bluuebunny/crossref_metadata_2025_split huggingface dataset:
Search for hybrid morphology radio galaxies from the FIRST survey at 1400 MHz
Authors: Kumari Shobha , Pal Sabyasachi 
Published: April 2022

ABSTRACT
Hybrid Morphology Radio Sources (HyMoRS) are a very rare subclass of radio galaxies with apparent mixed FR morphology, i.e. these galaxies seem to have an FR-I structure on one side of the core and an FR-II structure on the other side of the core. We systematically searched for HyMoRS using Very Large Array (VLA) Faint Images of the Radio Sky at Twenty-cm (FIRST) survey with 1400 MHz frequency and identified 33 candidate HyMoRS. Our finding significantly increased the known sample size of HyMoRS. HyMoRS may play an essential role in understanding the interaction of jets with the interstellar medium and the much-debated topic of the FR dichotomy. We identified optical counterparts for 29 sources in our catalogue. In our sample of sources, one source (J1106+1355) had quasar-like behaviour. Four sources were BRCLG (Brightest Cluster Galaxies) and six were LRG (Luminous Red Galaxies). We have estimated the spectral index and radio luminosity of HyMoRS in our catalogue, when possible. We found that J1136–0328 was the most luminous source in our sample (log L = 27.01 W Hz−1sr−1). It was also the farthest HyMoRS (with a redshift z = 0.82) in our sample. With the help of a large sample size of discovered sources, various statistical properties of detected galaxies were studied.
Cosmological simulations predict that AGN preferentially live in gas-rich, star-forming galaxies despite effective feedback
Authors: Ward S R , Harrison C M , Costa T , Mainieri V 
Published: April 2022

ABSTRACT
Negative feedback from active galactic nuclei (AGN) is the leading mechanism for the quenching of massive galaxies in the vast majority of modern galaxy evolution models. However, direct observational evidence that AGN feedback causes quenching on a population scale is lacking. Studies have shown that luminous AGN are preferentially located in gas-rich and star-forming galaxies, an observation that has sometimes been suggested to be in tension with a negative AGN feedback picture. We investigate three of the current cosmological simulations (illustrisTNG, EAGLE, and SIMBA) along with post-processed models for molecular hydrogen gas masses and perform similar tests to those used by observers. We find that the simulations predict: (i) no strong negative trends between Lbol and $f_{\mathrm{ H}_2}$ or specific star formation rate (sSFR); (ii) both high-luminosity ($L_{\rm {bol}} \ge 10^{44}\rm {\, erg\, s^{-1}}$) and high Eddington ratio (λEdd $\ge 1{{\ \rm per\ cent}}$) AGN are preferentially located in galaxies with high molecular gas fractions and sSFR; and (iii) that the gas-depleted and quenched fractions of AGN host galaxies are lower than a control sample of non-active galaxies. These three findings are in qualitative agreement with observational samples at z = 0 and z = 2 and show that such results are not in tension with the presence of strong AGN feedback, which all simulations we employ require to produce realistic massive galaxies. However, we also find quantifiable differences between predictions from the simulations, which could allow us to observationally test the different subgrid feedback models.
Decreased levels of histidine-rich glycoprotein and increased levels of high-mobility group box 1 are risk factors for refractory Kawasaki disease
Authors: Namba Takahiro , Yashiro Masato , Fujii Yosuke , Tsuge Mitsuru , Liu Keyue , Nishibori Masahiro , Tsukahara Hirokazu 
Published: April 2022

ABSTRACT

Objectives
Histidine-rich glycoprotein (HRG) and high-mobility group box 1 (HMGB1) regulate the activation of neutrophils and vascular endothelium. The aim of this study was to quantify HRG and HMGB1 levels in patients with Kawasaki disease (KD) and evaluate their use in the clinical management of KD.

Methods
This study was prospectively performed. Patients were divided into two groups and analysed depending on whether KD symptoms improved by Day 10 of illness. HRG, HMGB1, and other laboratory variables were measured before the first treatment in all cases and, in most cases, afterwards for assessing trends.

