julilili42/papers huggingface dataset:
Three-Dimensional (3D) Surface-Enhanced Raman Spectroscopy (SERS) Substrates for Sensing Low-Concentration Molecules in Solution
2024-10-29

The use of surface-enhanced Raman spectroscopy (SERS) in liquid solutions has always been challenging due to signal fluctuations, inconsistent data, and difficulties in obtaining reliable results, especially at very low analyte concentrations. In our study, we introduce a new method using a three-dimensional (3D) SERS substrate made of silica microparticles (SMPs) with attached plasmonic nanoparticles (NPs). These SMPs were placed in low-concentration analyte solutions for SERS analysis. In the first approach to perform SERS in a 3D environment, glycerin was used to immobilize the particles, which enabled high-resolution SERS imaging. Additionally, we conducted time-dependent SERS measurements in an aqueous solution, where freely suspended SMPs passed through the laser focus. In both scenarios, EFs larger than 200 were achieved, which enabled the detection of low-abundance analytes. Our study demonstrates a reliable and reproducible method for performing SERS in liquid environments, offering significant advantages for the real-time analysis of dynamic processes, sensitive detection of low-concentration molecules, and potential applications in biomolecular interaction studies, environmental monitoring, and biomedical diagnostics.
Evaluation of variation in preclinical electroencephalographic (EEG) spectral power across multiple laboratories and experiments: An EQIPD study
2024-10-29

The European Quality In Preclinical Data (EQIPD) consortium was born from the fact that publications report challenges with the robustness, rigor, and/or validity of research data, which may impact decisions about whether to proceed with further preclinical testing or to advance to clinical testing, as well as draw conclusions on the predictability of preclinical models. To address this, a consortium including multiple research laboratories from academia and industry participated in a series of electroencephalography (EEG) experiments in mice aimed to detect sources of variance and to gauge how protocol harmonisation and data analytics impact such variance. Ultimately, the goal of this first ever between-laboratory comparison of EEG recordings and analyses was to validate the principles that supposedly increase data quality, robustness, and comparability. Experiments consisted of a Localisation phase, which aimed to identify the factors that influence between-laboratory variability, a Harmonisation phase to evaluate whether harmonisation of standardized protocols and centralised processing and data analysis reduced variance, and a Ring-Testing phase to verify the ability of the harmonised protocol to generate consistent findings. Indeed, between-laboratory variability reduced from Localisation to Harmonisation and this reduction remained during the Ring-Testing phase. Results obtained in this multicentre preclinical qEEG study also confirmed the complex nature of EEG experiments starting from the surgery and data collection through data pre-processing to data analysis that ultimately influenced the results and contributed to variance in findings across laboratories. Overall, harmonisation of protocols and centralized data analysis were crucial in reducing laboratory-to-laboratory variability. To this end, it is recommended that standardized guidelines be updated and followed for collection and analysis of preclinical EEG data.
Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense
2024-10-29

Abstract Understanding the genomic basis of natural variation in plant pest resistance is an important goal in plant science, but it usually requires large and labour-intensive phenotyping experiments. Here, we explored the possibility that non-target reads from plant DNA sequencing can serve as phenotyping proxies for addressing such questions. We used data from a whole-genome and -epigenome sequencing study of 207 natural lines of field pennycress (Thlaspi arvense) that were grown in a common environment and spontaneously colonized by aphids, mildew and other microbes. We found that the numbers of non-target reads assigned to the pest species differed between populations, had significant SNP-based heritability, and were associated with climate of origin and baseline glucosinolates content. Specifically, pennycress lines from cold and thermally fluctuating habitats, presumably less favorable to aphids, showed higher aphid DNA load, i.e. decreased aphid resistance. Genome-wide association analyses identified genetic variants at known defense genes but also novel genomic regions associated with variation in aphid and mildew DNA load. Moreover, we found several differentially methylated regions associated with pathogen loads, in particular differential methylation at transposons and hypomethylation in the promoter of a gene involved in stomatal closure, likely induced by pathogens. Our study provides first insights into the defense mechanisms of Thlaspi arvense, a rising crop and model species, and demonstrates that non-target whole genome sequencing reads, usually discarded, can be leveraged to estimate intensities of plant biotic interactions. With rapidly increasing numbers of large sequencing datasets worldwide, this approach should have broad application in fundamental and applied research.
The Hungarian fossil record of the Pliocene pig Sus arvernensis (Suidae, Mammalia)
2024-10-29

