Miracle-dz/UniFAR-FTUs huggingface dataset:
Follow #eHealth2011: Measuring the Role and Effectiveness of Online and Social Media in Increasing the Outreach of a Scientific Conference

Background Social media promotion is increasingly adopted by organizers of industry and academic events; however, the success of social media strategies is rarely questioned or the real impact scientifically analyzed. Objective We propose a framework that defines and analyses the impact, outreach, and effectiveness of social media for event promotion and research dissemination to participants of a scientific event as well as to the virtual audience through the Web. Methods Online communication channels Twitter, Facebook, Flickr, and a Liveblog were trialed and their impact measured on outreach during five phases of an eHealth conference: the setup, active and last-minute promotion phases before the conference, the actual event, and after the conference. Results Planned outreach through online channels and social media before and during the event reached an audience several magnitudes larger in size than would have been possible using traditional means. In the particular case of eHealth 2011, the outreach using traditional means would have been 74 attendees plus 23 extra as sold proceedings and the number of downloaded articles from the online proceedings (4107 until October 2013). The audience for the conference reached via online channels and social media was estimated at more than 5300 in total during the event. The role of Twitter for promotion before the event was complemented by an increased usage of the website and Facebook during the event followed by a sharp increase of views of posters on Flickr after the event. Conclusions Although our case study is focused on a particular audience around eHealth 2011, our framework provides a template for redefining “audience” and outreach of events, merging traditional physical and virtual communities and providing an outline on how these could be successfully reached in clearly defined event phases.
Sequestrase chaperones protect against oxidative stress-induced protein aggregation and [PSI+] prion formation

Misfolded proteins are usually refolded to their functional conformations or degraded by quality control mechanisms. When misfolded proteins evade quality control, they can be sequestered to specific sites within cells to prevent the potential dysfunction and toxicity that arises from protein aggregation. Btn2 and Hsp42 are compartment-specific sequestrases that play key roles in the assembly of these deposition sites. Their exact intracellular functions and substrates are not well defined, particularly since no stress sensitivity has been reported in deletion mutants. We show here that Btn2 and Hsp42 are required for oxidant tolerance and act to sequestering misfolded proteins into defined PQC sites following ROS exposure. We have used the Sup35 translation termination factor as a model oxidized protein to show that protein aggregation is elevated and widespread in mutants lacking Btn2 and Hsp42. Oxidant-induced prion formation is also elevated in sequestrase mutants consistent with the idea that Btn2 and Hsp42 function to sequester oxidatively damaged Sup35, thus preventing templating to form its heritable prion form. Taken together, our data identify protein sequestration as key antioxidant defence mechanism that functions to mitigate the damaging consequences of protein oxidation-induced aggregation.
Exercise Training and Cold Exposure Trigger Distinct Molecular Adaptations to Inguinal White Adipose Tissue

Exercise training and cold exposure both improve systemic metabolism, but the mechanisms are not well-established. We tested the hypothesis that adaptations to inguinal white adipose tissue (iWAT) are critical for these beneficial effects by determining the impact of exercise-trained and cold-exposed iWAT on systemic glucose metabolism and the iWAT proteome and secretome. Transplanting trained iWAT into sedentary mice improved glucose tolerance, while cold-exposed iWAT transplantation showed no such benefit. Compared to training, cold led to more pronounced alterations in the iWAT proteome and secretome, downregulating >2,000 proteins but also boosting iWAT’s thermogenic capacity. In contrast, only training increased extracellular space and vesicle transport proteins, and only training upregulated proteins that correlate with favorable fasting glucose, suggesting fundamental changes in trained iWAT that mediate tissue-to-tissue communication. This study defines the unique exercise training- and cold exposure-induced iWAT proteomes, revealing distinct mechanisms for the beneficial effects of these interventions on metabolic health. GRAPHICAL ABSTRACT
Impaired emotion recognition in Cntnap2-deficient mice is associated with hyper-synchronous prefrontal cortex neuronal activity