Results
In this prospective study, we enrolled 60 patients with KD and 48 healthy controls. The HRG level in the KD group was significantly lower than that in the healthy control group; HMGB1 levels showed no obvious differences. In the KD group, HRG levels were negatively correlated with white blood cell and neutrophil counts. In the poor responders and responders groups, a tendency for a decrease in HRG and HMGB1 levels, respectively, was observed from pretreatment to post-treatment.

Conclusions
HRG and HMGB1 are related to the pathogenesis of KD; low HRG and high HMGB1 levels cause resistance against KD treatment.
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
Authors: Mungan Mehmet Direnç , Harbig Theresa Anisja , Perez Naybel Hernandez , Edenhart Simone , Stegmann Evi , Nieselt Kay , Ziemert Nadine 
Published: April 2022

Abstract
For decades, natural products have been used as a primary resource in drug discovery pipelines to find new antibiotics, which are mainly produced as secondary metabolites by bacteria. The biosynthesis of these compounds is encoded in co-localized genes termed biosynthetic gene clusters (BGCs). However, BGCs are often not expressed under laboratory conditions. Several genetic manipulation strategies have been developed in order to activate or overexpress silent BGCs. Significant increases in production levels of secondary metabolites were indeed achieved by modifying the expression of genes encoding regulators and transporters, as well as genes involved in resistance or precursor biosynthesis. However, the abundance of genes encoding such functions within bacterial genomes requires prioritization of the most promising ones for genetic manipulation strategies. Here, we introduce the ‘Secondary Metabolite Transcriptomic Pipeline’ (SeMa-Trap), a user-friendly web-server, available at https://sema-trap.ziemertlab.com. SeMa-Trap facilitates RNA-Seq based transcriptome analyses, finds co-expression patterns between certain genes and BGCs of interest, and helps optimize the design of comparative transcriptomic analyses. Finally, SeMa-Trap provides interactive result pages for each BGC, allowing the easy exploration and comparison of expression patterns. In summary, SeMa-Trap allows a straightforward prioritization of genes that could be targeted via genetic engineering approaches to (over)express BGCs of interest.
IBS 2.0: an upgraded illustrator for the visualization of biological sequences
Authors: Xie Yubin , Li Huiqin , Luo Xiaotong , Li Hongyu , Gao Qiuyuan , Zhang Luowanyue , Teng Yuyan , Zhao Qi , Zuo Zhixiang , Ren Jian 
Published: April 2022

Abstract
The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field of molecular and cellular biology. However, due to the limitations of the currently used applications, there are still considerable challenges in the preparation of biological schematic diagrams. Here, we present a professional tool called IBS 2.0 for illustrating the organization of both protein and nucleotide sequences. With the abundant graphical elements provided in IBS 2.0, biological sequences can be easily represented in a concise and clear way. Moreover, we implemented a database visualization module in IBS 2.0, enabling batch visualization of biological sequences from the UniProt and the NCBI RefSeq databases. Furthermore, to increase the design efficiency, a resource platform that allows uploading, retrieval, and browsing of existing biological sequence diagrams has been integrated into IBS 2.0. In addition, a lightweight JS library was developed in IBS 2.0 to assist the visualization of biological sequences in customized web services. To obtain the latest version of IBS 2.0, please visit https://ibs.renlab.org.
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples
Authors: Ianevski Aleksandr , Giri Anil K , Aittokallio Tero 
Published: April 2022

Abstract
SynergyFinder (https://synergyfinder.fimm.fi) is a free web-application for interactive analysis and visualization of multi-drug combination response data. Since its first release in 2017, SynergyFinder has become a popular tool for multi-dose combination data analytics, partly because the development of its functionality and graphical interface has been driven by a diverse user community, including both chemical biologists and computational scientists. Here, we describe the latest upgrade of this community-effort, SynergyFinder release 3.0, introducing a number of novel features that support interactive multi-sample analysis of combination synergy, a novel consensus synergy score that combines multiple synergy scoring models, and an improved outlier detection functionality that eliminates false positive results, along with many other post-analysis options such as weighting of synergy by drug concentrations and distinguishing between different modes of synergy (potency and efficacy). Based on user requests, several additional improvements were also implemented, including new data visualizations and export options for multi-drug combinations. With these improvements, SynergyFinder 3.0 supports robust identification of consistent combinatorial synergies for multi-drug combinatorial discovery and clinical translation.
Assessment of Internalizing Disorders
Authors: Naragon-Gainey Kristin , McMahon Tierney P. , Park Juhyun 
Published: April 2022

