bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing AlphaFold-Multimer-based Protein Complex Structure Prediction with MULTICOM in CASP15
Authors: Liu Jian , Guo Zhiye , Wu Tianqi , Roy Raj , Quadir Farhan , Chen Chen , Cheng Jianlin 
Published: June 2023

Abstract
AlphaFold-Multimer has emerged as the state-of-the-art tool for predicting the quaternary structure of protein complexes (assemblies or multimers) since its release in 2021. To further enhance the AlphaFold-Multimer-based complex structure prediction, we developed a new quaternary structure prediction system (MULTICOM) to improve the input fed to AlphaFold-Multimer and evaluate and refine the outputs generated by AlphaFold2-Multimer. Specifically, MULTICOM samples diverse multiple sequence alignments (MSAs) and templates for AlphaFold-Multimer to generate structural models by using both traditional sequence alignments and new Foldseek-based structure alignments, ranks structural models through multiple complementary metrics, and refines the structural models via a Foldseek structure alignment-based refinement method. The MULTICOM system with different implementations was blindly tested in the assembly structure prediction in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022 as both server and human predictors. Our server (MULTICOM_qa) ranked 3rd among 26 CASP15 server predictors and our human predictor (MULTICOM_human) ranked 7th among 87 CASP15 server and human predictors. The average TM-score of the first models predicted by MULTICOM_qa for CASP15 assembly targets is ~0.76, 5.3% higher than ~0.72 of the standard AlphaFold-Multimer. The average TM-score of the best of top 5 models predicted by MULTICOM_qa is ~0.80, about 8% higher than ~0.74 of the standard AlphaFold-Multimer. Moreover, the novel Foldseek Structure Alignment-based Model Generation (FSAMG) method based on AlphaFold-Multimer outperforms the widely used sequence alignment-based model generation.
Continuing vocational training in times of economic uncertainty - An event-study analysis in real time
Authors: Dauth Christine , Lang Julia 
Published: June 2023

Abstract
Continuing vocational training (CVT) is a key channel for employees to adapt their skills to changing requirements in the labor market due to structural changes and digitization. The COVID-19 pandemic and the energy crisis in consequence of the war in Ukraine may have accelerated these developments. Yet, it is unclear how the economic impacts of these crises affect individuals’ occupational preferences. In detail, we want to investigate how demand for CVT changes in times of economic uncertainty. We use Google Trends data for Germany and apply an event study analysis to examine how interest in CVT developed with the onset of the COVID-19 pandemic and the Russian attack on Ukraine. We find that the interest in CVT strongly declined during the first wave of the pandemic regardless of how severely a region was affected. During the second lockdown, the decline in CVT interest was more pronounced in the eastern German states where we find a general decline in search intensity since March 2020. Overall, we show that the search intensity for CVT decreased on average by 12 to 19 percent during the first 2.5 years of the pandemic, whereas the search intensity for online CVT increased by 39 to 45 percent. We also see a decrease in the search intensity for CVT at the beginning of the energy crisis.
JEL Codes: I18, J24
Biointerference-free signal generation via a self-floating transporter for early diagnosis of bladder cancer at the point of care
Authors: Keum Changjoon , Yeom Haejin , Noh Tae Il , Yi Seung Yong , Jin Soyeong , Kim Chaekyu , Shim Ji Sung , Yoon Sung Goo , Kim Hojun , Lee Kwan Hyi , Kang Seok Ho , Jeong Youngdo 
Published: June 2023

Abstract

At-home bladder cancer (BC) diagnostic kits using urine samples enable effective screening and surveillance, thereby facilitating its early detection, reducing the risk of BC progression, and improving patient survival rates. However, the complexity and heterogeneity of urine samples from BC patients with frequent hematuria interfere with signal transduction, leading to inaccurate diagnosis. Here, we developed a diagnostic platform that utilizes a separate biphasic system and a self-floating signal messenger to address the challenge of using untreated urine samples for at-home BC diagnosis. In our system, buoyant messengers are transferred from the urine to the organic phase autonomously in response to the biomarkers of BC; subsequently, a signal is generated in the organic layer where there are no interferents. We demonstrated the practicability of our system using 105 double-blind patient urine samples, including hematuria, andobtained ~89% accuracy, showing subequal diagnostic accuracy at the early stage of BC. This platform enabling accurate diagnosis without complex sample treatments would provide a convenient tool for screening cancers at home.
Effect of bio-inoculants and plant growth regulators on germination and seedling growth of wild ber (Ziziphus rotundifolia Lamk.) under in-vitro conditions
Authors: Singla Aayush , Kumar Mukesh , Sharma JR , Lamba Maya , kumar Manish , Dhundwal Arjoo , Dhattarwal Gurmeet , Gavri Ankit 
Published: June 2023

