bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis
Authors: Li Wei , Geng Ziwen , Zhang Cuiping , Wang Kuiling , Jiang Xinqiang 
Published: January 2021

Abstract
Background: Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. Results: Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusions: The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.
Tin isotopes via fs-LA-MC-ICP-MS analysis record complex fluid evolution in single cassiterite crystals
Authors: Liu Peng , Mao Jingwen , Lehmann Bernd , Weyer Stefan , Horn Ingo , Mathur Ryan , Wang Fangyue , Zhou Zhenhua 
Published: January 2021

Abstract
Tin isotope geochemistry of cassiterite may allow for reconstructing the fluid evolution of tin ore deposits. Here, we present cathodoluminescence (CL) imaging, trace element, and in situ Sn isotope compositions of two cassiterite crystals from an early and a relatively late stage of ore formation of the Xiling vein-style Sn deposit, southeastern China, by femtosecond laser ablation multi-collector inductively coupled plasma mass spectrometry (fs-LA-MC-ICP-MS). Our results show that the early-stage cassiterite from a high-temperature feldspar-stable hydrothermal environment has core, mantle, and rim zones with a systematic decrease in δ124/117Sn3161A (relative to the Sn standard NIST 3161 A) from +0.38 ± 0.06‰ in the crystal core to –0.12 ± 0.06‰ (2 SE) in the mantle zone. This isotopic evolution, also paralleled by a decrease in Ta content by two orders of magnitude, suggests a fluid batch evolving toward isotopically lighter Sn. The very rim zone of this crystal has an intermediate tin isotope composition at about +0.05‰ δ124/117Sn3161A, combined with elevated Ta, suggestive of a second fluid batch. The late-stage cassiterite crystal from a muscovite-stable hydrothermal environment has a core with an evolved Sn isotope composition at about –0.15‰ δ124/117Sn3161A combined with low Ta, and a rim with heavier Sn isotope compositions up to +0.30 ± 0.08‰ δ124/117Sn3161A and higher Ta contents. As for the early-stage crystal, two different fluid batches must be involved in the formation of this crystal. Our pilot study highlights the advantage of spatially resolved analysis compared to conventional, solution Sn-isotope analysis of bulk cassiterite crystals. The Sn isotope variations at the microscale reveal the complexity of cassiterite crystal growth by a combination of closed- and open-system fluid evolution and isotope fractionation.
Bennesherite, Ba2Fe2+Si2O7: A new melilite group mineral from the Hatrurim Basin, Negev Desert, Israel
Authors: Krzątała Arkadiusz , Krüger Biljana , Galuskina Irina , Vapnik Yevgeny , Galuskin Evgeny 
Published: January 2021

AbstractThe first barium member of the melilite group, bennesherite Ba2Fe2+Si2O7 [P421m, Z = 2, a = 8.2334(14) Å, c = 5.2854(8) Å, V = 359.29(13) Å3], was discovered in thin veins of rankinite paralava within pyrometamorphic gehlenite hornfels at Gurim Anticline, Hatrurim Basin, Negev Desert, Israel. Bennesherite occurs in small intergranular spaces between large crystals of rankinite, gehlenite, and garnet together with other Ba-minerals such as fresnoite, walstromite, zadovite, gurimite, hexacelsian, and celsian. It forms transparent, light yellow to lemon-colored crystals with a white streak and a vitreous luster. They exhibit good cleavage on (001), a brittle tenacity, and a conchoidal fracture. The estimated Mohs hardness is 5. Bennesherite has a melilite-type structure with the layers composed of disilicate (Si2O7)6− groups and (Fe2+O4)6− tetrahedra, connected by large eightfold-coordinated Ba atoms. In some grains, epitaxial intergrowths of bennesherite and fresnoite are observed. The structure of the fresnoite, Ba2TiO(Si2O7) with a P4bm space group and unit-cell parameters a = 8.5262(5) Å, c = 5.2199(4) Å, is closely related to the structure of bennesherite. Among all the known minerals of the melilite group, bennesherite has a structure characterized by the lowest misfit degree between the tetrahedral (T1 and T2 sites) and polyhedral (X-site) layers, as it was shown in both natural and synthetic melilite-type phases.
Celleriite, ☐(Mn22+Al)Al6(Si6O18)(BO3)3(OH)3(OH), a new mineral species of the tourmaline supergroup
Authors: Bosi Ferdinando , Pezzotta Federico , Altieri Alessandra , Andreozzi Giovanni B. , Ballirano Paolo , Tempesta Gioacchino , Cempírek Jan , Škoda Radek , Filip Jan , Čopjaková Renata , Novák Milan , Kampf Anthony R. , Scribner Emily D. , Groat Lee A. , Evans R. James 
Published: January 2021

