bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lipidome visualisation, comparison, and analysis in a vector space
Authors: Olzhabaev Timur , Müller Lukas , Krause Daniel , Schwudke Dominik , Torda Andrew Ernest 
Published: August 2024

AbstractA shallow neural network was used to embed lipid structures in a 2- or 3-dimensional space with the goal that structurally similar species have similar vectors. Tests on complete lipid databanks show that the method automatically produces distributions which follow conventional lipid classifications. The embedding is accompanied by the web-based software, Lipidome Projector. This displays user lipidomes as 2D or 3D scatterplots for quick exploratory analysis, quantitative comparison and interpretation at a structural level.Author summaryLipids are not just the basis of membranes. They carry signals and metabolic energy. This means that the presence, absence, and quantity of lipids reflects a cell’s biochemical state - starving, nourished, sick or healthy. Lipidomics (measuring all lipids in a biological specimen) provides lists of the chemical species and their quantities.We have used a shallow neural network from natural language modelling to embed lipids in a continuous vector space. Firstly, this means that similar molecules have similar positions in this space. Conventional lipid categories cluster automatically. Secondly, the accompanying web-based software, Lipidome Projector imports a lipidome and displays it as a set of points. Reading several lipidomes at once allows quantitative and structural comparisons. Combined with the ability to show structure and abundance diagrams, the software allows exploratory analysis and interpretation of lipidomics datasets.
Temporal kinetics of brain state effects on visual perception
Authors: Schmid Paul , Klein Timon , Minakowski Piotr , Sager Sebastian , Reichert Christoph , Knight Robert T. , Dürschmid Stefan 
Published: August 2024

AbstractWe investigated the effects of brain states on human perception and early visual response comparing focused wakefulness (ON state) to external inattention (OFF state). In two experiments, we investigated the temporal kinetics of brain states changes during stimulus processing and assessed fluctuations across extended periods of time. We used a classifier to distinguish between these states on a single trial level using theta activity in MEG sensors. We found that participants shifted from an ON to an OFF state as rapidly as two seconds. Visual target discrimination was comparable in both states, but reaction times were slower and more variable during the OFF state. Broad band high-frequency activity (BHA) recorded in MEG sensors covering the occipital cortex tracked target grating orientation. BHA was reduced during the OFF state but participants were still able to distinguish sensory information highlighting the role of BHA in visual perception across cognitive brain states.
Newly developed structure-based methods do not outperform standard sequence-based methods for large-scale phylogenomics
Authors: Mutti Giacomo , Ocaña-Pallarès Eduard , Gabaldón Toni 
Published: August 2024

AbstractRecent developments in protein structure prediction have allowed the use of this previously limited source of information at genome-wide scales. It has been proposed that the use of structural information may offer advantages over sequences in phylogenetic reconstruction, due to their slower rate of evolution and direct correlation to function. Here, we examined how recently developed methods for structure-based homology search and tree reconstruction compare to current state-of-the-art sequence-based methods in reconstructing genome-wide collections of gene phylogenies (i.e. phylomes). While structure-based methods can be useful in specific scenarios, we found that their current performance does not justify using the newly developed structured-based methods as a default choice in large-scale phylogenetic studies. On the one hand, the best performing sequence-based tree reconstruction methods still outperform structure-based methods for this task. On the other hand, structure-based homology detection methods provide larger lists of candidate homologs, as previously reported. However, this comes at the expense of missing hits identified by sequence-based methods, as well as providing homolog candidate sets with higher fractions of false positives. These insights help guide the use of structural data in comparative genomics and highlight the need to continue improving structure-based approaches. Our pipeline is fully reproducible and has been implemented in a snakemake workflow. This will facilitate a continuous assessment of future improvements of structure-based tools in the Alphafold era.
Tet2loss suppress α-synuclein pathology by stimulating ciliogenesis
Authors: Quansah Emmanuel , Vatsa Naman , Ensink Elizabeth , Brown Jaycie , Cave Tyce , Aguileta Miguel , Kuhn Emily , Lindquist Allison , Gilliland Carla , Steiner Jennifer A. , Escobar Galvis Martha L. , Milčiūtė Milda , Henderson Michael , Brundin Patrik , Brundin Lena , Marshall Lee L. , Gordevicius Juozas 
Published: August 2024