Abstract Sus arvernensis is a Pliocene species that occupies a key position in the evolution of suids (Suidae, Artiodactyla, Mammalia) in Eurasia, and besides, it is considered important for biochronological correlations and paleoecological inferences. However, our knowledge on S. arvernensis is largely based on fossil remains from southwestern Europe. Here, we present a revision of the Hungarian fossil record of S. arvernensis . Up to now, the species was known from only two localities of Hungary, Gödöllő (central Hungary) and Süttő (northwest Hungary), and the latter occurrence has even been questioned. After the comparison with other relevant samples of S. arvernensis , of the Early Pleistocene S. strozzii , and of the extant wild boar S. scrofa (motivated by previous attributions and the chronology of the localities), the presence of S. arvernensis from Gödöllő and Süttő is confirmed, and more material of the species is described from Beremend (southern Hungary) and Kisláng (western Hungary). Collectively, the results of the revision carried out herein reveal a relatively widespread distribution of S. arvernensis in Hungary, hence providing an important link from the eastern to western European fossil record of the species. The specimens from Gödöllő and Süttő are slightly larger than the other material of S. arvernensis from France and Italy included in the biometric comparison, although the paucity of the material precludes to evaluate whether these differences are significant and to relate them to a chronological and/or geographical context. The occurrence of S. arvernensis in the Hungarian localities considered in this work is a biochronological indication of an age older than at least 2.6 Ma, since the species is not recorded after the Pliocene–Pleistocene transition. This in agreement with the age estimates available so far for some of the localities or provides new insights. At Süttő, in particular, the identification of S. arvernensis reinforces the view that travertine deposition started already in the Pliocene.
Addressing the Anthropocene from the Global South: integrating paleoecology, archaeology and traditional knowledge for COP engagement
2024-10-29

The triple planetary crisis of climate change, pollution, and biodiversity loss necessitates more holistic, comprehensive, and integrated public policy approaches. Within the United Nations Framework Convention on Climate Change, this crisis highlights significant conflicts over forms of knowledge and conceptualization, affecting how international policies are formed. Indigenous knowledge systems have become increasingly acknowledged for their vital role in addressing the challenges of the Anthropocene. Conferences of the Parties institutions like the International Indigenous Peoples Forum on Climate Change emphasize the critical, although not always recognized, importance of Indigenous territories, which contain eighty percent of the world’s biodiversity. Here, we show that research in paleoecology, archaeology and history demonstrates the long-term significance of traditional knowledge and Indigenous land management practices for contemporary ecosystem dynamics. Drawing from these varied studies and perspectives also reveal the socio-economic inequalities resulting from centuries of European colonialism. We showcase three case studies on; (i) pastoralism in eastern Africa, (ii) natural resource management in southeast Asia and (iii) adaptation to sea level rise in the Caribbean, which touch upon highly diverse human resilience strategies across space and time. Despite efforts at the COP28 to accelerate climate action and incorporate diverse knowledge systems, significant challenges remain. The need for a pluralistic knowledge, rather than a one-size-fits-all approach, blending scientific language with artistic and narrative forms, is proposed as critical for fostering effective communication and developing more effective and equitable solutions for global environmental governance.
Inhibition of an Alzheimer’s disease–associated form of necroptosis rescues neuronal death in mouse models
2024-10-30