Abstract
Ziziphus rotundifolia Lamk. (Rhamnaceae) is an important rootstock for commercially cultivating ber orchard. There is problem in rapid seed germination and vigorous seedling availability by researchers and growers. So, improving germination and producing vigorous seedling through rootstocks is crucial as it is responsible to determine the quality of orchard. The prime motive of this experiment was to investigate the effectiveness of bio-inoculants and plant growth regulators (PGRs) in improving the germination rate and seedling growth of wild ber seeds under in-vitro conditions. The experiment was conducted at the Department of Seed Science and Technology, CCS Haryana Agricultural University, Hisar, India, during the season 2021-22. The seeds removed from stone were treated with five bio-inoculants viz, Azoteeka- Mac 27, Azoteeka- HT 54, Phosphoteeka- P36, Azospirillum-J11-12 and integrated biofertilizer (NPK- 1:1:1) by soaking for 30 min and dipped in six-plant growth regulators (PGRs) viz., 50 mg/L Gibberellic acid (GA3), 100 mg/L GA3, 50 mg/L 1-Naphthalene acetic acid (NAA), 100 mg/L NAA, 50 mg/L Indole-3-butyric acid (IBA), 100 mg/L IBA for 24 hrs and control. The experiment was conducted in CRD design with three replications. Among different treatments under laboratory conditions, maximum seed viability (92 ± 2.3%), maximum germination percentage (80.44 ± 1.84%), maximum vigour indices [vigour index- I (1633), vigour index- II (2762)] and the least mean germination time (9.7 ± 0.03 days) were recorded when seeds were treated with GA3 @100 mg/L for 24 hrs. Among different bio-inoculant treatments, the seed treated with integrated biofertilizer (NPK- 1:1:1) for 30 min led to the highest seedling length (20.33 ± 0.83 cm), maximum seedling fresh weight (159.8 ± 2.7 mg) and maximum seedling dry weight (35.06 ± 0.8 mg).
Epigenetic Regulation of Host Membrane Protein-Coding Genes Facilitates African Swine Fever Virus Infection
Authors: Qi Xiaolong , Xiang Yue , Sun Limeng , Xing Lingyu , Zhang Jinfu , Zhang SaiXian , Zhao Qiulin , Guo Yilin , Zhang Lu , Li Jingjin , Zhou Peng , Zheng Zhuqing , Dai Xueting , Jin Zhe , Jian Yaobang , Li Guosheng , Fu Yanan , Tan Yubei , Zhao Changzhi , Xie Shengsong , Cao Gang , Li Xinyun , Fang Lingzhao , Fu Liangliang , Peng Guiqing , Zhao Shuhong 
Published: June 2023

Abstract

African swine fever virus (ASFV) is a highly contagious pathogen that primarily affects domestic and wild pigs with specific tropism to porcine alveolar macrophages (PAMs), causing substantial economic losses in pig industry worldwide. Yet, host receptors and molecular mechanisms underlying the ASFV infection remain unknown, hindering the relevant vaccine development and precision breeding. Here, we present a comprehensive epigenetic atlas of ASFV-exposed PAMs by generating a total of 42 functional data at both bulk and single cell resolution. Suppressive expression regulation in ASFV-exposed cells showed that transcriptional activity of ARL4C was downregulated, leading to intracellular cholesterol accumulation for antiviral defense. In contrast, infection induced enhancer-promoter interactions in the host genome to boost transcriptional activity of membrane protein-coding genes, thereby contributing to macrophage activation. Moreover, actively infected macrophages (carrying viral DNA) exposed transcriptional induction of those genes. The following experimental validation highlighted CD244 as a potential host-receptor of ASFV, which was associated with host susceptibility. Our findings collectively provide novel insights into the molecular regulation of PAMs during ASFV infection, facilitating the identifion of new opportunities for vaccine development and precision breeding against ASFV infection.
The intensification of flash droughts across China from 1981 to 2021
Authors: Zhang Shuyi , Li Mingxing , Ma Zhuguo , Jian Dongnan , Lv Meixia , Yang Qing , Duan Yawen , Amin Doaa 
Published: June 2023

