julilili42/papers huggingface dataset:
Specialist reassociation and residence time modulate the evolution of defense in invasive plants: A meta‐analysis
2024-01-25

Abstract Invasive plants typically escape specialist herbivores but are often attacked by generalist herbivores in their introduced ranges. The shifting defense hypothesis suggests that this will cause invasive plants to evolve lower resistance against specialists, higher resistance against generalists, and greater tolerance to herbivore damage. However, the duration and direction of selective pressures can shape the evolutionary responses of resistance and tolerance for invasive plants. Two critical factors are (1) residence time (length of time that an invasive species has been in its introduced range) and (2) specialist herbivore reassociation (attack by purposely or accidentally introduced specialists). Yet, these two factors have not been considered simultaneously in previous quantitative syntheses. Here, we performed a meta‐analysis with 367 effect sizes from 70 studies of 35 invasive plant species from native and invasive populations. We tested how the residence time of invasive plant species and specialist reassociation in their introduced ranges affected evolutionary responses of defenses against specialists and generalists, including herbivore resistance traits (physical barriers, digestibility reducers and toxins), resistance effects (performance of and damage caused by specialists or generalists) and tolerance to damage (from specialists or generalists). We found that residence time and specialist reassociation each significantly altered digestibility reducers, specialist performance, generalist damage, and tolerance to specialist damage. Furthermore, residence time and specialist reassociation strongly altered toxins and generalist performance, respectively. When we restricted consideration to invasive plant species with both longer residence times and no reassociation with specialists, invasive populations had lower resistance to specialists, similar resistance to generalists, and higher tolerance to damage from both herbivore types, compared with native populations. We conclude that the duration and direction of selective pressure shape the evolutionary responses of invasive plants. Under long‐term (long residence time) and stable (no specialist reassociation) selective pressure, invasive plants generally decrease resistance to specialists and increase tolerance to generalist damage that provides mixed support for the shifting defense hypothesis.
The mobilization and transport of newly fixed carbon are driven by plant water use in an experimental rainforest under drought
2024-01-25

Abstract Non-structural carbohydrates (NSCs) are building blocks for biomass and fuel metabolic processes. However, it remains unclear how tropical forests mobilize, export, and transport NSCs to cope with extreme droughts. We combined drought manipulation and ecosystem 13CO2 pulse-labeling in an enclosed rainforest at Biosphere 2, assessed changes in NSCs, and traced newly assimilated carbohydrates in plant species with diverse hydraulic traits and canopy positions. We show that drought caused a depletion of leaf starch reserves and slowed export and transport of newly assimilated carbohydrates below ground. Drought effects were more pronounced in conservative canopy trees with limited supply of new photosynthates and relatively constant water status than in those with continual photosynthetic supply and deteriorated water status. We provide experimental evidence that local utilization, export, and transport of newly assimilated carbon are closely coupled with plant water use in canopy trees. We highlight that these processes are critical for understanding and predicting tree resistance and ecosystem fluxes in tropical forest under drought.
The Mongolian gerbil as an advanced model to study cone system physiology
2024-01-25