ABSTRACTThere are no approved treatments that slow Parkinson’s disease (PD) progression and therefore it is important to identify novel pathogenic mechanisms that can be targeted. Loss of the epigenetic marker,Tet2appears to have some beneficial effects in PD models, but the underlying mechanism of action is not well understood. We performed an unbiased transcriptomic analysis of cortical neurons isolated from patients with PD to identify dysregulated pathways and determine their potential contributions to the disease process. We discovered that genes associated with primary cilia, non-synaptic sensory and signaling organelles, are upregulated in both early and late PD patients. Enhancing ciliogenesis in primary cortical neurons via sonic hedgehog signaling suppressed the accumulation of α-synuclein pathologyin vitro. Interestingly, deletion ofTet2in mice also enhanced the expression of primary cilia and sonic hedgehog signaling genes and rescued the accumulation of α-synuclein pathology and dopamine neuron degenerationin vivo. Our findings demonstrate the crucial role ofTet2loss in regulating ciliogenesis and potentially affecting the progression of PD pathology.
Impact of Blended NPSB Fertilizer Rates on Sugarcane (Saccharum officinarumL.) Varieties: Seed Cane Yield and Quality Insights from North Western Ethiopia
Authors: Ali Solomon , Belay Bahiru , Abate Mesfin 
Published: August 2024

ABSTRACTSugarcane primarily cultivated for sugar production and other multiple uses. A field experiment was conducted at Tana Beles sugar project, North western Ethiopia during 2021 and 2022 cropping season to determine the optimum rate of NPSB fertilizer rate on three sugarcane varieties. The treatments were laid out in factorial randomized complete block design arranged with three replications. The experiment was arranged with five levels of NPSB blended fertilizer (0, 200, 260, 320 and 380 kg ha-1) combined with three sugarcane varieties (NCO-334, N-14 and C86/56). Among the parameters of seed cane crop; germination percent stalk weight, stalk diameter, node length, inter node number, plant height, stalk population, and sett yield for growth and yield parameters and sett moisture content, sett nitrogen content, reducing sugar content and total sugar content for seed cane quality parameters significantly affected by applied NPSB fertilizer, varieties and their interaction (p<0.05). Brix% and pol% were not significantly affected by different rates of NPSB fertilizer rates and varieties (p<0.05). The highest leaf area index, plant population, sett yield, average cane weight, seed cane moisture content and total nitrogen content was attained with 380 kg ha-1NPSB fertilizer applied on variety NCO-334 and N-14. Maximum population stand, average plant height, and sett yield of verity C86/56 were recorded at 320 kg ha-1NPSB fertilizer level. Sett yield, were positively correlated with germination percent, population stand count, inter node number, seed cane weight, seed cane diameter reducing sugar content, total sugar yield and sett moisture content. Therefore, it is advisable to recommend 380 kg NPSB ha1for variety NCO-334 and N-14, and 320 kg NPSB ha1for variety C86/56 with application of 160 kg ha-1urea at the age of two month and half for effective seed cane production. It was aimed to fill the seed cane fertilizer rate problems of different sugarcane varieties.
MiRNA-21-5p and MiRNA-125-5p Serve as Biomarkers for Diagnosis and Prognosis of Gastric Cancer
Authors: Zhang Xin , Xiang Yao , Wang Junpu 
Published: August 2024

AbstractBackgroundGastric cancer is one of the most common diseases worldwide. MicroRNAs (miRNAs) are small non-coding RNAs, typically 19-25 nucleotides in length, which represent potential targets for therapeutic intervention.Methods and ResultsIn this study, we performed a data mining analysis for gastric cancer (GC) by integrating differentially expressed genes obtained from the Gene Expression Omnibus (GEO) database with data from The Cancer Genome Atlas (TCGA) database. We compared the expression levels of miRNA-125-5p and miRNA-21-5p in cancer cells and GES-1 cells. Our analysis revealed up-regulation of these two miRNAs in both GEO and TCGA datasets, which was further validated by quantitative polymerase chain reaction (qPCR). Additionally, survival analysis, risk score analysis, and downstream analyses, including functional enrichment analysis, target gene prediction, and protein-protein interaction analysis, were conducted.ConclusionThe expression levels of miRNA-125-5p and miRNA-21-5p are upregulated in gastric cancer cells, which contribute to the diagnosis of gastric cancer and serve as novel biomarkers.
Silver Armor Against Bacteria: A Battle of Antimicrobial Effectiveness
Authors: Zaidi Alina 
Published: August 2024