Abstract

Flash droughts feature rapid onsets of soil moisture drought events and result in severe impacts and damages, especially on agricultural and ecological systems. How the flash drought regime across China varies on multitemporal scales with climate change is not fully clear yet. In this study, we extended the flash drought definition to apply to arid regions by adding an absolute soil moisture variation criterion. Then, we detected flash drought events across China during 1981–2021 and characterized their frequency, duration, and affected area changes on seasonal, annual, and decadal scales, using soil moisture data from the European Center for Medium-Range Weather Forecasts climate reanalysis-Land. Results show that hotspots of flash droughts appeared in North China and the Yangtze River Basin. During 1981–2021, the hotspots, even nationwide, underwent significant increases in frequencies, durations, and affected areas of flash droughts. The increases held in the extremely high values of the frequencies and durations in the decadal comparisons. Especially, North China saw the most extensive and rapid increases. Seasonally, flash drought frequencies and durations intensified more during spring and autumn, and seasonal hotspots in eastern China shifted in phase with spatial patterns of soil moisture loss balanced by precipitation and evapotranspiration. Thus, flash droughts tended to amplify atmospheric aridity. These findings on the hotspot regions and the spatiotemporal evolutions of flash droughts across China would pinpoint soil moisture responses to climate change and prepare for climate change impacts on local eco-environments.
Immunobiology of Cancer Stem Cells and their Immunoevasion Mechanisms
Authors: Marzban Havva , Pedram Nastaran , Amini Parnian , Gholampour Yasaman , Saranjam Navid , Moradi Samira , Rahvarian Jeiran 
Published: June 2023

Abstract

Cancer stem cells (CSCs) defined as a small fraction of cells within malignancies have been isolated from tumors with different histological origins with stem related characteristics such as self-replicating potential, tumorigenesis, and therapy resistance. The dynamic communication between CSCs and tumor microenvironment particularly immune cells orchestrates their fate and plasticity as well as the patient outcome. According to recent evidence, it has been reported that they harness different immunological pathways to escape immunosurveillance and express aberrantly immunomodulatory agents or decreased levels of factors forming antigen presenting machinery (APM), subsequently followed by impaired antigen presentation and suppressed immune detection. As effective therapies are expected to be able to eradicate CSCs, mechanistic understanding of such interactions can provide insights into causes of therapy failure particularly in immunotherapy. Also, it can contribute to enhance the practical interventions against CSCs and their immunomodulatory features resulting in CSCs eradication and improving patient clinical outcome. The aim of this review is to explain the present knowledge regarding the immunobiology of CSCs and the immunoevasion mechanisms they use.
Influence of hypergravity – a novel stimulus on root growth phenotype and physio-biochemical parameters in sorghum (Sorghum bicolor L.)
Authors: I Mahamed Ashiq , Honnutagi Sana B , Hosamani Ravikumar , B Deepthi R , Swamy Basavalingayya K , Sathasivam Malarvizhi , Bagewadi Basavaraj , Reddy Uday G , Hanamaratti N G 
Published: June 2023

Abstract
Plants on Earth are evolutionarily subjected to constant mechanical stimulation of the gravitational field. Earth’s gravity (1g) significantly influences the growth and morphogenesis of crop plants. Hypergravity, an evolutionarily novel environment has been exploited to comprehend the response of plants in the context of terrestrial and extra-terrestrial applications. Recently, researchers have shown that hypergravity induces desired phenotypic variability that can be utilized for improving terrestrial agriculture. In the present study, we tested the hypothesis that hypergravity can be used as a novel tool for inducing reliable phenotypes that can be further exploited for crop improvement programs. In the present investigation, screening is done with varied hypergravity regimen in sorghum, The acute hypergravity (1000g for 1 hr) regimen induced a significant increase in seedling vigor and plant growth parameters in both laboratory and greenhouse conditions. Among nine genotypes screened, three best-responding were chosen for further study. Additionally, we quantified associated biochemical, and hormonal changes. Resultant data revealed a significant increase in total dehydrogenase enzyme activity in seed; catalase, superoxide dismutase enzymes in seedlings, and elevated total chlorophyll content in response to hypergravity. Further, hypergravity elicits robust phytohormones dynamics in the root seedlings, and endogenous levels of 3-Indole Acetic Acid and indole-3-butyric acid are shown to have a direct correlation with the regulation of root phenotypes. Collectively, this work describes the utility of hypergravity as a novel tool for inducing phenotype/s that could be potentially exploited for improving crop plants in the future.
Challenges for research uptake for health policymaking and practice in low- and middle-income countries: a scoping review
Authors: Semahegn Agumasie , Manyazewal Tsagahun , Hanlon Charlotte , Getachew Eyerusalem , Fekadu Bethelhem , Assefa Esubalew , Kassa Munir , Hopkins Michael , Woldehana Tasew , Davey Gail , Fekadu Abebaw 
Published: June 2023