Necroptosis is a regulated form of cell death that has been observed in Alzheimer’s disease (AD) along with the classical pathological hallmark lesions of amyloid plaques and Tau neurofibrillary tangles. To understand the neurodegenerative process in AD, we studied the role of necroptosis in mouse models and primary mouse neurons. Using immunohistochemistry, we demonstrated activated necroptosis-related proteins in transgenic mice developing Tau pathology and in primary neurons from amyloid precursor protein (APP)–Tau double transgenic mice treated with phosphorylated Tau seeds derived from a patient with AD but not in APP transgenic mice that only exhibited β-amyloid deposits. Necroptosis proteins in granulovacuolar degeneration (GVD) bodies were associated with neuronal loss in mouse brain regions also known to be vulnerable to GVD in the human AD brain. Necroptosis inhibitors lowered the percentage of neurons showing GVD and reduced neuronal loss, both in transgenic mice and in primary mouse neurons. This suggests that a GVD-associated form of necroptosis that we refer to as “GVD-necroptosis” may represent a delayed form of necroptosis in AD. We propose that inhibition of necroptosis could rescue this type of neuronal death in AD.
Substantial in situ Ti isotope variations in rutile record source and fluid evolution of porphyry copper mineralization systems
2024-10-30

Abstract Titanium (Ti) and its stable isotopes have been widely used as tracers for magmatic processes. However, our understanding of Ti isotope behavior in magmatic-hydrothermal systems remains limited. Hence, the in situ Ti isotope composition (δ49Ti) of magmatic titanite and hydrothermal rutile associated with magnetite and chalcopyrite mineralization was determined for the first time in four well-characterized porphyry copper deposits in southern Tibet. The rutile formed through the alteration of primary Ti-rich minerals during fluid-rock interaction in the early high-temperature magnetite and later moderate-temperature chalcopyrite stages of mineralization. Hydrothermal rutile, altered from magmatic titanite, exhibits δ49Ti values similar to those of residual magmatic titanite. This suggests that hydrothermal rutile inherited the Ti isotope composition of magmatic titanite. The average δ49Ti values of rutile are negatively correlated with whole-rock εNd(t) and zircon εHf(t) data, and positively correlated with whole-rock (87Sr/86Sr)i values, which suggests that the initial Ti isotope compositions of hydrothermal rutile in porphyry copper deposits primarily reflect their source. Rutile from the Qulong deposit sometimes exhibits fractionation of δ49Ti at levels exceeding 0.5‰, displaying a negative correlation with Zr and FeO, which may be attributed to the formation of magnetite and rutile at an early potassic alteration stage. Isotopically light Ti is preferentially incorporated into magnetite and rutile. Thus, the rutile associated with sulfide mineralization that formed from the remaining fluids during a later stage of phyllic alteration is enriched in heavy δ49Ti. These findings contribute to the understanding of how rutile fractionates Ti isotopes in hydrothermal systems related to porphyry copper deposits. In local contexts, the substantial crystallization of magnetite, along with the preferential incorporation of isotopically light Ti during the early stages, leads to a decrease in oxygen fugacity within the ore-bearing fluid. This, in turn, facilitates the formation of sulfides during later stages. The results of this study demonstrate the efficacy of in situ Ti isotope analysis as a powerful tool for tracking fluid and metal sources, and can be used to help interpret ore precipitation throughout different stages of magmatic-to-hydrothermal ore-forming processes.
The rise and transformation of Bronze Age pastoralists in the Caucasus
2024-10-30

Abstract The Caucasus and surrounding areas, with their rich metal resources, became a crucible of the Bronze Age 1 and the birthplace of the earliest steppe pastoralist societies 2 . Yet, despite this region having a large influence on the subsequent development of Europe and Asia, questions remain regarding its hunter-gatherer past and its formation of expansionist mobile steppe societies 3–5 . Here we present new genome-wide data for 131 individuals from 38 archaeological sites spanning 6,000 years. We find a strong genetic differentiation between populations north and south of the Caucasus mountains during the Mesolithic, with Eastern hunter-gatherer ancestry 4,6 in the north, and a distinct Caucasus hunter-gatherer ancestry 7 with increasing East Anatolian farmer admixture in the south. During the subsequent Eneolithic period, we observe the formation of the characteristic West Eurasian steppe ancestry and heightened interaction between the mountain and steppe regions, facilitated by technological developments of the Maykop cultural complex 8 . By contrast, the peak of pastoralist activities and territorial expansions during the Early and Middle Bronze Age is characterized by long-term genetic stability. The Late Bronze Age marks another period of gene flow from multiple distinct sources that coincides with a decline of steppe cultures, followed by a transformation and absorption of the steppe ancestry into highland populations.
Evaluation and management of hepatic dysfunction, portal hypertension and portal/splanchnic vein thrombosis in patients with myelofibrosis undergoing allogeneic haematopoietic cell transplantation: A practice based survey on behalf of the Chronic Malignancies Working Party of the EBMT
2024-10-30