AbstractFor many farmers, there is a need to improve crop resistance to pathogenic organisms. Florida’s climate and hurricane-prone location promotes the spread of many crop pathogens making management difficult and expensive. Therefore, this study evaluates using a Do-It-Yourself, DIY, method to produce colloidal silver solutions that may be used as effective inhibitors of bacteria growth. The efficacy was compared across gram-negative and gram-positive bacteria species. Production of colloidal silver used an electric current from eight 9-volt batteries wired in series. The starting silver was a jewelry chain, approx. 98% silver, suspended in a container of distilled water. Treatment effects were compared to a commercially available silver solution (10K, ppm) as the positive controlviathe Kirby-Baur method. Each petri dish was divided into four quadrants, into which each had a treated cellulose square impregnated with a treatment solution. Treatments were: T1-10K ppm AgNp; T-2-5ppm AgNp, T3-3ppm AgNp; and positive control T4-blank water control. The dimensions of Zones of Clearance (ZOC) and the bacterial growth surrounding treated squares were analyzed. The experiment was replicated four times. Data analysis conducted using one-way ANOVA withpost hocseparation of means using the T test and Tukey’s HSD. The positive control solution was the most effective bactericide across all species, followed by Treatment-2 (5-ppm treatment), which caused ZOC in gram-negative species. Treatment-3, the 3ppm, did not significantly affect bacterial suppression, while activity at 5ppm suggests that simple home-based, DIY systems can produce low cost, bactericidal nano-silver solutions. In this experiment the bacterium that tested that is also beneficial to plants,R. rubrum, showed an increased tolerance to all silver treatments. Improving homemade, DIY, systems may provide low-cost treatment solutions against some bacteria species important to backyard agriculturists.
Prevalence of Mild and Severe Cognitive Impairment in World Trade Center Exposed Fire Department of the City of New York (FDNY) and General Emergency Responders
Authors: Mann Frank D. , Mueller Alexandra K. , Zeig-Owens Rachel , Choi Jaeun , Prezant David J. , Carr Melissa M. , Fels Alicia M. , Hennington Christina M. , Armstrong Megan P. , Barber Alissa , Fontana Ashley E. , Kroll Cassandra H. , Chow Kevin , Melendez Onix A. , Smith Abigail J. , Luft Benjamin J. , Hall Charles B. , Clouston Sean A. P. 
Published: August 2024

