bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel coating to avoid corrosion effect between eutectic gallium–indium alloy and heat sink metal for X-ray optics cooling
Authors: Tang Shanzhi , He Tian , Yu Haihan , Ou Zina , Ren Zhongrui , Li Ming , Sheng Weifan 
Published: December 2022

Owing to the parasitic vibration effect of the cooling medium and pipes of X-ray optics, the vibration decoupling cooling method based on eutectic gallium–indium (EGaIn) alloy has become very crucial for fourth generation synchrotron radiation advanced light sources. However, there is an issue that the corrosion of the EGaIn alloy to the heat sink metal [e.g., copper (Cu) plate] results in the solidification and the failure of eliminating the parasitic vibration effect. To deal with the problem, a novel anti-corrosion coating based on tungsten (W) is presented in this paper. It possesses better corrosion resistance performance compared with the traditional coating of nickel (Ni). The experimental investigation was carried out, in which the EGaIn alloy was exposed to several typical metal materials in conditions of various time durations and various temperatures, which were considered as controls. Furthermore, the corrosion effects are analyzed and evaluated in two aspects of micromorphology and the chemical composition by using an optical microscope and a scanning electron microscope as well as x-ray diffraction. The results show that non obvious corrosion occurred for W, 0.33 mm and 48 µm thick transition micro-area, respectively, for Cu and Ni. In addition, new substances CuGa2 and Ni3Ga7 occurred, respectively, for Cu and Ni for 36 hours at 250 °C. The EGaIn alloy will freeze after corroding 18 µm substrate for Ni or 30 µm for Cu. Furthermore, the W coating that was prepared by magnetron sputtering has been implemented for feasibility validation.
Single and double thermal reduction processes for synthesis reduced graphene oxide assisted by a muffle furnace: A facile robust synthesis and rapid approach to enhance electrical conductivity
Authors: Al-Mufti Salah M. S. , Almontasser Asma , Rizvi S. J. A. 
Published: December 2022

Nowadays, with the rapid development of electronic devices, it is increasingly important to enhance the electrical conductivity of reduced graphene oxide (rGO). Thermal reduction (TR) temperature and time play the most crucial role as they control the electrical conductivity of rGO in terms of removal of oxygen-containing functional (OCF) groups. This work proposes a novel systematic approach for quick calibration of the OCF groups and lattice defects of GO to increase the conductivity by tuning the temperature and exposure time of the sample to the temperature. Single TR (STR) and double TR (DTR) processes were used in the current work, in which samples were exposed to temperatures of 500, 700, and 900 °C for 5 min. Further annealing took place for each sample at the same temperature with various reduction times. The results indicate that the DTR process improved the electrical conductivity of rGO samples. The highest enhancement of rGO500-5, rGO700-5, and rGO900-5 conductivities was 52.36%, 57.58%, and 231.81%, respectively. Consequently, this material can be used as a filler to get a well dispersed nanocomposite by accurate addition of rGO in a matrix, which enhances its electrical properties. Based on x-ray diffraction, scanning electron microscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, and electrical analyses, the plausible STR and DTR mechanism of GO to rGO is effectively proposed.
Lion (Panthera leo) diet and cattle depredation on the Kuku Group Ranch Pastoralist area in southern Maasailand, Kenya
Authors: Olivier Iain R. , Tambling Craig J. , Müller Lana , Radloff Frans G. T. 
Published: December 2022