Heterogeneous approaches exist in regard to the management of disease-related co-morbidities in potential allogeneic haematopoietic cell transplantation (allo-HCT) candidates with myelofibrosis (MF). The EBMT Chronic Malignancies Working Party launched an electronic survey to evaluate how MF-specific comorbidities are approached and whether they ultimately affect the decision to transplant. A total of 41/63 (65%) Centers, all of whom were experienced in the management of MF allo-HCT, responded. Responses were aggregated and reported in a comparative fashion. Screening for portal hypertension (PH) was routinely performed in 54% centers, never in 12% and guided by clinical manifestations in the remaining. Involvement of hepatologists/gastroenterologists was always/very often considered in patients with signs of PH prior to transplant. Centers reported that radiological evidence of PH did not routinely represent a formal contraindication for allo-HCT in most cases (78%). Of note, most centers (61%) did not perform routine screening for gastroesophageal varices; this was systematically considered or guided by clinical manifestations in only 7% and 32% centers, respectively. Presence of gastroesophageal varices was always (15%) or occasionally (19%) considered a formal contraindication to allo-HCT. A prior history of portal vein thrombosis never (78%) or occasionally (15%) represented a formal contraindication. Three Centers would not proceed to transplant in such cases. Less importance was assigned to non-portal splanchnic vein thrombosis (SVT), with all but one centre proceeding to transplant regardless of prior SVT. This survey highlights a considerable heterogeneity across responding centers in approaching MF-related comorbidities prior to transplant, suggesting that harmonisation guidelines are needed to address these issues in this patient population.
Real-time imaging of cGMP signaling shows pronounced differences between glomerular endothelial cells and podocytes
2024-10-30

Abstract Recent clinical trials of drugs enhancing cyclic guanosine monophosphate (cGMP) signaling for cardiovascular diseases have renewed interest in cGMP biology within the kidney. However, the role of cGMP signaling in glomerular endothelial cells (GECs) and podocytes remains largely unexplored. Using acute kidney slices from mice expressing the FRET-based cGMP biosensor cGi500 in endothelial cells or podocytes enabled real-time visualization of cGMP. Stimulation with atrial natriuretic peptide (ANP) or SNAP (NO donor) and various phosphodiesterase (PDE) inhibitors elevated intracellular cGMP in both cell types. GECs showed a transient cGMP response upon particulate or soluble guanylyl cyclase activation, while the cGMP response in podocytes reached a plateau following ANP administration. Co-stimulation (ANP + SNAP) led to an additive response in GECs. The administration of PDE inhibitors revealed a broader basal PDE activity in GECs dominated by PDE2a. In podocytes, basal PDE activity was mainly restricted to PDE3 and PDE5 activity. Our data demonstrate the existence of both guanylyl cyclase pathways in GECs and podocytes with cell-specific differences in cGMP synthesis and degradation, potentially suggesting new therapeutic options for kidney diseases.
Stable isotope analysis of faunal remains from Bronze Age Kaymakçı, Western Anatolia
2024-10-30

This paper presents the results of stable carbon ( δ 13 C) and nitrogen ( δ 15 N) isotopic analysis of bulk bone collagen from faunal remains from the Bronze Age site of Kaymakçı in western Anatolia. We use the isotopic values in conjunction with zooarchaeological data and contextual archaeological information to examine human-environment interactions; in particular, animal management and husbandry. Middle and Late Bronze Age agricultural systems in western and central Anatolia remain poorly understood, and this research aims to contribute to rectifying this research gap. We obtained stable isotopic values from both wild and domestic species, including deer, hare, birds, catfish, dogs, pigs, caprids and cattle. The δ 13 C values range from −22.0‰ to −16.9‰ and the δ 15 N values range from 2.3‰ to 10.3‰. For cattle, the δ 13 C values suggest that some specimens were subject to different management strategies, likely related to feeding or herding patterns or even the movement of animals in and around the region through some exchange mechanism. There appears to be no fixed location or strategy for the management of caprids and, furthermore, there is evidence to suggest that the herding/management areas of some caprids overlapped with those of wild animals such as deer and hare. Variation in δ 15 N values for pigs may indicate that whilst some animals in the sampled assemblage were free-roaming, others were penned. For the pigs and some other herbivorous domesticated species variation in δ 15 N values may also point to the exploitation of the wetland areas around Lake Marmara.
Non‐Native, Non‐Naturalised Plants Suffer Less Herbivory Than Native Plants Across European Botanical Gardens
2024-10-30

