Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial patterns of nitrogen mineralization, fertilizer distribution and roots explain nitrate leaching from mature Amazonian oil palm plantation

Abstract. The African oil palm (Elaeis guineensis) is relatively well adapted to the pedoclimatic conditions of central Amazonia. The clayey upland soils of the region are well supplied with nitrogen, although they are deficient in most other nutrients. Under these conditions, oil palm does not respond to N fertilization with yield increases. In this research, the N status of a central Amazonian upland soil was evaluated after having supported a productive oil palm plantation for 15 years without N fertilization. Mineral N in the upper 2 m of soil showed pronounced spatial patterns, with very low concentrations close to the palms, indicative of efficient N uptake by the palms, and evidence for nitrate leaching into the subsoil in the inter‐tree spaces despite the near‐absence of a leguminous cover crop during the previous ten years. The pronounced increases of mineral N with increasing tree distance were explained by increases in N mineralization and a strong decrease in fine root length density of the palms, especially in the subsoil. Failure of the palms to fully occupy the available soil volume with their roots was apparently related to fertilizer placement close to the stem base, which over the years had led to steep fertility gradients between the soil under the trees and the inter‐tree spaces. Broadcast fertilization would have presumably favoured a more extensive lateral root development of the palms, and consequently improved nutrient and water uptake from the inter‐tree spaces. The incomplete soil occupation by the palm roots also suggests that young oil palms can be associated with shade tolerant crops without much risk of root competition. These conclusions may be valid also for other tree crops and may help to reduce nitrate leaching and consequently the need for N fertilization in Amazonian tree crop agriculture.
The Less Said The Better: Dewey, Neurath, and Mid-Century Theories of Truth

Abstract John Dewey’s theory of truth is widely viewed as proposing to substitute “warranted assertibility” for “truth,” a proposal that has faced serious objections since the late 1930s. By examining Dewey’s theory in its historical context – and, in particular, by drawing parallels with Otto Neurath’s concurrent attempts to develop a non-correspondence, non-formal theory of truth – I aim to shed light on Dewey’s underlying objectives. Dewey and Neurath were well-known to each other and, as their writing and correspondence make clear, they took similar paths over the mid-century philosophical terrain. I conclude that Dewey’s account of truth is more principled, and more relevant to historical debates, than it first appears.
Comparing Different Designs and Scales of Bubble Columns for Their Effectiveness in Treating Kraft Pulp Mill Effluents

Abstract The experimental results obtained in three different types of ozone contactors were analyzed to study the effects of the ozone contactor design, configuration, operating conditions, and scale-up on the: (1) ozonation process induced reduction efficiencies of color, AOX, COD, and TOC from biologically treated Kraft pulp mill effluents; (2) the increase in biodegradability of this type of wastewater; and (3) the dynamics of the ozone gas absorption process. The three types of ozone contactors included: (1) an extra-coarse-bubble diffuser ozone contactor; (2) an impinging-jet ozone contactor; and (3) a fine-bubble diffuser ozone contactor. Similar treatment levels were achieved in those ozone contactors although the impinging-jet bubble column was more effective in treating Kraft pulp mill effluents due to its smaller reactor volume and lower off-gas ozone concentrations. Consequently, the operating costs of an ozonation process and ozone off-gas destruction facilities will be greatly reduced when using the impinging-jet bubble column design for treating Kraft pulp mill effluents.
Tillage system and seeding rate effects on the performance of Brassica carinata