Individuals diagnosed with autism spectrum disorder (ASD) show difficulty in recognizing emotions in others, a process termed emotion recognition. While human fMRI studies linked multiple brain areas to emotion recognition, the specific mechanisms underlying impaired emotion recognition in ASD are not clear, partially due to the lack of appropriate tests in animal models. Here, we employed an emotional state preference (ESP) task to show that Cntnap2-knockout (KO) mice, an established ASD model, do not distinguish between conspecifics according to their emotional state. We assessed brain-wide local-field potential (LFP) signals during various social behavior tasks and found that Cntnap2-KO mice exhibited higher LFP theta and gamma rhythmicity than did C57BL/6J mice, even at rest. Specifically, Cntnap2-KO mice showed increased theta coherence, especially between the prelimbic cortex (PrL) and the hypothalamic paraventricular nucleus, during social behavior. Moreover, we observed significantly increased Granger causality of theta rhythmicity between these two brain areas, across all types of social behavior. Finally, optogenetic stimulation of PrL pyramidal neurons in C57BL/6J mice impaired their social discrimination abilities, including ESP behavior. Together, these results suggest that increased activity of PrL pyramidal neurons and their augmented synchronization with specific brain regions are involved in the impaired emotion recognition exhibited by Cntnap2-KO mice.
GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT

There has been significant recent progress in leveraging large-scale gene expression data to develop foundation models for single-cell biology. Models such as Geneformer and scGPT implicitly learn gene and cellular functions from the gene expression profiles of millions of cells, which requires extensive data curation and resource-intensive training. Here we explore a much simpler alternative by leveraging ChatGPT embeddings of genes based on literature. Our proposal, GenePT, uses NCBI text descriptions of individual genes with GPT-3.5 to generate gene embeddings. From there, GenePT generates single-cell embeddings in two ways: (i) by averaging the gene embeddings, weighted by each gene’s expression level; or (ii) by creating a sentence embedding for each cell, using gene names ordered by the expression level. Without the need for dataset curation and additional pretraining, GenePT is efficient and easy to use. On many downstream tasks used to evaluate recent single-cell foundation models — e.g., classifying gene properties and cell types — GenePT achieves comparable, and often better, performance than Geneformer and other models. GenePT demonstrates that large language model embedding of literature is a simple and effective path for biological foundation models.
Mutualist-Provided Resources Increase Susceptibility to Parasites

Mutualistic microbes often increase their host’s susceptibility to parasite infection. We tested two competing hypotheses to identify the cause of this phenomenon. First, mutualist-provided resources could attract antagonists by making hosts more resource-rich. Second, mutualism establishment itself might increase host vulnerability to antagonists. To test which mechanism underlies increased parasite susceptibility, we experimentally decoupled mutualism establishment and mutualist-provided resources in the legume-rhizobia mutualism. We measured parasite load on Medicago truncatula plants infected with root-knot nematodes in a full-factorial design, in which we independently manipulated rhizobia nodulation (mutualism establishment) and nitrogen availability (mutualist-provided resources). We found little effect of mutualism establishment on susceptibility, as nodulation without nitrogen fixation did not significantly increase parasite infection. By contrast, nitrogen did increase parasite infection, but with non-linear effects not fully explained by nitrogen assimilation into tissues. Our results suggest that mutualist-provided resources are an important but complex driver of indirect ecological costs of mutualism.
Global control of cellular physiology by biomolecular condensates through modulation of electrochemical equilibria