ABSTRACT Aim The enemy release hypothesis states that the invasion success of non‐native species is partly due to their escape from natural enemies, e.g., herbivores. Large‐scale studies of herbivory using multiple species across multiple sites are needed to test the generality of herbivory release in non‐native plants. Location Europe. Methods We carried out leaf‐herbivory surveys from 2007 to 2021 in 15 botanical gardens ranging in latitude from 47°N (Switzerland) to 63°N (Norway) to investigate how herbivory levels differed between (i) native and non‐native species, and (ii) native and non‐naturalised or naturalised species. Results Overall, we found that herbivory levels were lower on non‐native than native species. In addition, we found that non‐naturalised plants suffered less herbivory than natives and that naturalised plants showed similar levels of herbivory to native plants. Main Conclusions We find broad support for lower herbivory of non‐native plant species compared to natives. However, the stronger reduction in herbivory for non‐naturalised plants suggests that herbivore release may be transient and less pronounced for naturalised non‐native species that have become abundant and integrated into resident communities. This has implications for the management of naturalised non‐native plants, which are performing well in their non‐native ranges despite suffering comparable herbivory levels to native species.
Resistance of Anopheles gambiae s.s. against commonly used insecticides and implication of cytochrome P450 monooxygenase in resistance to pyrethroids in Lambaréné (Gabon)
2024-10-30

Abstract Background Insecticides are a crucial component of vector control. However, resistance constitute a threat on their efficacy and the gains obtained over the years through malaria vector control. In Gabon, little data on phenotypic insecticide resistance in Anopheles vectors are published, compromising the rational implementation of resistance management strategies. We assessed the susceptibility to pyrethroids, carbamates and organophosphates of Anopheles gambiae sensu lato ( s.l. ) and discuss the mechanisms involved in the pyrethroid resistance-phenotype. Methods A. gambiae s.l. larvae were collected from breeding sites in Lambaréné. Emerging adults were used in WHO tube assays at an insecticide concentration that defines resistance (diagnostic concentration). Subsequently, deltamethrin and permethrin were used at 5x and 10x diagnostic concentrations and after preexposure with the cytochrome p450 (and glutathione S-transferase) inhibitor piperonyl butoxide (PBO). A subset of mosquitoes was typed by molecular methods and screened using Taqman assays for mutations conferring target site resistance at the Voltage-gated sodium channel 1014 ( Vgsc-1014 ) locus and the acetylcholinesterase ( Ace-1 ) gene. Results All mosquitoes were A. gambiae sensu stricto ( s.s. ) and resistant to permethrin, deltamethrin and alphacypermethrin (mortality less than 98%). However, mosquitoes were susceptible to malathion but resistant to bendiocarb. The level of resistance was high for permethrin and at least moderate for deltamethrin. Pre-exposure to PBO significantly increased the mortality of resistant mosquitoes ( P &lt; 0.0001). They became fully susceptible to deltamethrin and permethrin-induced mortality increased 4-fold. The G119S Ace-1 resistance allele, which confers resistance to both organophosphates and carbamates, was not present. All sampled mosquitoes were either homozygous for the Vgsc-L1014F or heterozygous for Vgsc-L1014F/L1014S , a marker for resistance to pyrethroids and organochlorides. Conclusion These findings demonstrate a role of cytochrome P450 monooxygenases in the pyrethroid-resistance of A. gambiae s.s . from Lambaréné. Combining PBO with pyrethroids, as done in second generation bednets, may be used to revert resistance. In addition, malathion could also be used in combination with pyrethroids-based methods for resistance management.