Brassica carinata, a nonfood oilseed crop, is used to produce renewable fuels because of its high oil content and favorable fatty acid profile. Production in the southeastern United States is relatively new, and information on agronomic management practices to optimize growth and yield is limited. Since optimal seeding rate may depend on the land preparation method for this small‐seeded crop, a study was conducted to evaluate the effect of tillage system (conventional, no‐till, broadcast‐disc, and ripper‐roller) and seeding rate (1.12, 5.60, 10.09, and 14.57 kg seed ha−1) on the performance of B. carinata. A randomized complete block design with a strip‐plot restriction on randomization and four replications was implemented in Headland, AL, Jay, FL, and Quincy, FL, over five site‐years during the 2017–2018 and 2018–2019 growing seasons. Data were collected on soil residue cover; plant population; soil penetrometer resistance and moisture; biomass (including carbon and nitrogen); stalk diameter; yield and yield components; seed oil, protein, and glucosinolates concentration; and oil composition. Soil penetrometer resistance was significantly affected by tillage system, with the ripper‐roller consistently having the lowest penetration resistance values across all site‐years. Ripper‐roller tillage had the highest oil content and lowest protein and glucosinolate contents. Yield response to tillage system was variable. Among seeding rate treatments, yield was lowest at 1.12 kg seed ha−1 and similar among 5.60, 10.09, and 14.57 kg seed ha−1 at all site‐years. There was no tillage by seeding rate interaction for yield. Results indicate that among seeding rate treatments used, 5.6 kg seed ha−1 rate was optimal at all site‐years regardless of land preparation method and is thus the recommended seeding rate for commercial carinata production in the Southeastern United States.
Characterization, Classification and Evaluation of Soils on Different Landforms in Ramachandrapuram Mandal of Chittoor District in Andhra Pradesh for Sustainable Land Use Planning

Typical pedons representing major landforms of Ramachandrapuram mandal in Chittoor district of Andhra Pradseh viz., plain, upland and hill slope developed from alluvium and granite–gneiss occurring under varying land use were characterized, classified and assessed for their nutrient status. The soils were moderately deep to very deep in depth, light yellowish brown to dark red in colour, slightly acidic to moderately alkaline in reaction and low to medium in organic carbon and cation exchange capacity. Further, the soils were low in available nitrogen, low to medium in available phosphorus, medium to high in available potassium and deficient in available sulphur. The soils were deficient in DTPA–extractable zinc and iron while these were sufficient in DTPA–extractable copper and manganese. Pedons 1 and 3, occupying plains, showed cambic (Bw) sub-surface diagnostic horizon and were classified as Vertic Haplustepts and Typic Haplustepts, respectively. Pedon 2 also occurring in plain did not exhibit any diagnostic horizon and was classified as Typic Ustipsamment. Pedon 4 on upland showed argillic (Bt) sub-surface diagnostic horizon and was classified as Typic Haplustalf. In contrast, the pedon 5 on upland did not show any diagnostic horizon and was classified as Typic Ustifluvent. However, pedons 6 and 7 located on hill slope did not show any diagnostic horizon, and were classified as Typic Ustorthents. On the basis of major soil constraints, suitable land use plan for the Ramachandrapuram mandal was also suggested for sustainable management of soils.
Fluorescence-Guided High-Grade Glioma Surgery More Than Four Hours After 5-Aminolevulinic Acid Administration

Background: Fluorescence-guided surgery (FGS) using 5-aminolevulic acid (5-ALA) is a widely used strategy for delineating tumor tissue from surrounding brain intraoperatively during high-grade glioma (HGG) resection. 5-ALA reaches peak plasma levels ~4 h after oral administration and is currently approved by the FDA for use 2–4 h prior to induction to anesthesia. Objective: To demonstrate that there is adequate intraoperative fluorescence in cases undergoing surgery more than 4 h after 5-ALA administration and compare survival and radiological recurrence to previous data. Methods: Retrospective analysis of HGG patients undergoing FGS more than 4 h after 5-ALA administration was performed at two institutions. Clinical, operative, and radiographic pre- and post-operative characteristics are presented. Results: Sixteen patients were identified, 6 of them female (37.5%), with mean (SD) age of 59.3 ± 11.5 years. Preoperative mean modified Rankin score (mRS) was 2 ± 1. All patients were dosed with 20 mg/kg 5-ALA the morning of surgery. Mean time to anesthesia induction was 425 ± 334 min. All cases had adequate intraoperative fluorescence. Eloquent cortex was involved in 12 cases (75%), and 13 cases (81.3%) had residual contrast enhancement on postoperative MRI. Mean progression-free survival was 5 ± 3 months. In the study period, 6 patients died (37.5%), mean mRS was 2.3 ± 1.3, Karnofsky score 71.9 ± 22.1, and NIHSS 3.9 ± 2.4. Conclusion: Here we demonstrate that 5-ALA-guided HGG resection can be performed safely more than 4 h after administration, with clinical results largely similar to previous reports. Relaxation of timing restrictions could improve procedure workflow in busy neurosurgical centers, without additional risk to patients.
The Tree Shrew as a Model for Cancer Research