BackgroundThe emergency personnel who responded to the World Trade Center (WTC) attacks endured severe occupational exposures, yet the prevalence of cognitive impairment remains unknown among WTC-exposed-FDNY-responders. The present study screened for mild and severe cognitive impairment in WTC-exposed FDNY responders using objective tests, compared prevalence rates to a cohort of non-FDNY WTC-exposed responders, and descriptively to meta-analytic estimates of MCI from global, community, and clinical populations.MethodsA sample of WTC-exposed-FDNY responders (n = 343) was recruited to complete an extensive battery of cognitive, psychological, and physical tests. The prevalences of domain-specific impairments were estimated based on the results of norm-referenced tests, and the Montreal Cognitive Assessment (MoCA), Jak/Bondi criteria, Petersen criteria, and the National Institute on Aging and Alzheimer’s Association (NIA-AA) criteria were used to diagnose MCI. NIA-AA criteria were also used to diagnose severe cognitive impairment. Generalized linear models were used to compare prevalence estimates of cognitive impairment to a large sample of WTC-exposed-non-FDNY responders from the General Responder Cohort (GRC; n = 7102) who completed the MoCA during a similar time frame.ResultAmong FDNY responders under 65 years, the unadjusted prevalence of MCI varied from 52.57% to 71.37% depending on the operational definition of MCI, apart from using a conservative cut-off applied to MoCA total scores (18 < MoCA < 23), which yielded a markedly lower crude prevalence (24.31%) compared to alternative criteria. The prevalence of MCI was higher among WTC-exposed-FDNY-responders, compared to WTC-exposed-non-FDNY-GRC-responders (adjustedRR= 1.53,95% C.I. = [1.24, 1.88],p< .001) and meta-analytic estimates from different global, community, and clinical populations. Following NIA-AA diagnostic guidelines, 4.96% of WTC-exposed-FDNY-responders met the criteria for severe impairments (95% CI = [2.91% to 7.82%]), a prevalence that remained largely unchanged after excluding responders over the age of 65 years.DiscussionThere is a high prevalence of mild and severe cognitive impairment among WTC-responders highlighting the putative role of occupational/environmental and disaster-related exposures in the etiology of accelerated cognitive decline.
Assessing the Role of Red Blood Cell Distribution Width in Hospital Mortality Among Elderly and Non-Elderly COVID-19 Patients: A Prospective Study in a Brazilian University Hospital
Authors: Duani Helena , Cabral Máderson Alvares de Souza , Machado Carla Jorge , Fonseca Thalyta Nogueira , Marcolino Milena Soriano , Nobre Vandack Alencar , Ravetti Cecilia Gómez , Vassallo Paula Frizera , Tupinambás Unaí 
Published: August 2024

SummaryThis study investigated the role of red blood cell distribution width (RDW) as a risk factor for hospital mortality in COVID-19 patients at a public hospital in Minas Gerais, Brazil. The study included 161 patients over 16 years old hospitalized between May and October 2020, with 39 (24.2%) deaths. Key mortality risk factors identified were age over 70 years (RR=2.78; p<0.001), male sex (RR=2.28; p=0.005), cardiovascular disease (RR=1.8; p=0.044), and abnormal chest X-ray upon admission (RR=3.07; p=0.022). Although high RDW at admission did not significantly predict mortality (31.1% vs 21.7%; RR=1.43; p=0.413), it was linked to higher mortality in patients aged 70 and over (66.7% vs 33.3%; RR=2; p=0.029). High RDW during hospitalization was a strong mortality factor for the entire cohort (41.1% vs 10.2%; RR=4.03; p<0.001) and at any time during the stay (39.7% vs 9.6%; RR=4.14; p<0.001). The Cox model analysis showed that age >70 years (HR=4.8; p<0.001), white race (HR=3.2; p=0.018), need for invasive ventilation (HR=3.8; p=0.001), and abnormal chest X-ray (HR=3.5; p=0.044) were significant risk factors, but RDW was not associated with mortality.
Standing Strong: A Systematic Review of Multifaceted Fall Prevention in Older Adults
Authors: Thomas Mony , Kirk Johnson , Patel Raul , Fred Mary 
Published: August 2024

AbstractBackgroundFalls among older adults are a major public health concern, leading to significant morbidity, mortality, and healthcare costs. This systematic review and meta-analysis aimed to evaluate the effectiveness of falls prevention interventions for community-dwelling older adults aged 65 and above.MethodsWe searched PubMed, Cochrane Library, CINAHL, Embase, and Web of Science databases for randomized controlled trials published between January 1, 2000, and December 31, 2023. Studies evaluating interventions designed to reduce fall incidence or fall-related injuries in community-dwelling older adults were included. Two reviewers independently screened studies, extracted data, and assessed risk of bias using the RoB 2 tool. Meta-analyses were conducted using random-effects models.ResultsForty-seven studies met the inclusion criteria, involving 23,584 participants across 15 countries. The mean age of participants was 76.3 years (SD 4.7), and 68% were female. Overall, interventions significantly reduced fall rates (Rate Ratio 0.80, 95% CI 0.75-0.86, I2=67%). Multifaceted interventions showed the greatest reduction in fall rates (RR 0.75, 95% CI 0.68-0.82), followed by exercise interventions alone (RR 0.85, 95% CI 0.78-0.92). Interventions also reduced the risk of becoming a faller (Risk Ratio 0.85, 95% CI 0.80-0.90) and the risk of fall-related injuries (Risk Ratio 0.83, 95% CI 0.76-0.91). Subgroup analyses revealed greater effectiveness in high-risk populations (RR 0.72, 95% CI 0.65-0.80). Longer interventions (12 months or more) showed greater reductions in fall rates. The mean adherence rate was 76%, with no serious adverse events reported.ConclusionsThis review provides strong evidence supporting the implementation of multifaceted falls prevention programs for community-dwelling older adults, with a particular emphasis on exercise interventions. Future research should focus on long-term adherence, cost-effectiveness, and innovative approaches to fall prevention in diverse populations and settings.
Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing
Authors: Voorhies Mark , Joehnk Bastian , Uehling Jessie , Walcott Keith , Dubin Claire , Mead Heather L. , Homer Christina M. , Galgiani John N. , Barker Bridget M. , Brem Rachel B. , Sil Anita 
Published: August 2024