In this work, we introduce a diurnal rodent, the Mongolian gerbil ( Meriones unguiculatus ) (MG) as an alternative to study retinal cone system physiology and pathophysiology in mice. The cone system is of particular importance, as it provides high-acuity and color vision and its impairment in retinal disorders is thus especially disabling. Despite their nocturnal lifestyle, mice are currently the most popular animals to study cone-related diseases due to the high availability of genetically modified models. However, the potential for successful translation of any cone-related results is limited due to the substantial differences in retinal organization between mice and humans. Alternatively, there are diurnal rodents such as the MG with a higher retinal proportion of cones and a macula-like specialized region for improved visual resolution, the visual streak. The focus of this work was the evaluation of the MG’s cone system functionality using full-field electroretinography (ERG), together with a morphological assessment of its retinal/visual streak organization via angiography, optical coherence tomography (OCT), and photoreceptor immunohistochemistry. We found that rod system responses in MGs were comparable or slightly inferior to mice, while in contrast, cone system responses were much larger, more sensitive, and also faster than those in the murine counterparts, and in addition, it was possible to record sizeable ON and OFF ERG components. Morphologically, MG cone photoreceptor opsins were evenly distributed throughout the retina, while mice show a dorsoventral M- and S-opsin gradient. Additionally, each cone expressed a single opsin, in contrast to the typical co-expression of opsins in mice. Particular attention was given to the visual streak region, featuring a higher density of cones, elongated cone and rod outer segments (OSs), and an increased thickness of the inner and outer retinal layers in comparison to peripheral regions. In summary, our data render the MG a supreme model to investigate cone system physiology, pathophysiology, and to validate potential therapeutic strategies in that context.
Surface-Mediated Modulation of Different Biological Responses on Anatase-Coated Titanium
2024-01-25

Various surface modification strategies are being developed to endow dental titanium implant surfaces with micro- and nano-structures to improve their biocompatibility, and first of all their osseointegration. These modifications have the potential to address clinical concerns by stimulating different biological processes. This study aims to evaluate the biological responses of ananatase-modified blasted/etched titanium (SLA-anatase) surfaces compared to blasted/acid etched (SLA) and machined titanium surfaces. Using unipolar pulsed direct current (DC) sputtering, a nanocrystalline anatase layer was fabricated. In vitro experiments have shown that SLA-anatase discs can effectively promote osteoblast adhesion and proliferation, which are regarded as important features of a successful dental implant with bone contact. Furthermore, anatase surface modification has been shown to partially enhance osteoblast mineralization in vitro, while not significantly affecting bacterial colonization. Consequently, the recently created anatase coating holds significant potential as a promising candidate for future advancements in dental implant surface modification for improving the initial stages of osseointegration.
Nanoparticle Interferometer by Throw and Catch
2024-01-25

Matter wave interferometry with increasingly larger masses could pave the way to understanding the nature of wavefunction collapse, the quantum to classical transition, or even how an object in a spatial superposition interacts with its gravitational field. In order to improve upon the current mass record, it is necessary to move into the nanoparticle regime. In this paper, we provide a design for a nanoparticle Talbot–Lau matter wave interferometer that circumvents the practical challenges of previously proposed designs. We present numerical estimates of the expected fringe patterns that such an interferometer would produce, considering all major sources of decoherence. We discuss the practical challenges involved in building such an experiment, as well as some preliminary experimental results to illustrate the proposed measurement scheme. We show that such a design is suitable for seeing interference fringes with 106 amu SiO2 particles and that this design can be extended to even 108 amu particles by using flight times below the typical Talbot time of the system.
Detection of Reduced Diameter of the Cochlear Nerve in Long-term Deaf Patients Quantified With Semiautomatic Measurement of Nerve Cross-sectional Area Using 3T MRI Data
2024-01-25

Hypothesis: High-resolution parallel transmit T2 sampling perfection with application optimized contrast using different flip angle evolution sequence with improved edge discrimination and semiautomatic determination of nerve cross-sectional area (CSA) can be used to evaluate nerve degeneration in the inner auditory canal (IAC) in long-term deaf patients. Background: In patients with hearing loss, temporal bone MRI is routinely acquired to evaluate the morphology of the nerves within the IAC. Earlier studies have shown that the diameter of the cochlear nerve can be used as prognostic marker for the auditory performance after cochlear implantation in postlingually deaf patients. Methods: Eighty-two consecutive MRI scans were analyzed using a semiautomatic tool to measure CSA of cranial nerves in the IAC. Results were correlated with patient history and audiology testing as well as with age and gender. Results: There was a significant reduced CSA of the cochlear nerve in ears with moderate-to-profound hearing loss and deafness compared with ears with normal hearing, but no significant difference in ears with mild-to-moderate hearing loss compared with normal hearing. In detail, normal hearing ears had a CSA of 1.23 ± 0.11 mm 2 , whereas ears with pantonal hearing loss of more than 40 dB had 1.02 ± 0.05 mm 2 ( P = 0.026). Maximal CSA of the facial nerve was not different among all groups (average, 1.04 mm 2 ± 0.03; linear regression, P = 0.001) and stable with age. However, vestibular nerve CSA decreased significantly with age (average, 1.78 ± 0.05 mm 2 ; linear regression, P = 0.128). Conclusions: In long-term deaf patients, smaller the diameter of cochlear nerve is the more severe the hearing loss is. The new semiautomatic tool can primarily be used to assess nerve diameter and possibly determine ears with nerve degeneration.
Evidence for a causal link between intra-pancreatic fat deposition and pancreatic cancer: A prospective cohort and Mendelian randomization study
2024-01-26