Animal disease models are necessary in medical research, and an appropriate animal model is of great importance for studies about the prevention or treatment of cancer. The most important thing in the selection of animal models is to consider the similarity between animals and humans. The tree shrew (Tupaia belangeri) is a squirrel-like mammal which placed in the order Scandentia. Whole-genome sequencing has revealed that tree shrews are extremely similar to primate and humans than to rodents, with many highly conserved genes, which makes the data from studies that use tree shrews as models more convincing and the research outcomes more easily translatable. In tumor research, tree shrews are often used as animal models for hepatic and mammary cancers. As research has progressed, other types of tree shrew tumor models have been developed and exhibit clinical manifestations similar to those of humans. Combining the advantages of both rodents and primates, the tree shrew is expected to be the most powerful animal model for studying tumors.
Ototoxicity of Non-aminoglycoside Antibiotics

It is well-known that aminoglycoside antibiotics can cause significant hearing loss and vestibular deficits that have been described in animal studies and in clinical reports. The purpose of this review is to summarize relevant preclinical and clinical publications that discuss the ototoxicity of non-aminoglycoside antibiotics. The major classes of antibiotics other than aminoglycosides that have been associated with hearing loss in animal studies and in patients are discussed in this report. These antibiotics include: capreomycin, a polypeptide antibiotic that has been used to treat patients with drug-resistant tuberculosis, particularly in developing nations; the macrolides, including erythromycin, azithromycin and clarithromycin; and vancomycin. These antibiotics have been associated with ototoxicity, particularly in neonates. It is critical to be aware of the ototoxic potential of these antibiotics since so much attention has been given to the ototoxicity of aminoglycoside antibiotics in the literature.
Retinoic Acid Signaling Plays a Crucial Role in Excessive Caffeine Intake-Disturbed Apoptosis and Differentiation of Myogenic Progenitors

Whether or not the process of somitogenesis and myogenesis is affected by excessive caffeine intake still remains ambiguous. In this study, we first showed that caffeine treatment results in chest wall deformities and simultaneously reduced mRNA expressions of genes involved in myogenesis in the developing chicken embryos. We then used embryo cultures to assess in further detail how caffeine exposure affects the earliest steps of myogenesis, and we demonstrated that the caffeine treatment suppressed somitogenesis of chicken embryos by interfering with the expressions of crucial genes modulating apoptosis, proliferation, and differentiation of myogenic progenitors in differentiating somites. These phenotypes were abrogated by a retinoic acid (RA) antagonist in embryo cultures, even at low caffeine doses in C2C12 cells, implying that excess RA levels are responsible for these phenotypes in cells and possibly in vivo. These findings highlight that excessive caffeine exposure is negatively involved in regulating the development of myogenic progenitors through interfering with RA signaling. The RA somitogenesis/myogenesis pathway might be directly impacted by caffeine signaling rather than reflecting an indirect effect of the toxicity of excess caffeine dosage.
The Role of Chromatid Interference in Determining Meiotic Crossover Patterns