Abstract
Internalizing disorders, which include depression and anxiety as well as several other syndromes, are common and impairing conditions that form one of the spectra in structural models of psychopathology (i.e., the Hierarchical Taxonomy of Psychopathology). This chapter reviews the hierarchical structure and contents of the Internalizing spectrum, as well as their key features and challenges that commonly arise when assessing these symptoms. Four types of assessment tools are presented—self-report measures, clinical interviews, ambulatory assessment, and performance-based clinician-rated measures (i.e., behavioral avoidance tasks)—along with their strengths and limitations, applications, and example measures as they relate to the Internalizing spectrum. The chapter also discusses considerations for assessment of internalizing symptoms in diverse populations and future directions in this area.
Construct Validation of Personality Measures
Authors: Smith Gregory T. , Atkinson Emily A. 
Published: April 2022

Abstract
Current construct validity theory emphasizes the following points. The process of validating measures of unobservable constructs is also the process of validating theories of psychological functioning. That process is ongoing for each measure and theory: Construct validity is never fully established but, rather, evidence for the validity of measures and theories accrues over time. To facilitate the process, researchers should conduct validation tests that are as informative as possible—that is, that directly address core components of one’s theory. Measure and theory validation should be conducted on measures of homogeneous constructs: The use of single scores to represent multidimensional entities cannot be defended. An important issue concerning validating the claims of personality theory involves understanding the relationship between self-reports of general tendencies and daily moment-to-moment reports of reactions and behavior. Noting the significant amount of variance shared between various forms of psychopathology and facets of personality, researchers have utilized bifactor modeling to extract general factors of psychopathology and personality. These new models present unique challenges for construct validation. Extraordinary progress has been made in the study of personality, and the further implementation of sound construct validation principles will lead to continued, improved, and successful measure and theory validation in the future.
Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance
Authors: Wei Hua , Xu Hang , Su Chen , Wang Xiling , Wang Lei 
Published: April 2022

AbstractThe circadian clock facilitates the survival and reproduction of crop plants under harsh environmental conditions such as drought and osmotic and salinity stresses, mainly by reprogramming the endogenous transcriptional landscape. Nevertheless, the genome-wide roles of core clock components in rice (Oryza sativa L.) abiotic stress tolerance are largely uncharacterized. Here, we report that CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1), a vital clock component in rice, is required for tolerance to salinity, osmotic, and drought stresses. DNA affinity purification sequencing coupled with transcriptome analysis identified 692 direct transcriptional target genes of OsCCA1. Among them, the genes involved in abscisic acid (ABA) signaling, including group A protein phosphatase 2C genes and basic region and leucine zipper 46 (OsbZIP46), were substantially enriched. Moreover, OsCCA1 could directly bind the promoters of OsPP108 and OsbZIP46 to activate their expression. Consistently, oscca1 null mutants generated via genome editing displayed enhanced sensitivities to ABA signaling. Together, our findings illustrate that OsCCA1 confers multiple abiotic stress tolerance likely by orchestrating ABA signaling, which links the circadian clock with ABA signaling in rice.
Circadian entrainment in Arabidopsis
Authors: Wang Shouming , Steed Gareth , Webb Alex A R 
Published: April 2022

Abstract
Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.
Geochemical ice-core constraints on the timing and climatic impact of Aniakchak II (1628 BCE) and Thera (Minoan) volcanic eruptions
Authors: Pearson Charlotte , Sigl Michael , Burke Andrea , Davies Siwan , Kurbatov Andrei , Severi Mirko , Cole-Dai Jihong , Innes Helen , Albert Paul G , Helmick Meredith 
Published: April 2022

