bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity
Authors: Raza Ali , Salehi Hajar , Bashir Shanza , Tabassum Javaria , Jamla Monica , Charagh Sidra , Barmukh Rutwik , Mir Rakeeb Ahmad , Bhat Basharat Ahmad , Javed Muhammad Arshad , Guan Dong-Xing , Mir Reyazul Rouf , Siddique Kadambot H. M. , Varshney Rajeev K. 
Published: February 2024

AbstractThe escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.
The value of C-reactive protein, leucocytes and vital signs in detecting major complications after oncological colorectal surgery
Authors: Gielen Anke H. C. , Schoenmakers Maud , Breukink Stephanie O. , Winkens Bjorn , van der Horst Jischmaël , Wevers Kevin P. , Melenhorst Jarno 
Published: February 2024

Abstract
Purpose
To assess the association of postoperative C-reactive protein (CRP), leucocytes and vital signs in the first three postoperative days (PODs) with major complications after oncological colorectal resections in a tertiary referral centre for colorectal cancer in The Netherlands.

Methods
A retrospective cohort study, including 594 consecutive patients who underwent an oncological colorectal resection at Maastricht University Medical Centre between January 2016 and December 2020. Descriptive analyses of patient characteristics were performed. Logistic regression models were used to assess associations of leucocytes, CRP and Modified Early Warning Score (MEWS) at PODs 1–3 with major complications. Receiver operating characteristic curve analyses were used to establish cut-off values for CRP.

Results
A total of 364 (61.3%) patients have recovered without any postoperative complications, 134 (22.6%) patients have encountered minor complications and 96 (16.2%) developed major complications. CRP levels reached their peak on POD 2, with a mean value of 155 mg/L. This peak was significantly higher in patients with more advanced stages of disease and patients undergoing open procedures, regardless of complications. A cut-off value of 170 mg/L was established for CRP on POD 2 and 152 mg/L on POD 3. Leucocytes and MEWS also demonstrated a peak on POD 2 for patients with major complications.

Conclusions
Statistically significant associations were found for CRP, Δ CRP, Δ leucocytes and MEWS with major complications on POD 2. Patients with CRP levels ≥ 170 mg/L on POD 2 should be carefully evaluated, as this may indicate an increased risk of developing major complications.
COVID-19 in the Netherlands: lessons from a nationwide query of dutch autopsy, histology, and cytology pathological reports
Authors: Lopuhaä Boaz , Voorham Q. J. M. , van Kemenade Folkert J. , von der Thüsen Jan H. 
Published: February 2024

AbstractSince the onset of the COVID-19 pandemic, autopsies have played a valuable role in understanding the pathophysiology of COVID-19. In this study, we have analyzed COVID-19-related pathology reports from autopsies, histology, and cytology on a nationwide level. Pathology reports from all 43 pathology laboratories in the Netherlands stating “COVID,” “Corona,” and/or “SARS” were queried from the Dutch Nationwide Pathology Database (Palga). Consecutive reports of the included patients were also retrieved. Out of 5065 entries, a total of 1833 eligible COVID-19-related pathology reports between January 2020 and June 2021 were included in this collection of reports. Lung histopathology reports reflected differences in the severity of abnormalities (acute diffuse alveolar damage, alveolar histiocytes, and thrombi during the first three pandemic waves (Wuhan variant) versus the fourth wave (alpha variant)). Autopsy reports from 2020 state significantly shorter disease duration and younger age of death compared to autopsy reports from 2021. All reports together reflected a more granular pathology with comorbidities such as chronic histiocytic intervillositis, perniosis, and thrombi found in a variety of organs (lungs, kidneys, and small and large intestines). This nationwide overview of pathology reports provides data related to deaths as well as comorbidities in a clinical setting of COVID-19. Certain findings reported in SARS-CoV-infected lungs and placentas were also reported in post-COVID-19 tissue of the same kind. Consecutive reports after the earliest reports with COVID-19 allowed for follow-up reports. These follow-up reports can help with post-viral studies regarding long-term effects of COVID-19 as well as identifying the effects of different SARS-CoV-2 variants.
Determinants of health-related quality of life in healthy children and adolescents during the COVID-19 pandemic: Results from a prospective longitudinal cohort study
Authors: Haile Sarah R. , Peralta Gabriela P. , Raineri Alessia , Rueegg Sonja , Ulytė Agnė , Puhan Milo A. , Radtke Thomas , Kriemler Susi 
Published: February 2024