Plants, like all sexually reproducing organisms, create genetic variability by reshuffling parental alleles during meiosis. Patterns of genetic variation in the resulting gametes are determined by the independent assortment of chromosomes in meiosis I and by the number and positioning of crossover (CO) events during meiotic recombination. On the chromosome level, spatial distribution of CO events is biased by multiple regulatory mechanisms, such as CO assurance, interference and homeostasis. However, little is known about how multiple COs are distributed among the four chromatids of a bivalent. Chromatid interference (CI) has been proposed as a regulatory mechanism that biases distribution of multiple COs toward specific chromatid partners, however, its existence has not been well-studied and its putative mechanistic basis remains undescribed. Here, we introduce a novel method to quantitatively express CI, and take advantage of available tetrad-based genotyping data from Arabidopsis and maize male meiosis to quantify CI effects on a genome-wide and chromosomal scale. Overall, our analyses reveal random involvement of sister chromatids in double CO events across paired chromosomes, indicating an absence of CI. However, on a genome-wide level, CI was found to vary with physical distance between COs, albeit with different effects in Arabidopsis and maize. While effects of CI are minor in Arabidopsis and maize, the novel methodology introduced here enables quantitative interpretation of CI both on a local and genome-wide scale, and thus provides a key tool to study CI with relevance for both plant genetics and crop breeding.
Invertebrates in Science Communication: Confronting Scientists’ Practices and the Public’s Expectations

Good science communication should give the public the tools to make informed decisions and take action, which can be particularly important for nature conservation. The crisis in invertebrate conservation might be rooted in public prejudices against invertebrate animals, which are perceived as the unpopular 97% of Earth’s animal biodiversity. As such, how we approach science communication regarding those animals might yet play a critical role in their conservation. Given how specialized a topic invertebrate biology is, a large part of its communication fall to scientists. Here, we surveyed both scientists and members of the public about the former’s approaches and assumptions and the latter’s interest and expectations regarding invertebrate science communication, confronting the results of each survey. Our findings show that scientists and the public are only tangentially aligned; there is plenty of ground scientists and communicators need to pay attention to and explore better in order to achieve more meaningful and balanced science communication. Among other findings, topics and approaches that could be used to greater effect include (depending on age groups of the audience) history, folklore, pop culture, and pathology. Our results have unveiled some issues in science communication of invertebrates and are thus a good first approach to start defining the way forward.
Identifying the Signatures and Rules of Circulating Extracellular MicroRNA for Distinguishing Cancer Subtypes

Cancer is one of the most threatening diseases to humans. It can invade multiple significant organs, including lung, liver, stomach, pancreas, and even brain. The identification of cancer biomarkers is one of the most significant components of cancer studies as the foundation of clinical cancer diagnosis and related drug development. During the large-scale screening for cancer prevention and early diagnosis, obtaining cancer-related tissues is impossible. Thus, the identification of cancer-associated circulating biomarkers from liquid biopsy targeting has been proposed and has become the most important direction for research on clinical cancer diagnosis. Here, we analyzed pan-cancer extracellular microRNA profiles by using multiple machine-learning models. The extracellular microRNA profiles on 11 cancer types and non-cancer were first analyzed by Boruta to extract important microRNAs. Selected microRNAs were then evaluated by the Max-Relevance and Min-Redundancy feature selection method, resulting in a feature list, which were fed into the incremental feature selection method to identify candidate circulating extracellular microRNA for cancer recognition and classification. A series of quantitative classification rules was also established for such cancer classification, thereby providing a solid research foundation for further biomarker exploration and functional analyses of tumorigenesis at the level of circulating extracellular microRNA.
Rapid Changes in the Phytoplankton Community of a Subtropical, Shallow, Hypereutrophic Lake During the Rainy Season