Abstract

Background: An estimated 85% of research resources are wasted worldwide, while there is growing demand for context-based evidence-informed health policymaking. In low and middle-income countries (LMICs), research uptake for health policymaking and practice is low, while little is known about the barriers to the translation of health evidence to policy and local implementation. We conducted a scoping review to identify research uptake challenges for health policymaking and practice in LMICs.
Methods: The scoping review followed the preferred reporting items for systematic review and meta-analysis-extension for scoping reviews (PRISMA-ScR) and the Arksey and O'Malley framework. Both published and unpublished evidence on research uptake were systematically searched from major databases (PubMed, Cochrane Library, CINAHL(EBSCO), Global Health (Ovid)) and direct Google Scholar. Literature exploring barriers to uptake of research evidence in health policy and practice in LMICs were included and their key findings were synthesized using thematic areas to address the review question.
Results:A total of 4,291 literature were retrieved in the initial searches, of which 142 were included in the review as they met the eligibility criteria. The findings revealed low research uptake for policymaking and practice in LMICs. The challenges of research uptake were related to lack of understanding the local contexts, political priorities, poor stakeholder engagement and partnership, resource and capacity constraints, limited research infrastructure and institution support, low leadership commitment, lack of accountability and pathway, lack of communication and dissemination platforms.
Conclusion: Multiple barriers exist in LMICs that hinder the translation of health research evidence into policy and practice. This calls for designing pragmatic strategies that facilitate an in-depth understanding of the local contexts, a conducive environment for researchers and policymakers to work closely with, and government ownership mitigating the barriers to low evidence uptake.
Assessment of house hold water treatment practice in Endamehoni district, northern, Ethiopia: 2020: A community based cross-sectional study
Authors: Beyene Berhe , Teka Girmay , Gebremariam Brhane 
Published: June 2023

Abstract

Objective Water born disease is one of the major public health problems throughout the world. Drinking unsafe water is one of the front risk factor for the occurrence of waterborne diseases particularly in sub-Saharan African countries including Ethiopia. This study aims to assess household water treatment practice in Endamehoni district, northern Ethiopia. Results Practicing house hold water treatment was 47.0% (95% CI: 43.3–50.5). Being young age [AOR = 2.22; 95% CI: (1.93–13.01)], female [AOR = 3.9; 95% CI: (2.45–6.32), married marital status [AOR = 2.1; 95% CI: (0.84–11.10)], Secondary and above educational level[AOR = 2.2; 95% CI: (1.87–11.45)] and get unimproved source of drinking water [AOR = 6.8; 95% CI: (3.35–12.59)] were significantly associated with household water treatment practice. Water treatment at house hold level is low. Providing community based health education and providing improved water source may improve house hold water treatment practice.
The hidden factors of regional prevalence of intussusception in children under two years: Interdisciplinary examination using exploratory geostatistical analysis
Authors: Dixit Shikha , Das Manoja Kumar , Ramadugu Durga Chitra , Arora Narendra Kumar , Group The INCLEN Intussusception Surveillance Network Study 
Published: June 2023