AbstractUnderstanding health-related quality of life (HRQOL) in children and adolescents, during a pandemic and afterwards, aids in understanding how circumstances in their lives impact their well-being. We aimed to identify determinants of HRQOL from a broad range of biological, psychological, and social factors in a large longitudinal population-based sample. Data was taken from a longitudinal sample (n = 1843) of children and adolescents enrolled in the prospective school-based cohort study Ciao Corona in Switzerland. The primary outcome was HRQOL, assessed using the KINDL total score and its subscales (each from 0, worst, to 100, best). Potential determinants, including biological (physical activity, screen time, sleep, etc.), psychological (sadness, anxiousness, stress), and social (nationality, parents’ education, etc.) factors, were assessed in 2020 and 2021 and HRQOL in 2022. Determinants were identified in a data-driven manner using recursive partitioning to define homogeneous subgroups, stratified by school level. Median KINDL total score in the empirically identified subgroups ranged from 68 to 83 in primary school children and from 69 to 82 in adolescents in secondary school. The psychological factors sadness, anxiousness, and stress in 2021 were identified as the most important determinants of HRQOL in both primary and secondary school children. Other factors, such as physical activity, screen time, chronic health conditions, or nationality, were determinants only in individual subscales.Conclusion: Recent mental health, more than biological, physical, or social factors, played a key role in determining HRQOL in children and adolescents during pandemic times. Public health strategies to improve mental health may therefore be effective in improving HRQOL in this age group.

What is Known:• Assessing health-related quality of life (HRQOL) in children and adolescents aids in understanding how life circumstances impact their well-being.• HRQOL is a complex construct, involving biological, psychological, and social factors. Factors driving HRQOL in children and adolescents are not often studied in longitudinal population-based samples.

What is New:• Mental health (stress, anxiousness, sadness) played a key role in determining HRQOL during the coronavirus pandemic, more than biological or social factors.• Public health strategies to improve mental health may be effective in improving HRQOL in children.
Bartonella in bat flies from the Egyptian fruit bat in the Middle East
Authors: Špitalská Eva , Ševčík Martin , Peresh Yevheniy-Yuliy , Benda Petr 
Published: February 2024

AbstractIn the family of fruit bats, Pteropodidae Gray, 1821, as in the third most diverse group of bats (Chiroptera), the bacterium of the genus Bartonella was detected in several species as well as in a few species of their insect ectoparasites in some tropical and sub-tropical regions of the Old World. The Egyptian fruit bat, Rousettus aegyptiacus (Geoffroy, 1810), is one of the most widespread fruit bats, occurring between South Africa, Senegal, and Pakistan. In this bat species, Candidatus Bartonella rousetti has been detected in three African populations in Nigeria, Kenya, and Zambia. This fruit bat, however, also occurs in the Palaearctic, an area isolating the species geographically and phylogenetically from the Afrotropical part of its distribution range. We screened the blood-sucking bat flies (family Nycteribiidae) from R. aegyptiacus for the presence of the Bartonella bacteria. A rich material of bat fly Eucampsipoda aegyptia (Macquart, 1850), a monoxenous ectoparasite of the Egyptian fruit bats, was collected at 26 localities in seven countries (Egypt, Iran, Jordan, Lebanon, Oman, United Arab Emirates, and Yemen) of the Middle East in 2007–2013. The DNA isolates from the bat flies were subjected to a three-marker (gltA, ssrA, and intergenic spacer region, ITS) multilocus sequence analysis. Based on the amplification of the fragment of ssrA gene by a real-time PCR, 65 E. aegyptia samples from 19 localities in all seven countries were positive for the bacteria. One to five Bartonella-positive individuals of E. aegyptia were collected per one individual of R. aegyptiacus. An analysis of the ITS and gltA genes indicated the presence of an uncultured Bartonella sp., belonging to the Cand. B. rousetti genogroup, identified from populations of the Egyptian fruit bat in Africa. These results support the hypothesis that Bartonella’s diversity corresponds to its host’s diversity (and phylogenetic structure). Specific lineages of pathogens are present in specific phylogenetic groups of bats.
Detecting SQL injection attacks by binary gray wolf optimizer and machine learning algorithms
Authors: Arasteh Bahman , Aghaei Babak , Farzad Behnoud , Arasteh Keyvan , Kiani Farzad , Torkamanian-Afshar Mahsa 
Published: February 2024

AbstractSQL injection is one of the important security issues in web applications because it allows an attacker to interact with the application's database. SQL injection attacks can be detected using machine learning algorithms. The effective features should be employed in the training stage to develop an optimal classifier with optimal accuracy. Identifying the most effective features is an NP-complete combinatorial optimization problem. Feature selection is the process of selecting the training dataset's smallest and most effective features. The main objective of this study is to enhance the accuracy, precision, and sensitivity of the SQLi detection method. In this study, an effective method to detect SQL injection attacks has been proposed. In the first stage, a specific training dataset consisting of 13 features was prepared. In the second stage, two different binary versions of the Gray-Wolf algorithm were developed to select the most effective features of the dataset. The created optimal datasets were used by different machine learning algorithms. Creating a new SQLi training dataset with 13 numeric features, developing two different binary versions of the gray wolf optimizer to optimally select the features of the dataset, and creating an effective and efficient classifier to detect SQLi attacks are the main contributions of this study. The results of the conducted tests indicate that the proposed SQL injection detector obtain 99.68% accuracy, 99.40% precision, and 98.72% sensitivity. The proposed method increases the efficiency of attack detection methods by selecting 20% of the most effective features.
Advancing 3D printed microfluidics with computational methods for sweat analysis
Authors: Ece Emre , Ölmez Kadriye , Hacıosmanoğlu Nedim , Atabay Maryam , Inci Fatih 
Published: February 2024