Lake Cajititlán is a small, shallow, subtropical lake located in an endorheic basin in western Mexico. It is characterized by a strong seasonality of climate with pronounced wet and dry seasons and has been classified as a hypereutrophic lake. This eutrophication was driven by improperly treated sewage discharges from four municipal wastewater treatment plants (WWTPs) and by excessive agricultural activities, including the overuse of fertilizers that reach the lake through surface runoff during the rainy season. This nutrient rich runoff has caused algal blooms, which have led to anoxic or hypoxic conditions, resulting in large-scale fish deaths that have occurred during or immediately after the rainy season. This study investigated the changes in the phytoplankton community in Lake Cajititlán during the rainy season and the association between these changes and the physicochemical water quality and environmental parameters measured in the lake’s basin. Planktothrix and Cylindrospermopsis were the dominant genera of the cyanobacterial community, while the Chlorophyceae, Chrysophyceae, and Trebouxiophyceae classes dominated the microalgae community. However, the results showed a significant temporal shift in the phytoplankton communities in Lake Cajititlán induced by the rainy season. The findings of this study suggest that significant climatic variations cause high seasonal surface runoff and rapid changes in the water quality (Chlorophyll-a, DO, NH4+, and NO3–) and in variations in the composition of the phytoplankton community. Finally, an alternation between phosphorus and nitrogen limitation was observed in Lake Cajititlán during the rainy season, clearly correlating to the presence of Planktothrix when the lake was limited by phosphorus and to the presence of Cylindrospermopsis when the lake was limited by nitrogen. The evidence presented in this study supports the idea that the death of fish in Lake Cajititlán could be mainly caused by anoxia, caused by rapid changes in water quality during the rainy season. Based on our review of the literature, this is the first study on the phytoplankton community in a subtropical lake during the rainy season using high throughput 16S rRNA and 18S rRNA amplicon sequencing.
Risk of Clinically Relevant Venous Thromboembolism in Critically Ill Patients With COVID-19: A Systematic Review and Meta-Analysis

Background: Early during the course of the ongoing COVID-19 pandemic, reports suggested alarmingly high incidences for thromboembolic events in critically ill patients with COVID-19. However, the clinical relevance of these events was not reported in several studies. Additionally, more recent research showed contradictory results and suggested substantially lower rates of venous thromboembolism. Thus, the aim of the present study was to summarize evidence on the incidence of clinically relevant venous thromboembolism (VTE)—defined as VTE excluding isolated subsegmental pulmonary embolism (PE) and distal deep vein thrombosis (DVT)—in adult critically ill patients with COVID-19. Methods: We performed a systematic review of studies reporting the incidence of clinically relevant PE and/or DVT in critically ill patients with COVID-19. Scientific reports published in the English language between January and October 2020 were included. We conducted a random-effects model meta-analysis to calculate incidence estimates of clinically relevant VTE and bleeding events. We also performed exploratory meta-regression and subgroup analyses of different diagnostic approaches and additional factors that possibly influenced the incidence of these outcomes. Results: Fifty-four articles (5,400 patients) fulfilled the predefined inclusion criteria, of which 41 had a high risk of bias. The majority of included patients were male, > 60 years, and overweight. Twenty-one studies reported the use of prophylactic doses of heparin. Pooled incidences for clinically relevant PE were estimated at 8% (95% CI, 4–11%), for proximal DVT at 14% (95% CI, 9–20%), and—after exclusion of studies with a high risk of bias—for the composite outcome of VTE at 18% (95% CI, 13–24%). Clinically relevant bleeding occurred at a rate of 6% (95% CI, 2–9%). Conclusions: We summarized currently available data on the rate of clinically relevant VTE in critically ill patients with COVID-19. Pooled incidence estimates were lower than those reported by previous review articles. In the absence of evidence-based anticoagulation guidelines for critically ill patients with COVID-19, the results of our study provide clinically important information for an individual risk-benefit assessment in this context. Registration: The study protocol was prospectively registered in PROSPERO on June 22, 2020 (CRD42020193353; https://www.crd.york.ac.uk/prospero).