Abstract

Both developed and developing countries carry a large burden of pediatric intussusception. Epidemiological studies conducted so far have highlighted the huge difference in the regional prevalence of intussusception cases. Through the lens of interdisciplinary exploratory geospatial analysis this manuscript attempts to relook at the regional prevalence data reported from the hospital based sentinel surveillance. The objectives of this study are to see the geospatial pattern of the hospital confirmed childhood intussusception, to check the geospatial pattern of cases and assessment of the potential reasons behind the existing geospatial pattern. Study utilizes address information of the cases documented in the INCLEN’s intussusception surveillance study (n 2221) conducted in between 2010 and 2017 after removing the personal identifiers. Majority of cases were concentrated in geographical clusters (Moran’s- I index 0.071 at the statistically significant (p value < 0.0010) Z score of 16.147. Out of the 2221 locations (residence of children with intussusception) across the country, 14 locations (6 in Kerala and 8 in Tamil Nadu) emerged as the hotspots (95% CI). Geostatistical analysis at the granular scale indicated that the 67% of the reported cases resided within < 50 km distance from the hospitals and average distance travelled by the patients to the sentinel hospital site was ~ 47 kms (CI 95%: min1km- max 378 km). The potential cause of the higher caseloads from a few sentinel sites were facility preference. We recommend designing community based surveillance studies for building better understanding of the incidence and epidemiological burden of intussusception.
Hydrogen sulfide maintains redox homeostasis and suppresses ganoderic acids biosynthesis under heat stress via S-sulfhydrating thioredoxin 1 in Ganoderma lucidum
Authors: Shangguan Jiaolei , Han Xiaofei , Qiao Jinjin , Qiu Hao , Liu He , Liu Rui , Ren Ang , Shi Liang , Zhu Jing , Zhao Mingwen 
Published: June 2023

Abstract
Hydrogen sulfide (H2S) is considered to be a novel gaseous signalling molecule with multiple physiological functions. Recently, the identification of sulfhydrated proteins has become a new hotspot in the analysis of the underlying mechanism of H2S. Our preliminary study has shown that H2S negatively regulates the heat-induced accumulation of ganoderic acids (GAs)，a major secondary metabolite in Ganoderma lucidum. However, a comprehensive understanding of its mechanism is lacking. In this study, sulfhydrated proteins in G. lucidum were quantified by quantitative proteomic mass spectrometry (MS), and the role of H2S in maintaining redox homeostasis under heat stress (HS) was determined. A redox-regulated protein, thioredoxin 1 (Trx1), was selected as a potential target of H2S. Further research revealed that the activity of Trx1 was provoked by sulfhydration at Cys31 and Cys34, contributing to the negative regulation of H2S to ROS accumulation and GAs biosynthesis under HS in G. lucidum. Our results provide a novel target for investigating the molecular mechanism of H2S physiological function. Moreover, new evidence is provided regarding the interaction mechanism between the H2S and ROS signalling pathways.
TERT RNAscope analysis of papillary thyroid carcinomas ≤1cm and synchronous lymph node metastases.
Authors: Eich Marie-Lisa , Jeske Wiebke , Zenz Uschi , Chiapponi Costanza , Alidousty Christina , Merkelbach-Bruse Sabine , Buettner Reinhard , Schultheis Anne Maria 
Published: June 2023

Abstract
Introduction Small papillary thyroid cacinomas measuring ≤ 1 cm usually have a good prognosis, however in a significant number of cases lymph node metastases can be observed.Material and Methods 22 cases of papillary thyroid carcinomas ≤ 1 cm with synchronous lymph node metastases were examined regarding morphological patterns and immunohistochemical status of p53 and Ki-67. Immunohistochemical BRAF V660E status was examined in primary tumors, whereas TERT alterations in lymph node metastases were evaluated by RNAScope®.Results Morphological patterns were heterogeneous in both primary tumors and lymph node metastases. Proliferation indices measured by Ki-67 were low. Both primary and lymph node metastases were wild type for p53 by immunohistochemical analysis. No lymph node metastasis showed TERT expression by RNAScope®.Discussion Our data indicate that TERT aberrations are not involved in the development of early lymph node metastasis in patients with PTC measuring ≤ 1cm.
Two-bit Analog to Digital Converter based on Acoustic Directional Coupler
Authors: Tahriri Kimiya , Bahrami Ali , Motaei Farzaneh 
Published: June 2023

Abstract
This study explores the novel application of a solid-state phononic crystal (PnC)-based analog-to-digital converter (ADC). To ensure a ripple-free output, a coupler is utilized, enabling 2-bit quantization. As the input amplitude increases, the structure exhibits non-linear behavior. This non-linearity emerges from an augmented displacement gradient, resulting in a corresponding alteration in mass density. The phononic crystal matrix consists of a 13×20 array of iron rods embedded within a PMMA host material. The system operates at a frequency of 67.5 kHz. A directional coupler is utilized to direct the emitted wave. For the designed model, we have considered transmission less than 0.3 to be logically equivalent to "0" and more than that to be logically equivalent to "1". Also, in order for both outputs to be on, transmission from 0.4 to 0.6 is equivalent to " 1" we have considered. The manufacturing tolerance of the converter is 0.03.