AbstractNext generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungusCoccidioides posadasiiand infer the strain compositions for large mixed pools of these strains after competition at 37°C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition.Author summaryThe diversity of the gene pool in natural populations encodes a wealth of information about its molecular biology. This is an especially valuable resource for non-model organisms, from humans to many microbial pathogens, lacking traditional genetic approaches. An effective method for reading out this population genetic information is a genome wide association study (GWAS) which searches for genotypes correlated with a phenotype of interest. With the advent of cheap genotyping, high throughput phenotyping is the primary bottleneck for GWAS, particularly for microbes that are difficult to manipulate. Here, we take advantage of the fact that the naturally occurring genetic variation within each individual strain can be used as an intrinsic barcode, which can be used to read out relative abundance of each strain as a quantitative phenotype from a mixed culture.Coccidioides posadasii, the causative agent of Valley Fever, is a fungal pathogen that must be manipulated under biosafety level 3 conditions, precluding many high-throughput phenotyping approaches. We apply our method to pooled competitions ofC. posadasiistrains at environmental and host temperatures. We identify robustly growing and temperature-sensitive strains, confirm these inferences in validation pooled growth experiments, and successfully demonstrate their use in GWAS.
The Diffusion Exchange Ratio (DEXR): A minimal sampling of diffusion exchange spectroscopy to probe exchange, restriction, and time-dependence
Authors: Cai Teddy X. , Williamson Nathan H. , Ravin Rea , Basser Peter J. 
Published: August 2024

AbstractWater exchange is increasingly recognized as an important biological process that can affect the study of biological tissue using diffusion MR. Methods to measure exchange, however, remain immature as opposed to those used to characterize restriction, with no consensus on the optimal pulse sequence(s) or signal model(s). In general, the trend has been towards data-intensive fitting of highly parameterized models. We take the opposite approach and show that a judicious sub-sample of diffusion exchange spectroscopy (DEXSY) data can be used to robustly quantify exchange, as well as restriction, in a data-efficient manner. This sampling produces a ratio of two points per mixing time: (i) one point with equal diffusion weighting in both encoding periods, which gives maximal exchange contrast, and (ii) one point with the sametotaldiffusion weighting in just the first encoding period, for normalization. We call this quotient the Diffusion EXchange Ratio (DEXR). Furthermore, we show that it can be used to probe time-dependent diffusion by estimating the velocity autocorrelation function (VACF) over intermediate to long times (∼ 2 − 500 ms). We provide a comprehensive theoretical framework for the design of DEXR experiments in the case of static or constant gradients. Data from Monte Carlo simulations and experiments acquired in fixed and viableex vivoneonatal mouse spinal cord using a permanent magnet system are presented to test and validate this approach. In viable spinal cord, we report the following apparent parameters from just 6 data points:τk= 17 ± 4 ms,fNG= 0.71 ± 0.01,Reff= 1.10 ± 0.01μm, andkeff= 0.21 ± 0.06μm/ms, which correspond to the exchange time, restricted or non-Gaussian signal fraction, an effective spherical radius, and permeability, respectively. For the VACF, we report a long-time, power-law scaling with ≈t− 2.4, which is approximately consistent with disordered domains in 3-D. Overall, the DEXR method is shown to be highly efficient, capable of providing valuable quantitative diffusion metrics using minimal MR data.