Prior observational studies suggest an association between intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC); however, the causal relationship is unclear. To elucidate causality, we conduct a prospective observational study using magnetic resonance imaging (MRI)-measured IPFD data and also perform a Mendelian randomization study using genetic instruments for IPFD. In the observational study, we use UK Biobank data (N = 29,463, median follow-up: 4.5 years) and find that high IPFD (>10%) is associated with PDAC risk (adjusted hazard ratio [HR]: 3.35, 95% confidence interval [95% CI]: 1.60-7.00). In the Mendelian randomization study, we leverage eight out of nine IPFD-associated genetic variants (p < 5 × 10<sup>-8</sup>) from a genome-wide association study in the UK Biobank (N = 25,617) and find that genetically determined IPFD is associated with PDAC (odds ratio [OR] per 1-standard deviation [SD] increase in IPFD: 2.46, 95% CI: 1.38-4.40) in the Pancreatic Cancer Cohort Consortium I, II, III (PanScan I-III)/Pancreatic Cancer Case-Control Consortium (PanC4) dataset (8,275 PDAC cases and 6,723 non-cases). This study provides evidence for a potential causal role of IPFD in the pathogenesis of PDAC. Thus, reducing IPFD may lower PDAC risk.
Microbiome Dysbiosis With Enterococcus Presence in the Upper Gastrointestinal Tract Is a Risk Factor for Mortality in Patients Undergoing Surgery for Pancreatic Cancer
2024-01-26

Background: Recent retrospective studies suggest a role for distinct microbiota in the perioperative morbidity and mortality of pancreatic head resections. Objective: We aimed to prospectively investigate the microbial colonization of critical operative sites of pancreatic head resections to identify microbial stratification factors for surgical and long-term oncologic outcomes. Methods: Prospective biomarker study applying 16S rRNA sequencing and microbial culturing to samples collected from various sites of the gastrointestinal tract and surgical sites of patients during pancreatic head resections at a German single high-volume pancreatic center. Results: A total of 101 patients were included {38 noncancer, 63 cancer patients [50 pancreatic ductal adenocarcinoma (PDAC) patients]} in the study. In a first data analysis series, 16S rRNA sequencing data were utilized from 96 patients to assess associations of microbiome profiles with clinical parameters and outcomes. In general, microbiome composition varied according to sampling site, cancer, age or preoperative endoscopic retrograde cholangiopancreatography (ERCP) intervention, notably for the bile microbiome. In the PDAC subcohort, the compositional variance of the bile or periampullary microbiome was significantly associated with postoperative complications such as intensive care unit admission; on a taxonomic level we observed Enterococcus spp. to be significantly more abundant in patients developing deep or organ-space surgical site infections (SSI). Elevated Enterococcus relative abundances in the upper gastrointestinal tract, in turn, were associated with 6 months mortality rates. In a second step, we focused on microbiological cultures collected from bile aspirates during surgery and investigated associations with perioperative complications and long-term survival. Notably, Enterococcus spp. were among the most prevalent pathobiont isolates observed in cancer patient bile specimens that were associated with severe SSIs, and thereby elevated mortality rates up to 24 months. Clinically relevant postoperative pancreatic fistulas or severe SSI were found as other major variables determining short-term mortality in this cancer patient cohort. In the context of adverse microbiological factors, a preoperative ERCP was also observed to segregate long-term survival, and it appeared to interact with the presence of Enterococcus spp. as highest mortality rates were observed in PDAC patients with both preoperative ERCP and presence of E. faecalis in bile aspirates. Conclusions: The presence of Enterococcus spp. in bile ducts of PDAC patients undergoing pancreatic surgery represents a significant risk factor for perioperative infections and, thereby, elevated postoperative and long-term mortality. This finding supports previous data on the use of the antibiotic drug piperacillin-tazobactam as appropriate perioperative antibiotic prophylaxis for preventing adverse outcomes after pancreatoduodenectomy.
In vitro and in vivo models define a molecular signature reference for human embryonic notochordal cells
2024-01-26