AbstractThe intricate tapestry of biomarkers, including proteins, lipids, carbohydrates, vesicles, and nucleic acids within sweat, exhibits a profound correlation with the ones in the bloodstream. The facile extraction of samples from sweat glands has recently positioned sweat sampling at the forefront of non-invasive health monitoring and diagnostics. While extant platforms for sweat analysis exist, the imperative for portability, cost-effectiveness, ease of manufacture, and expeditious turnaround underscores the necessity for parameters that transcend conventional considerations. In this regard, 3D printed microfluidic devices emerge as promising systems, offering a harmonious fusion of attributes such as multifunctional integration, flexibility, biocompatibility, a controlled closed environment, and a minimal requisite analyte volume—features that leverage their prominence in the realm of sweat analysis. However, formidable challenges, including high throughput demands, chemical interactions intrinsic to the printing materials, size constraints, and durability concerns, beset the landscape of 3D printed microfluidic devices. Within this paradigm, we expound upon the foundational aspects of 3D printed microfluidic devices and proffer a distinctive perspective by delving into the computational study of printing materials utilizing density functional theory (DFT) and molecular dynamics (MD) methodologies. This multifaceted approach serves manifold purposes: (i) understanding the complexity of microfluidic systems, (ii) facilitating comprehensive analyses, (iii) saving both cost and time, (iv) improving design optimization, and (v) augmenting resolution. In a nutshell, the allure of 3D printing lies in its capacity for affordable and expeditious production, offering seamless integration of diverse components into microfluidic devices—a testament to their inherent utility in the domain of sweat analysis. The synergistic fusion of computational assessment methodologies with materials science not only optimizes analysis and production processes, but also expedites their widespread accessibility, ensuring continuous biomarker monitoring from sweat for end-users.
Graphical Abstract
The restorative and state enhancing potential of abstract fractal-like imagery and interactive mindfulness interventions in virtual reality
Authors: Barton Adam C. , Do Michael , Sheen Jade , Byrne Linda K. 
Published: February 2024

AbstractThe restorative and mental state enhancing effects of brief mindfulness-based interventions (MBIs) and restorative environments such as nature has been supported in the research literature. However, regular adoption of these practices is limited by practical constraints and motivational barriers. The current study addressed these challenges by introducing two novel approaches which utilise the immersive and interactive qualities of virtual reality (VR). This included an interactive MBI and an abstract restorative environment using fractal-like imagery. These approaches were explored using a comparative evaluation of two short (6 min) VR interventions: Passive VR (applying principles from restorative interventions) and Interactive VR (implementing a focused attention form of mindfulness meditation). A mixed methods approach revealed increased state mindfulness, reduced mental fatigue, and enhanced aspects of mood (calm/relaxation, anxiety) consistently between conditions. Between group differences revealed additional benefits for cognition (focus), mood (happiness and sadness), and motivational value with the interactive intervention. The abstract environment, used in both interventions, maintained comparable levels of perceived restoration with a nature VR control condition. The results provide preliminary evidence supporting the use of interactive approaches for mindfulness interventions and abstract versions of restorative environments.
Current status of head and neck sarcomas in Japan in 2016–2019: an analysis using the national cancer registry
Authors: Rikitake Ryoko , Mizushima Yu , Yoshimoto Seiichi , Higashi Takahiro , Satake Tomoyuki , Morizane Chigusa , Kawai Akira 
Published: February 2024

Abstract
Background
Head and neck sarcomas are especially rare in Asia, leading to limited clinical evidence. This study aimed to investigate the incidence, clinical features, treatment status, and outcome of these sarcomas using data from the National Cancer Registry in Japan.

Methods
All head and neck sarcomas diagnosed between 2016 and 2019 and recorded in the National Cancer Registry were analyzed. Data on sex, age, primary site, histological type, stage, treatment modality, and prognostic information were collected. Age-adjusted incidence and 3-year survival rates of patients with head and neck sarcomas were calculated.