Context African lion (Panthera leo) populations are declining throughout Africa, but the problem is particularly acute in southern Kenya, where human–lion conflict is common. Aims Using the Kuku Group Ranch (KGR) in southern Kenya as a case study, we investigated lion diet and the potential drivers of temporal variation in cattle depredation. Methods Using GPS clusters, we investigated the main prey species consumed by lions to determine lion diet. Prey preference of lions in relation to prey availability was then assessed using a Jacobs index to determine whether cattle or wild prey were preferred. We used reported depredation events recorded by verification officers over 36 months (2016–2018) to investigate whether temporal variation in cattle depredation by lions was linked to variation in lag rainfall, normalised difference vegetation index (NDVI) or availability of the most important large non-domestic prey items. Key results Six prey species (cattle, Bos taurus; Burchell’s zebra, Equus quagga; Coke’s hartebeest, Alcelaphus cokeii; Maasai giraffe, Giraffa tippelskirchi; blue wildebeest, Connochaetes taurinus; and eland, Tragelaphus oryx) made up 92% of the biomass consumed by lions on KGR. Cattle are the most consumed prey item and contribute the second most to consumed biomass after giraffe. However, once prey availability is considered, lions preferred wild prey. Verification officers identified 330 cattle depredation events over 3 years, and we show that the most important predictor of monthly cattle depredation by lions was cumulative rainfall in the preceding 3 months. Conclusions Our results on cattle depredation by lions showed that rainfall and its influence on the environment are important drivers of cattle depredation. Understanding the mechanistic link between lion depredation and rainfall enables us to predict when depredation events may increase and allows hypotheses on the reason why this spike in depredation takes place to be explored. Implications Given that climate-change models indicate that East Africa will experience prolonged and increased seasonal rainfall, we predict that periods when cattle are vulnerable to lion depredation may increase. Therefore, it is imperative to ensure that cattle husbandry is improved during these wetter periods to minimise the risk of conflict and retaliatory killing of lions.
Transcriptional repressor RST1 controls salt tolerance and grain yield in rice by regulating gene expression of asparagine synthetase
Authors: Deng Ping , Jing Wen , Cao Chengjuan , Sun Mingfa , Chi Wenchao , Zhao Shaolu , Dai Jinying , Shi Xingyu , Wu Qi , Zhang Baolong , Jin Zhuo , Guo Chunxia , Tian Quanxiang , Shen Like , Yu Jun , Jiang Ling , Wang Chunming , Chin Joong Hyoun , Yuan Jingya , Zhang Qun , Zhang Wenhua 
Published: December 2022

Salt stress impairs nutrient metabolism in plant cells, leading to growth and yield penalties. However, the mechanism by which plants alter their nutrient metabolism processes in response to salt stress remains elusive. In this study, we identified and characterized the rice (
Oryza sativa
)
rice salt tolerant 1
(
rst1
) mutant, which displayed improved salt tolerance and grain yield. Map-based cloning revealed that the gene
RST1
encoded an auxin response factor (OsARF18). Molecular analyses showed that RST1 directly repressed the expression of the gene encoding asparagine synthetase 1 (OsAS1). Loss of
RST1
function increased the expression of
OsAS1
and improved nitrogen (N) utilization by promoting asparagine production and avoiding excess ammonium (NH
4
+
) accumulation.
RST1
was undergoing directional selection during domestication. The superior haplotype RST1
Hap III
decreased its transcriptional repression activity and contributed to salt tolerance and grain weight. Together, our findings unravel a synergistic regulator of growth and salt tolerance associated with N metabolism and provide a new strategy for the development of tolerant cultivars.
Supporting university students’ argumentative source-based writing
Authors: Marttunen Miika , Kiili Carita 
Published: December 2022

AbstractArgumentative writing from sources is a literacy practice that students commonly find challenging. The present article reports a descriptive study where students’ source-based writing in small groups was supported with either print-based or digital scaffolding. Students analyzed source texts given to them and used their analysis to compose a position paper on a controversial educational topic. Position papers were analyzed for depth and breadth of argumentation, stand and justifications, degree of transformation of source texts’ argumentation, and structure. The study suggests that students in both scaffolding groups were fairly capable of identifying relevant reasons representing various perspectives on the topic in source texts and using them to build an argument in their position papers. However, students seldom transformed the arguments by adding their own thoughts or connecting arguments across the texts. Further, quite a few students seem to struggle in structuring their essays: 41% of essays in the print-based scaffolding group and 24% of essays in the digital scaffolding group were unstructured. Instructional implications are discussed.
Investigation of the time resolution of 3D silicon sensors
Authors: Diehl L. , Ferrer O. , Hauser M. , Jakobs K. , King M. , Kramberger G. , Moffat N. , Parzefall U. , Pellegrini G. , Sperlich D. 
Published: December 2022