Abstract
Celleriite, ☐(Mn22+Al)Al6(Si6O18)(BO3)3(OH)3(OH), is a new mineral of the tourmaline supergroup. It was discovered in the Rosina pegmatite, San Piero in Campo, Elba Island, Italy (holotype specimen), and in the Pikárec pegmatite, western Moravia, Czech Republic (co-type specimen). Celleriite in hand specimen is violet to gray-blue (holotype) and dark brownish-green (co-type) with a vitreous luster, conchoidal fracture, and white streak. Celleriite has a Mohs hardness of ~7 and a calculated density of 3.13 and 3.14 g/cm3 for holotype and its co-type, respectively. In plane-polarized light in thin section, celleriite is pleochroic (O = pale violet and E = light gray-blue in holotype; O = pale green and E = colorless in co-type) and uniaxial negative. Celleriite has trigonal symmetry: space group R3m, Z = 3, a = 15.9518(4) and 15.9332(3) Å, c = 7.1579(2) and 7.13086(15) Å, V = 1577.38(9) and 1567.76(6) Å3 for holotype and co-type, respectively (data from single-crystal X-ray diffraction). The crystal structure of the holotype specimen was refined to R1 = 2.89% using 1696 unique reflections collected with MoKα X-ray intensity data. Structural, chemical, and spectroscopic analyses resulted in the formulas:
x ( ◻ 0.58 N a 0.42 ) Σ 1.00 Y ( M n 1.39 2 + F e 0.16 2 + M g 0.01 A l 1.14 F e 0.01 3 + L i 0.28 T i 0.01 ) Σ 3.00 Z A l 6 [ T ( S i 5.99 A l 0.01 ) Σ 6.00 O 18 ] ( B O 3 ) 3 ( O H ) 3 w [ ( O H ) 0.65 F 0.03 O 0.32 ] Σ 1.00 ( for holotype )
and
x ( ◻ 0.51 N a 0.49 ) Σ 1.00 Y ( M n 0.90 2 + F e 0.50 2 + A l 1.36 F e 0.04 3 + L i 0.17 Zn 0.04 ) Σ 3.00 Z A l 6 [ T ( S i 5.75 B 0.25 ) Σ 6.00 O 18 ] ( B O 3 ) 3 ( O H ) 3 w [ ( O H ) 0.35 F 0.17 O 0.48 ] Σ 1.00 ( for co-type )
Celleriite is a hydroxy species belonging to the X-site vacant group of the tourmaline supergroup. The new mineral was approved by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association, proposal no. 2019-089.
In the Rosina pegmatite, celleriite formed an overgrowth at the analogous pole of elbaite–fluorelbaite–rossmanite crystals during the latest stage of evolution of pegmatite cavities after an event of a pocket rupture. In the Pikárec pegmatite, celleriite occurs as an intermediate growth sector of elbaite, princivalleite, and fluor-elbaite.
The influence of the SCM structure parameters on the engine vibration and optimization the engine power
Authors: Yan Dingao , Nguyen Vanliem 
Published: January 2021

In this paper, based on the slider-crank-mechanism (SCM) dynamics model, the dynamic parameters of the engine including the eccentricity (e) between crankshaft centre and cylinder centre of the SCM, the length and radius of the connecting rod and crankshaft, and engine speed are researched on the engine vibration and power, respectively. The dynamic parameters are then optimized based on the multi-objective genetic algorithm developed in MATLAB software to improve the vibration and power of the engine. Both the values of the maximum friction force and maximum torque are chosen as the objective functions. The research results show that the length of the connecting rod (L), radius of the crankshaft (R), eccentricity e, and engine speed (ne) significantly affect the vibration and power of the engine. With the optimized dynamic parameters of L= 136 mm, R= 45 mm, e= 14 mm, and ne= 1850 rpm, the amplitude of oscillation of piston acceleration and the maximum friction force are reduced by 36.3 % and 12.5 % while the maximum torque is increased by 18.6 % in comparison without optimization. Therefore, the vibration and power of the engine are improved.
Comparative Analysis of Fracture Strength of Remaining Tooth Structure after Endodontic Treatment with Various Access Cavity Preparation Techniques
Authors: Mustafa Mohammed , AlJeaidi Zaid A. , AlQahtani Ali Robaian , Abuelqomsan Mohammed Ali Salem , Alofi Raneem Suleiman , Alghomlas Ziyad Ibrahim , Abdullah AlOthman Tameem 
Published: January 2021