Abstract
Decades of research have focused on establishing the exact year and climatic impact of the Minoan eruption of Thera, Greece (c.1680 to 1500 BCE). Ice cores offer key evidence to resolve this controversy, but attempts have been hampered by a lack of multivolcanic event synchronization between records. In this study, Antarctic and Greenland ice-core records are synchronized using a double bipolar sulfate marker, and calendar dates are assigned to each eruption revealed within the ‘Thera period’. From this global-scale sequence of volcanic sulfate loading, we derive indications toward each eruption’s latitude and potential to disrupt the climate system. Ultrafine sampling for sulfur isotopes and tephra conclusively demonstrate a colossal eruption of Alaska’s Aniakchak II as the source of stratospheric sulfate in the now precisely dated 1628 BCE ice layer. These findings end decades of speculation that Thera was responsible for the 1628 BCE event, and place Aniakchak II (52 ± 17 Tg S) and an unknown volcano at 1654 BCE (50 ± 13 Tg S) as two of the largest Northern Hemisphere sulfur injections in the last 4,000 years. This opens possibilities to explore widespread climatic impacts for contemporary societies and, in pinpointing Aniakchak II, confirms that stratospheric sulfate can be globally distributed from eruptions outside the tropics. Dating options for Thera are reduced to a series of precisely dated, constrained stratospheric sulfur injection events at 1611 BCE, 1561/1558/1555BCE, and c.1538 BCE, which are all below 14 ± 5 Tg S, indicating a climatic forcing potential for Thera well below that of Tambora (1815 CE).
Graphene oxide and mineralized collagen-functionalized dental implant abutment with effective soft tissue seal and romotely repeatable photodisinfection
Authors: Gao Yichun , Kang Ke , Luo Bin , Sun Xiaoqing , Lan Fang , He Jing , Wu Yao 
Published: April 2022

Abstract
Grasping the boundary of antibacterial function may be better for the sealing of soft tissue around dental implant abutment. Inspired by ‘overdone is worse than undone’, we prepared a sandwich-structured dental implant coating on the percutaneous part using graphene oxide (GO) wrapped under mineralized collagen. Our unique coating structure ensured the high photothermal conversion capability and good photothermal stability of GO. The prepared coating not only achieved suitable inhibition on colonizing bacteria growth of Streptococcus sanguinis, Fusobacterium nucleatum and Porphyromonas gingivalis but also disrupted the wall/membrane permeability of free bacteria. Further enhancements on the antibacterial property were generally observed through the additional incorporation of dimethylaminododecyl methacrylate. Additionally, the coating with sandwich structure significantly enhanced the adhesion, cytoskeleton organization and proliferation of human gingival fibroblasts, which was effective to improve soft tissue sealing. Furthermore, cell viability was preserved when cells and bacteria were cultivated in the same environment by a coculture assay. This was attributed to the sandwich structure and mineralized collagen as the outmost layer, which would protect tissue cells from photothermal therapy and GO, as well as accelerate the recovery of cell activity. Overall, the coating design would provide a useful alternative method for dental implant abutment surface modification and functionalization.
Critically ill COVID-19 patients in northeast Brazil: mortality predictors during the first and second waves including SAPS 3
Authors: Lázaro Ana Paula Pires , Albuquerque Polianna Lemos Moura Moreira , Meneses Gdayllon Cavalcante , Zaranza Marza de Sousa , Batista Ana Beatriz , Aragão Natalia Linhares Ponte , Beliero Andrea Mazza , Guimarães Álvaro Rolim , Aragão Nilcyeli Linhares , Leitão Alessandra Marjorye Maia , de Carvalho Marcelo Costa Freire , Cavalcante Maria Isabel de Alencar , Mota Fabio Augusto Xerez , Daher Elizabeth De Francesco , Martins Alice Maria Costa , da Silva Junior Geraldo Bezerra 
Published: April 2022

Abstract

Background
The Simplified Acute Physiology Score (SAPS) 3 is a reliable score to predict mortality. This study aims to investigate the predictive values of SAPS 3 and other clinical parameters for death in critically ill coronavirus disease 2019 (COVID-19) patients.

Methods
This is a prospective study in a tertiary hospital for patients who required intensive care due to COVID-19 infection in northeast Brazil. Two distinct groups were constructed according to the epidemiological data: first wave and second wave. The severity of patients admitted was estimated using the SAPS 3 score.