Results
Overall, 635 head and neck sarcoma patients were identified. Head and neck sarcoma occurred more frequently in men and patients in their 70 s. The age-adjusted annual incidence rate was 0.125 per 100,000 patients in the 2015 Japanese model or 0.089 per 100,000 patients in the world population model. The nasal cavity and paranasal sinuses were the most frequent primary sites, with rhabdomyosarcoma as the most common histologic type. Treatment typically involved chemotherapy and/or radiation therapy for rhabdomyosarcoma and Ewing’s sarcoma, whereas surgical approaches for other types. Three-year survival rate of head and neck sarcoma patients was 64.8%.

Conclusions
Head and neck sarcomas occurred rarely, but most frequently in the nasal cavity and paranasal sinuses in Japan. Poor outcomes were observed for sarcoma patients than for non-sarcoma head and neck cancer patients.
Assessment of health state utilities associated with adult and pediatric acid sphingomyelinase deficiency (ASMD)
Authors: Matza Louis S. , Stewart Katie D. , Fournier Marie , Rowen Donna , Lachmann Robin , Scarpa Maurizio , Mengel Eugen , Obermeyer Travis , Ayik Evren , Laredo Fernando , Pulikottil-Jacob Ruth 
Published: February 2024

Abstract
Introduction
Acid sphingomyelinase deficiency (ASMD) type B is a rare genetic disorder leading to enlargement of the spleen and liver, pulmonary dysfunction, and other symptoms. Cost-utility analyses are often conducted to quantify the value of new treatments, and these analyses require health state utilities. Therefore, the purpose of this study was to estimate utilities associated with varying levels of severity of adult and pediatric ASMD type B.

Methods
Seven adult and seven child health state vignettes describing ASMD were developed based on published literature, clinical trial results, and interviews with clinicians, patients with ASMD, and parents of children with ASMD. The health states were valued in time trade-off interviews with adult general population respondents in the UK.

Results
Interviews were completed with 202 participants (50.0% female; mean age = 41.3 years). The health state representing ASMD without impairment had the highest mean utility for both the adult and child health states (0.92/0.94), and severe ASMD had the lowest mean utility (0.33/0.45). Every child health state had a significantly greater utility than the corresponding adult health state. Differences between adult/child paired states ranged from 0.02 to 0.13. Subgroup analyses explored the impact of parenting status on valuation of child health states.

Discussion
Greater severity of ASMD was associated with lower mean utility. Results have implications for valuation of pediatric health states. The resulting utilities may be useful in cost-utility modeling estimating the value of treatment for ASMD.
The past, present, and a future for native charr in Japan
Authors: Fausch Kurt D. , Morita Kentaro , Tsuboi Jun-ichi , Kanno Yoichiro , Yamamoto Shoichiro , Kishi Daisuke , Dunham Jason B. , Koizumi Itsuro , Hasegawa Koh , Inoue Mikio , Sato Takuya , Kitano Satoshi 
Published: February 2024

AbstractCharrs (Salvelinus) reach their southernmost distribution in Japan, and are uniquely adapted to the short, steep streams of this island archipelago. Southern Asian Dolly Varden (Salvelinus curilus) occur only in Hokkaido Island, whereas white-spotted charr (Salvelinus leucomaenis) range to southern Honshu. Both species diverged from an ancestral lineage during the late Pliocene/early Pleistocene, when lowered sea levels created semi-enclosed water bodies in the seas of Japan and Okhotsk. Genetic analyses showed S. curilus represents the most ancient divergence from the Dolly Varden (Salvelinus malma) - Arctic charr (Salvelinus alpinus) group, and revealed five lineages of S. leucomaenis which align differently than traditional subspecies. Japanese charr display diverse and flexible life histories including anadromous fish with partial migration, and fluvial, adfluvial, and resident forms. In Hokkaido, Dolly Varden are distributed upstream and white-spotted charr downstream. They coexist in narrow sympatric zones through adaptive shifts by Dolly Varden in behavior and morphology that facilitate benthic foraging. Both species hybridize with native and nonnative salmonids, and are displaced from microhabitats and decline in abundance when rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta) invade. Japan streams contain over 95,000 erosion control dams which create short stream fragments (medians ~200 m). This has increased extirpation of charr populations via lower genetic diversity and stochastic and demographic factors. Tributaries provide complex rearing habitats, afford refuges from floods, and supply recruits that sustain populations in mainstem fragments and create metapopulations in connected riverscapes. Charr play central roles in linked stream-riparian food webs, and cause direct and indirect effects that cascade to streambed algae and riparian predators when linkages are disrupted by anthropogenic effects or altered by native parasites. Many charr populations are threatened by habitat fragmentation and introgression or invasion by nonnative forms, but efforts to conserve charr are growing. These include restoring connectivity among pure populations above barriers that prevent invasions, protecting tributary nurseries, and instituting angling regulations to protect headwater populations. Key steps include inventorying pure populations, identifying conservation units, selecting appropriate management based on connectivity and biotic interactions, and engaging stakeholders and youth to engender an ethic for conserving irreplaceable charr lineages.