Background:A perfect balance needs to be maintained between various types of endodontic access cavity preparation designs like - Traditional and conservative designed preparation to have access to the root canal system for proper cleaning and shaping of root canals without compromising the fracture resistance of the tooth structure.Aims and Objectives:We aimed to assess as well as draw comparisons of resistance against fracture of remaining tooth structure post the endodontic treatment after preparing access cavity through a variety of techniques so that we can estimate which type of cavity design technique will help endodontically treated teeth to withstand excessive load without fracture.Methods:Forty-two intact teeth (mandibular molars) were randomly selected and then were assigned to 07 different groups, inclusive of control and test groups. Various designs of access cavity preparation were done on sample teeth. The groups were divided based on different access cavity preparation designs as well as residual walls. The samples were then mounted on a composite cylinder, which was loaded under a mechanical testing machine at 0.5mm/min speed till the tooth structure fractured. This measurement of force was denoted in newton. The later analysis was carried out with the help of two-way Analysis of Variance (ANOVA) as well as Tukey’s post-hoc statistical tests.Results:There was negligible statistically relevant variance in strength towards fracture between traditional and conservative designs in teeth having three remaining walls. However, teeth with only two remaining walls fractured easily.Conclusion:Fracture resistance of teeth with remaining 03 residual walls did not show any significant difference among Traditional (TEC) and Conservative Cavity (CEC) design groups, but increased fracture strength was reported in CEC with 02 residual walls.
Natural Language Processing and Machine Learning for Identifying Incident Stroke From Electronic Health Records: Algorithm Development and Validation
Authors: Zhao Yiqing , Fu Sunyang , Bielinski Suzette J , Decker Paul A , Chamberlain Alanna M , Roger Veronique L , Liu Hongfang , Larson Nicholas B 
Published: January 2021

Background
Stroke is an important clinical outcome in cardiovascular research. However, the ascertainment of incident stroke is typically accomplished via time-consuming manual chart abstraction. Current phenotyping efforts using electronic health records for stroke focus on case ascertainment rather than incident disease, which requires knowledge of the temporal sequence of events.

Objective
The aim of this study was to develop a machine learning–based phenotyping algorithm for incident stroke ascertainment based on diagnosis codes, procedure codes, and clinical concepts extracted from clinical notes using natural language processing.

Methods
The algorithm was trained and validated using an existing epidemiology cohort consisting of 4914 patients with atrial fibrillation (AF) with manually curated incident stroke events. Various combinations of feature sets and machine learning classifiers were compared. Using a heuristic rule based on the composition of concepts and codes, we further detected the stroke subtype (ischemic stroke/transient ischemic attack or hemorrhagic stroke) of each identified stroke. The algorithm was further validated using a cohort (n=150) stratified sampled from a population in Olmsted County, Minnesota (N=74,314).

Results
Among the 4914 patients with AF, 740 had validated incident stroke events. The best-performing stroke phenotyping algorithm used clinical concepts, diagnosis codes, and procedure codes as features in a random forest classifier. Among patients with stroke codes in the general population sample, the best-performing model achieved a positive predictive value of 86% (43/50; 95% CI 0.74-0.93) and a negative predictive value of 96% (96/100). For subtype identification, we achieved an accuracy of 83% in the AF cohort and 80% in the general population sample.

Conclusions
We developed and validated a machine learning–based algorithm that performed well for identifying incident stroke and for determining type of stroke. The algorithm also performed well on a sample from a general population, further demonstrating its generalizability and potential for adoption by other institutions.
Characterizing the Anticancer Treatment Trajectory and Pattern in Patients Receiving Chemotherapy for Cancer Using Harmonized Observational Databases: Retrospective Study
Authors: Jeon Hokyun , You Seng Chan , Kang Seok Yun , Seo Seung In , Warner Jeremy L , Belenkaya Rimma , Park Rae Woong 
Published: January 2021

Background
Accurate and rapid clinical decisions based on real-world evidence are essential for patients with cancer. However, the complexity of chemotherapy regimens for cancer impedes retrospective research that uses observational health databases.

Objective
The aim of this study is to compare the anticancer treatment trajectories and patterns of clinical events according to regimen type using the chemotherapy episodes determined by an algorithm.

Methods
We developed an algorithm to extract the regimen-level abstracted chemotherapy episodes from medication records in a conventional Observational Medical Outcomes Partnership (OMOP) common data model (CDM) database. The algorithm was validated on the Ajou University School Of Medicine (AUSOM) database by manual review of clinical notes. Using the algorithm, we extracted episodes of chemotherapy from patients in the EHR database and the claims database. We also developed an application software for visualizing the chemotherapy treatment patterns based on the treatment episodes in the OMOP-CDM database. Using this software, we generated the trends in the types of regimen used in the institutions, the patterns of the iterative chemotherapy use, and the trajectories of cancer treatment in two EHR-based OMOP-CDM databases. As a pilot study, the time of onset of chemotherapy-induced neutropenia according to regimen was measured using the AUSOM database. The anticancer treatment trajectories for patients with COVID-19 were also visualized based on the nationwide claims database.