Abstract
Collider experiments as the upcoming Phase II-LHC or the future circular collider (FCC) will increase the demands on tracking detectors. In the FCC hadron collider, sensors will not only face fluences up to 1 × 1017 neq/cm2, but also high pile-up scenarios. Therefore, sensors will be required not only to have a good spatial resolution and a very high radiation hardness, but also an excellent time resolution of the order of 5 ps. Currently, Low Gain Avalanche Diodes (LGADs) are one of the main candidates when it comes to timing, achieving a resolution well below 30 ps. However, their radiation hardness is not sufficient for future colliders. 3D sensors are an interesting alternative due to their superior radiation hardness. In 3D sensors, which already have been thoroughly investigated for tracking purposes, the drift distances are short, the depletion voltage is very low and the electric field can be very high, thus the signals are fast and short.
In this study, the time resolution of different 3D sensors was investigated with signals generated by MIP-like electrons, as well as by measurements using a laser with an infrared wavelength. It is shown that 3D pixel sensors can achieve time resolutions competitive with those of LGADs. Additionally, Transient Current Technique (TCT) timing measurements have been conducted. These allow to study the position dependence of the time resolution, which is interesting for 3D sensors due to their complex electric field structure. The measurements prove the direct correlation between the time resolution and the electric field configuration. Furthermore, the performance of the sensors is demonstrated before and after irradiation with reactor neutrons.
annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing
Authors: Farkas Carlos , Recabal Antonia , Mella Andy , Candia-Herrera Daniel , Olivero Maryori González , Haigh Jody Jonathan , Tarifeño-Saldivia Estefanía , Caprile Teresa 
Published: December 2022

Abstract

Background
The advancement of hybrid sequencing technologies is increasingly expanding genome assemblies that are often annotated using hybrid sequencing transcriptomics, leading to improved genome characterization and the identification of novel genes and isoforms in a wide variety of organisms.

Results
We developed an easy-to-use genome-guided transcriptome annotation pipeline that uses assembled transcripts from hybrid sequencing data as input and distinguishes between coding and long non-coding RNAs by integration of several bioinformatic approaches, including gene reconciliation with previous annotations in GTF format. We demonstrated the efficiency of this approach by correctly assembling and annotating all exons from the chicken SCO-spondin gene (containing more than 105 exons), including the identification of missing genes in the chicken reference annotations by homology assignments.

Conclusions
Our method helps to improve the current transcriptome annotation of the chicken brain. Our pipeline, implemented on Anaconda/Nextflow and Docker is an easy-to-use package that can be applied to a broad range of species, tissues, and research areas helping to improve and reconcile current annotations. The code and datasets are publicly available at https://github.com/cfarkas/annotate_my_genomes
Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts
Authors: Tang Kecong , Naseri Ardalan , Wei Yuan , Zhang Shaojie , Zhi Degui 
Published: December 2022

Abstract
In the recent biobank era of genetics, the problem of identical-by-descent (IBD) segment detection received renewed interest, as IBD segments in large cohorts offer unprecedented opportunities in the study of population and genealogical history, as well as genetic association of long haplotypes. While a new generation of efficient methods for IBD segment detection becomes available, direct comparison of these methods is difficult: existing benchmarks were often evaluated in different datasets, with some not openly accessible; methods benchmarked were run under suboptimal parameters; and benchmark performance metrics were not defined consistently. Here, we developed a comprehensive and completely open-source evaluation of the power, accuracy, and resource consumption of these IBD segment detection methods using realistic population genetic simulations with various settings. Our results pave the road for fair evaluation of IBD segment detection methods and provide an practical guide for users.
The opportunities of research parasitism: A case study using the Barcode of Life Data System (BOLD)
Authors: Pilgrim Jack 
Published: December 2022

Abstract
The Barcode of Life Data System (BOLD) is primarily used to identify biological specimens based on a mitochondrial gene sequence and has been an underpinning resource for life science researchers. Importantly, curators of BOLD archive DNA extracts where possible, and also record contaminant sequences that can be made available on request. This collegial offering of samples and data led to our work describing the serendipitous discovery of new interactions between a Torix Rickettsia bacterium and their arthropod hosts and resulted in winning the 2022 Junior Research Parasite Award. A case study of this work is presented, which discusses the opportunities provided by secondary data and how careful maintenance of such large-scale repositories plays a vital role in scientific research that goes beyond obvious lines of enquiry.
Depression in Women With Inflammatory Bowel Disease: A Multifaceted Approach for a Multidimensional Problem
Authors: Bommena Shoma , Goldberg Aaron , Amini Mona , Alishahi Yasmin 
Published: December 2022