Results
A total of 767 patients were included: 290 were enrolled in the first wave and 477 in the second wave. Patients in the first wave had more comorbidities, were put on mechanical ventilation and required dialysis and vasopressors more frequently (p&lt;0.05). During the second wave, non-invasive ventilation was more often required (p&lt;0.05). In both periods, older patients and higher SAPS 3 scores on admission were associated with death (p&lt;0.05). Non-invasive ventilation use showed a negative association with death only in the second wave period. In the first wave, the SAPS 3 score was more useful (area under the curve [AUC] 0.897) in predicting death in critically ill COVID-19 patients than in the second wave (AUC 0.810).

Conclusion
The SAPS 3 showed very reliable predictive values for death during the waves of the COVID-19 pandemic, mostly together with kidney and pulmonary dysfunction.
Increased Fatigability in Women With Persistent Cancer-Related Fatigue After Breast Cancer Treatment: A Pilot Study
Authors: Wood Magee Lisa J. , Kneiss Janet , Wechsler Stephen , Singh Ayesha Bani , Fox Annie B. , Peppercorn Jeffrey , Pirl William F. 
Published: April 2022

Purpose:
To examine whether survivors of breast cancer (SBC) with persistent cancer-related fatigue (CRF) have greater fatigability than their nonfatigued counterparts.

Methods:
Measures of fatigability, including endurance, perceived exertion, lower extremity muscle force and power, and sit-to-stand time (STST), were assessed in 43 women (21 with persistent CRF) after a sit-to-stand fatigue (STSF) task. Group differences in fatigability outcomes were examined using analysis of variance.

Results:
SBC with persistent CRF had lower endurance (P = .003, ηp
2 = 0.205) and reported greater perceived exertion (P < .001, ηp
2 = 0.284) during the STSF task, and demonstrated lower postexertional force (P = .035, ηp
2 = 0.109), power (P = .001, ηp
2 = 0.242), and slower STST (P = .001, ηp
2 = 0.258) compared with SBC without CRF.

Conclusions:
SBC with persistent CRF have increased fatigability compared with those without CRF. Our findings suggest that exercise recommendations for women with persistent CRF after breast cancer treatment should include activities that increase lower limb muscle force and power, such as heavy resistance or explosive-type strength training.
Impact of Heat Inactivation of Blood Samples on Therapeutic Drug Monitoring of 5 Second-Generation Antipsychotics and Their Metabolites
Authors: Ding Jing , Yang Liu , Zhang Yan , Zhang Suo , Meng Zhuocheng 
Published: April 2022

Background:
The severe acute respiratory syndrome coronavirus 2 outbreak has been classified as a pandemic. Because many coronaviruses are heat sensitive, heat inactivation of patient samples at 56°C before testing reduces the risk of transmission. The aim of this study is to assess the impact of heat inactivation of patient blood samples on plasma concentrations of 5 second-generation antipsychotics and their metabolites.

Methods:
Blood samples were collected during routine clinical therapeutic drug monitoring examination between April 3, 2021, and April 19, 2021. Samples were divided into 2 groups: group A, noninactivated raw sample, and group B, inactivated samples. Inactivation was performed by a 30-minute incubation at 56°C. The levels of the 5 drugs and their metabolites before and after sample heat inactivation were measured using liquid chromatography-tandem mass spectrometry and compared. Furthermore, correlation and Bland–Altman analyses were conducted.

Results:
No statistically significant difference was observed between the levels of the 5 drugs and their metabolites (ie, risperidone, 9-OH-risperidone, aripiprazole, dehydroaripiprazole, olanzapine, quetiapine, norquetiapine, clozapine, and norclozapine) in the noninactivated group A and the inactivated group B (P > 0.05). Each drug's concentration values in inactivated and noninactivated treatments correlated (Spearman r
s > 0.98; P < 0.001). The results of the noninactivated treatment methods and samples alone showed good consistency via Bland–Altman analysis.

Conclusions:
Blood sample heat inactivation had no significant effect on the therapeutic drug monitoring of 5 second-generation antipsychotics and their metabolites. This inactivated treatment method should be recommended to effectively protect laboratory staff from virus contamination.