Understanding the emergence of human notochordal cells (NC) is essential for the development of regenerative approaches. We present a comprehensive investigation into the specification and generation of <i>bona fide</i> NC using a straightforward pluripotent stem cell (PSC)-based system benchmarked with human fetal notochord. By integrating <i>in vitro</i> and <i>in vivo</i> transcriptomic data at single-cell resolution, we establish an extended molecular signature and overcome the limitations associated with studying human notochordal lineage at early developmental stages. We show that TGF-β inhibition enhances the yield and homogeneity of notochordal lineage commitment <i>in vitro</i>. Furthermore, this study characterizes regulators of cell-fate decision and matrisome enriched in the notochordal niche. Importantly, we identify specific cell-surface markers opening avenues for differentiation refinement, NC purification, and functional studies. Altogether, this study provides a human notochord transcriptomic reference that will serve as a resource for notochord identification in human systems, diseased-tissues modeling, and facilitating future biomedical research.
Spyglass: a framework for reproducible and shareable neuroscience research
2024-01-26

Abstract Scientific progress depends on reliable and reproducible results. Progress can be accelerated when data are shared and re-analyzed to address new questions. Current approaches to storing and analyzing neural data involve bespoke formats and software that make replication and reuse of data difficult. To address these challenges, we created Spyglass, an open-source data management and analysis framework written in Python. Spyglass provides reproducible pipelines for common neuroscience analyses and sharing of raw data, intermediate analyses and final results within and across labs. Spyglass uses the Neurodata Without Borders (NWB) standard and includes pipelines for spectral filtering, spike sorting, pose tracking, and neural decoding. Spyglass can be extended to apply existing and newly developed pipelines to datasets from multiple sources. We demonstrate these features in the context of a cross-laboratory replication by applying advanced state space decoding algorithms to publicly available data. New users can try out Spyglass on a Jupyter Hub hosted by HHMI and 2i2c: https://spyglass.hhmi.2i2c.cloud/ .
Beyond the MEP Pathway: A novel kinase required for prenol utilization by malaria parasites
2024-01-26