Results
We generated 178,360 treatment episodes for patients with colorectal, breast, and lung cancer for 85 different regimens. The algorithm precisely identified the type of chemotherapy regimen in 400 patients (average positive predictive value >98%). The trends in the use of routine clinical chemotherapy regimens from 2008-2018 were identified for 8236 patients. For a total of 12 regimens (those administered to the largest proportion of patients), the number of repeated treatments was concordant with the protocols for standard chemotherapy regimens for certain cases. In addition, the anticancer treatment trajectories for 8315 patients were shown, including 62 patients with COVID-19. A comparative analysis of neutropenia showed that its onset in colorectal cancer regimens tended to cluster between days 9-15, whereas it tended to cluster between days 2-8 for certain regimens for breast cancer or lung cancer.

Conclusions
We propose a method for generating chemotherapy episodes for introduction into the oncology extension module of the OMOP-CDM databases. These proof-of-concept studies demonstrated the usability, scalability, and interoperability of the proposed framework through a distributed research network.
Determinan Perempuan Keluar dari Praktik Kawin Anum Suku Banjar
Authors: Kartika Norma Yuni , Darwin Muhadjir , Sukamdi Sukamdi 
Published: January 2021

“Kawin anum” dalam bahasa Banjar berarti perkawinan di bawah 16 tahun. Penelitian ini dilakukan di Kelurahan Raya Belanti, Kecamatan Binuang, Kabupaten Tapin, Provinsi Kalimantan Selatan dengan praktik kawin anum yang dipraktikkan oleh 90,26 persen penduduk perempuannya. Tujuan penelitian ini adalah mengetahui determinan perempuan keluar dari praktik kawin anum Suku Banjar. Penelitian ini menggunakan desain sequential explanatory method. Tahap pertama adalah melakukan survei terhadap 127 responden yang terdiri atas 37 perempuan yang menikah di bawah 16 tahun (pelaku kawin anum) dan 90 perempuan yang menikah pada usia 16-30 tahun, dan kemudian hasil analisis tahap pertama dieksplorasi lebih lanjut pada tahap kedua dengan metode kualitatif. Pada tahap kedua, informan dipilih berdasarkan hasil analisis tahap pertama dan 14 perempuan yang menolak desakan untuk segera menikah, 14 orang tua dan 9 stakeholders. Hasil penelitian ini menunjukkan bahwa terdapat empat variabel yang menjadi determinan perempuan keluar dari praktik kawin anum, yaitu variabel individual (berpendidikan tinggi dan bekerja), interpersonal (tingkat ekonomi keluarga asal perempuan tinggi), institusional (syarat menikah sudah memiliki kartu tanda penduduk) dan sosietal (memenuhi syarat usia minimal resmi yang diijinkan untuk menikah menurut undang-undang perkawinan).Kawin anum in local languange of Banjar means that a marriage conducted those who are under 16 years old. The research of kawin anum is located in Raya Belanti Village, Binuang District, Tapin District, South Kalimantan Province where kawin anum was practiced by 90.26 percent of female residents. The purpose of this study was to find out the determinants of women who got out of kawin anum practice in Banjar Tribe. This study uses a sequential explanatory method design. The first stage was conducting a survey to 127 respondents, consisted of 37 women married under 16 (perpetrators of kawin anum) and 90 women who were married at the age of 16-30 years. The results of first phase of analysis were further explored in the second stage using a qualitative method. For the second stage, the informants were chosen based on the results of the first phase analysis and 14 women who refused the urge to get married immediately, 14 parents and 9 stakeholders were selected. The results showed that there were four variables which were the determinants of women getting out of kawin anum practices, namely individual variables (highly educated and working women), interpersonal (women came from families with high level of economy), institutional (to get married, one must had an identification card) and societal (has fulfiled the minimum legal age requirements in order to be permitted to marry according to marriage law).
Optimalisasi Modal Sosial Keluarga Muda dalam Membangun Ketahanan Ekonomi di Era Covid-19: Studi Kasus di Perdesaan Jawa
Authors: Setiadi Setiadi 
Published: January 2021

The Covid-19 pandemic has caused acute non-health impacts for various levels of society, including young families in rural areas of Java. This study presents the results of research that focus on the experiences of young families who work in the informal sector in overcoming the economic impacts due to the Covid-19 pandemic. The young families in this study were those who got married less than 10 years and/or had the oldest child aged less than 10 years. By using an anthropological approach and applying data collection method through participatory observations and in-depth interviews, this study concluded that there were two factors that made them be the most vulnerable group, yet they could face economic emergencies at the same time, such as first, their ability to optimize social capital to increase their own capacity and their family’s capacity in the face of economic vulnerability. They did productive economic activities by optimizing very limited work networks to survive their life. Second, they carefully performed minimal income management so that they could survive and fulfill the minimum household needs as a household unit.