Abstract
The prevalence of depression is higher in patients with inflammatory bowel disease (IBD) than in the general population. Women are more significantly affected by depression among those with IBD and in the general population. This review presents evidence on sex-based differences in depression pathogenesis and the effect of depression on various factors associated with IBD that affect women’s lives, including sexual dysfunction, body image dissatisfaction, fertility, and overall quality of life. We also discuss sex-specific effects on IBD treatment, disease activity, and health care costs. Interestingly, women with IBD tend to seek and are more receptive to depression-related information. Given the underdiagnosis and undertreated nature of depression in individuals with IBD, effective screening and an optimal integrative treatment approach with relevant sex-specific needs are discussed. Evidence regarding the efficacy of psychotherapy, antidepressant pharmacotherapy, and IBD-specific therapy for depression is discussed. This review summarizes evidence of the effect of depression on both personal and professional aspects of the daily lives of women with IBD, which extends beyond negative moods. It applies this information to screening and integrative treatment, resulting in a holistic approach to this multidimensional problem. We also discuss how depression affects males with IBD differently from females. Finally, we discuss the need for gender-based studies on depression in individuals with IBD.
New Synthetic Cannabinoid ADB-BUTINACA-Related Death of a Police Dog
Authors: Tokarczyk Bogdan , Suchan Marta , Adamowicz Piotr 
Published: December 2022

Abstract
The popularity of synthetic cannabinoids puts police sniffer dogs at risk of accidental introduction of such substances into the body. The extreme efficacy and potency of many new synthetic cannabinoids are associated with a high risk of serious poisonings and even deaths. The paper presents the toxicological findings in an intoxication of a police dog, in which a new synthetic cannabinoid ADB-BUTINACA was detected and quantified in postmortem materials. The screening analyses were performed by liquid chromatography with tandem mass spectrometry (LC–MS-MS) and liquid chromatography--quadrupole/time-of-flight mass spectrometry (LC–QTOF-MS). LC–MS-MS was also used for quantitative analyses, while LC–QTOF-MS for metabolite identification. Due to unusual matrices, the standard addition method was used for the quantitative determination of ADB-BUTINACA. The determined concentrations of ADB-BUTINACA in blood, lung, stomach, liver and kidney were 8.1 ng/mL, 6.4 ng/g, 1.5 ng/g, 1.8 ng/g and 0.4 ng/g, respectively. Apart from ADB-BUTINACA, the monohydroxylated metabolites and the dihydrodiol metabolite were detected and identified in all analyzed materials, and moreover the product of N-debutylation was found in blood and liver. The described case presents the identification and quantitation of a new synthetic cannabinoid ADB-BUTINACA in postmortem dog specimens. Although the cause of death was acute gastric dilatation, it cannot be ruled out that this process was the result of synthetic cannabinoid inhalation. Due to dogs’ sensitivity to cannabinoids, ADB-BUTINACA poisoning cannot be excluded either. The described case suggests that ADB-BUTINACA elicits serious adverse effects in dogs. The article also indicates the dangers to which police dogs coming into contact with extremely potent drugs may be exposed.
Building structure with elastoplastic bilinear model under multi-dimensional earthquake forces
Authors: Hong Hong-Ki , Liu Li-Wei , Shiao Ya-Po , Chang Cheng-Jih 
Published: December 2022