A proposed treatment for malaria is a combination of fosmidomycin and clindamycin. Both compounds inhibit the methylerythritol 4-phosphate (MEP) pathway, the parasitic source of farnesyl and geranylgeranyl pyrophosphate (FPP and GGPP, respectively). Both FPP and GGPP are crucial for the biosynthesis of several essential metabolites such as ubiquinone and dolichol, as well as for protein prenylation. Dietary prenols, such as farnesol (FOH) and geranylgeraniol (GGOH), can rescue parasites from MEP inhibitors, suggesting the existence of a missing pathway for prenol salvage via phosphorylation. In this study, we identified a gene in the genome of P . falciparum , encoding a transmembrane prenol kinase (PolK) involved in the salvage of FOH and GGOH. The enzyme was expressed in Saccharomyces cerevisiae , and its FOH/GGOH kinase activities were experimentally validated. Furthermore, conditional knockout parasites (Δ-PolK) were created to investigate the biological importance of the FOH/GGOH salvage pathway. Δ-PolK parasites were viable but displayed increased susceptibility to fosmidomycin. Their sensitivity to MEP inhibitors could not be rescued by adding prenols. Additionally, Δ-PolK parasites lost their capability to utilize prenols for protein prenylation. Experiments using culture medium supplemented with whole/delipidated human plasma in transgenic parasites revealed that human plasma has components that can diminish the effectiveness of fosmidomycin. Mass spectrometry tests indicated that both bovine supplements used in culture and human plasma contain GGOH. These findings suggest that the FOH/GGOH salvage pathway might offer an alternate source of isoprenoids for malaria parasites when de novo biosynthesis is inhibited. This study also identifies a novel kind of enzyme related to isoprenoid metabolism.
Global heterogeneity of latitudinal patterns in herbivory between native and exotic plants
2024-01-26

Abstract Latitudinal gradient of herbivory that differs between native and exotic plants has been an open issue. It is expected that a latitudinal gradient of herbivory will be evident for native plants; this gradient in exotic plants may lag behind native plants in terms of co-evolution with local abiotic and biotic factors in introduced area. Our study aims to elucidate the difference in latitudinal gradient of herbivory between native and exotic plants globally, while exploring the underlying mechanisms driving the latitudinal gradient of herbivory with biotic and abiotic factors. To achieve this, we analyzed herbivory data from 94 studies and calculated 862 herbivory effect sizes ( z r ) to quantitatively characterize the intensity of latitudinal herbivory gradient. For each herbivory data, we matched the corresponding plant identity (native/exotic), herbivore feeding guilds and climate data to reveal the contribution of these factors to z r . Our findings demonstrate a significant decrease in the latitudinal gradients of with increasing latitude for native plants, a pattern not observed for exotic plants. The heterogeneity in latitudinal gradients of herbivory between native and exotic plants is mediated by herbivore feeding guilds. There is a significant influence of climatic factors on the latitudinal gradient of herbivory for native plants, but not for exotic plants. Overall, our results underscore a general heterogeneity in global macroecological herbivory patterns between native and exotic plants, and highlight the role of biotic and abiotic factors in explaining these global-scale differences.
People with a tobacco use disorder exhibit misaligned Bayesian belief updating by falsely attributing non-drug cues as worse predictors of positive outcomes compared to drug cues
2024-01-26

Adaptive behaviours depend on dynamically updating internal representations of the world based on the ever-changing environmental contingencies. People with a substance use disorder (pSUD) show maladaptive behaviours with high persistence in drug-taking, despite severe negative consequences. We recently proposed a salience misattribution model for addiction (SMMA; Kalhan et al., 2021), arguing that pSUD have aberrations in their updating processes where drug cues are misattributed as strong predictors of positive outcomes, but weaker predictors of negative outcomes. We also argued that conversely, non-drug cues are misattributed as weak predictors of positive outcomes, but stronger predictors of negative outcomes. We tested these hypotheses using a multi-cue reversal learning task, with reversals in whether drug or non-drug cues are relevant in predicting the outcome (monetary win or loss). We show that people with a tobacco use disorder (pTUD), do form misaligned internal representations. We found that pTUD updated less towards learning the drug cue's relevance in predicting a loss. Further, when neither drug nor non-drug cue predicted a win, pTUD updated more towards the drug cue being relevant predictors of that win. Our Bayesian belief updating model revealed that pTUD had a low estimated likelihood of non-drug cues being predictors of wins, compared to drug cues, which drove the misaligned updating. Overall, several hypotheses of the SMMA were supported, but not all. Our results implicate that strengthening the non-drug cue association with positive outcomes may help restore the misaligned internal representation in pTUD, and offers a quantifiable, computational account of these updating processes.