Abstract
Developed herein is an analysis procedure based on closed-form solutions to elastoplastic bilinear model of building structures accounted for different stiffnesses and yielding forces in different directions and rotated yield ellipses in different floor levels due to the layout of buildings and the complexity of structural members. The seismic design often considers earthquake forces on multiple floor levels but usually only in a single direction. However, in reality, the direction of the earthquake is not limited to one particular direction. Therefore, studying the influence of a two-way, furthermore multi-dimensional, earthquake on buildings is of great value. To estimate the total seismic demand on inelastic building structures subjected to multi-dimensional loading, this paper aims to find closed-form solution responses to an input rectilinear force path for the elastoplastic bilinear model of Hong and Liu (1999) which already has available closed-form solution responses to an input rectilinear displacement path. In this paper the elastoplastic bilinear model of building structures and Minkowski spacetime are adapted to accommodate such situations as different stiffnesses and yielding forces in different directions and rotated yield ellipses in different floor levels.
Association of circulating markers with cognitive decline after radiation therapy for brain metastasis
Authors: Huntoon Kristin , Anderson S Keith , Ballman Karla V , Twohy Erin , Dooley Katharine , Jiang Wen , An Yi , Li Jing , von Roemeling Christina , Qie Yaqing , Ross Owen A , Cerhan Jane H , Whitton Anthony C , Greenspoon Jeffrey N , Parney Ian F , Ashman Jonathan B , Bahary Jean-Paul , Hadjipanayis Constantinos , Urbanic James J , Farace Elana , Khuntia Deepak , Laack Nadia N , Brown Paul D , Roberge David , Kim Betty Y S 
Published: December 2022

AbstractBackgroundA recent phase III trial (NCT01372774) comparing use of stereotactic radiosurgery [SRS] versus whole-brain radiation therapy [WBRT] after surgical resection of a single brain metastasis revealed that declines in cognitive function were more common with WBRT than with SRS. A secondary endpoint in that trial, and the primary objective in this secondary analysis, was to identify baseline biomarkers associated with cognitive impairment after either form of radiotherapy for brain metastasis. Here we report our findings on APOE genotype and serum levels of associated proteins and their association with radiation-induced neurocognitive decline.MethodsIn this retrospective analysis of prospectively collected samples from a completed randomized clinical trial, patients provided blood samples every 3 months that were tested by genotyping and enzyme-linked immunosorbent assay, and results were analyzed in association with cognitive impairment.ResultsThe APOE genotype was not associated with neurocognitive impairment at 3 months. However, low serum levels of ApoJ, ApoE, or ApoA protein (all P &lt; .01) and higher amyloid beta (Aβ 1–42) levels (P = .048) at baseline indicated a greater likelihood of neurocognitive decline at 3 months after SRS, whereas lower ApoJ levels were associated with decline after WBRT (P = .014).ConclusionsPatients with these pretreatment serum markers should be counseled about radiation-related neurocognitive decline.
UB2/UB3/TSH4-anchored transcriptional networks regulate early maize inflorescence development in response to simulated shade
Authors: Kong Dexin , Li Changyu , Xue Weicong , Wei Hongbin , Ding Hui , Hu Guizhen , Zhang Xiaoming , Zhang Guisen , Zou Ting , Xian Yuting , Wang Baobao , Zhao Yongping , Liu Yuting , Xie Yurong , Xu Miaoyun , Wu Hong , Liu Qing , Wang Haiyang 
Published: December 2022

Abstract
Increasing planting density has been adopted as an effective means to increase maize (Zea mays) yield. Competition for light from neighbors can trigger plant shade avoidance syndrome, which includes accelerated flowering. However, the regulatory networks of maize inflorescence development in response to high-density planting remain poorly understood. In this study, we showed that shade-mimicking treatments cause precocious development of the tassels and ears. Comparative transcriptome profiling analyses revealed the enrichment of phytohormone-related genes and transcriptional regulators among the genes co-regulated by developmental progression and simulated shade. Network analysis showed that three homologous Squamosa promoter binding protein (SBP)-like (SPL) transcription factors, Unbranched2 (UB2), Unbranched3 (UB3), and Tasselsheath4 (TSH4), individually exhibited connectivity to over 2,400 genes across the V3-to-V9 stages of tassel development. In addition, we showed that the ub2 ub3 double mutant and tsh4 single mutant were almost insensitive to simulated shade treatments. Moreover, we demonstrated that UB2/UB3/TSH4 could directly regulate the expression of Barren inflorescence2 (BIF2) and Zea mays teosinte branched1/cycloidea/proliferating cell factor30 (ZmTCP30). Furthermore, we functionally verified a role of ZmTCP30 in regulating tassel branching and ear development. Our results reveal a UB2/UB3/TSH4-anchored transcriptional regulatory network of maize inflorescence development and provide valuable targets for breeding shade-tolerant maize cultivars.