Control of the electrochemical environment in living cells is typically attributed to ion channels. Here we show that the formation of biomolecular condensates can modulate the electrochemical environment in cells, which affects processes globally within the cell and interactions of the cell with its environment. Condensate formation results in the depletion or enrichment of certain ions, generating intracellular ion gradients. These gradients directly affect the electrochemical properties of a cell, including the cytoplasmic pH and hyperpolarization of the membrane potential. The modulation of the electrochemical equilibria between the intra- and extra-cellular environments by biomolecular condensates governs charge-dependent uptake of small molecules by cells, and thereby directly influences bacterial survival under antibiotic stress. The shift of the intracellular electrochemical equilibria by condensate formation also drives a global change of the gene expression profile. The control of the cytoplasmic environment by condensates is correlated with their volume fraction, which can be highly variable between cells due to the stochastic nature of gene expression at the single cell level. Thus, condensate formation can amplify cell-cell variability of the environmental effects induced by the shift of cellular electrochemical equilibria. Our work reveals new biochemical functions of condensates, which extend beyond the biomolecules driving and participating in condensate formation, and uncovers a new role of biomolecular condensates in cellular regulation.
Angiopoietin-like protein 2 mediates vasculopathy driven fibrogenesis in a mouse model of systemic sclerosis

Vasculopathy is a common hallmark of various fibrotic disorders including systemic sclerosis (SSc), yet its underlying etiology and contribution to fibrogenesis remain ill-defined. In SSc the vasculopathy typically precedes the onset of fibrosis and we observed that this phenomenon is recapitulated in the Snail transgenic mouse model of SSc. The vascular anomalies manifest as deformed vessels, endothelial cell dysfunction and vascular leakage. Our investigation into the underlying mechanism of this phenotype revealed that Angiopoietin-like protein 2 (Angptl2), secreted by the Snail transgenic keratinocytes, is a principal driver of fibrotic vasculopathy. In endothelial cells, Angptl2 upregulates pro-fibrotic genes, downregulates the tight junction protein Claudin 5, and prompts the acquisition of mesenchymal characteristics. Inhibiting endothelial cell junctional instability and consequently vascular leakage with a synthetic analog of the microbial metabolite Urolithin A (UAS03) effectively mitigated the vasculopathy and inhibited fibrogenesis. Thus, Angptl2 emerges as a promising early biomarker of the disease and inhibiting the vasculopathy inducing effects of this protein with agents such as UAS03 presents an appealing therapeutic avenue to reduce disease severity. These insights hold the potential to revolutionize the approach to the treatment of fibrotic diseases by targeting the vascular defects.
The panC-encoded pantothenate synthetase to tackle carbapenem-resistant OprD Pseudomonas aeruginosa mutant revealed through Tn-Seq

For the World Health Organization, carbapenem-resistant Pseudomonas aeruginosa is a critical priority for which new antimicrobial drugs are needed. Consequently, understanding the underlying mechanisms of resistant bacteria infection will enable the identification of new therapeutic targets. Loss of the OprD porin is the main determinant of resistance to the last resort carbapenem antibiotics and has been described to enhance fitness in vivo and virulence. Transposon sequencing is a high-throughput sequencing technique that makes it possible to identify essential genes (EGs) that may turn out to be therapeutic targets. However, such a strategy has not yet been used for OprD-deficient P. aeruginosa. In this study, we identified the EGs specific to PA14 OprD mutant for LB growth and we established a list of 30 EGs among these, we highlighted the panC gene encoding pantothenate synthetase as a promising target. Using CRISPRi, we confirmed that silencing panC reduced LB growth, and decreased sigX expression, whose overexpression is associated with membrane fluidity, as well as the expression of genes involved in the fatty acid synthesis (FAS). Taking into account the weakness of PA14 OprD mutant due to an altered membrane consecutive to a decrease in unsaturated FAS in the absence of panC, we showed that silencing panC extended the destruction time of 16HBE airway cells. Overall, our findings highlighted the anti-virulence potential of panC inhibition and shed new light on its inhibition as a target for treating carbapenem-resistant OprD-defective PA lung infections.
Evaluating Persistent Memory Range Indexes

Persistent memory (PM) is fundamentally changing the way database index structures are built by enabling persistence, high performance, and (near) instant recovery all on the memory bus. Prior work has proposed many techniques to tailor index structure designs for PM, but they were mostly based on volatile DRAM with simulation due to the lack of real PM hardware. Until today is it unclear how these techniques will actually perform on real PM hardware. With the recent released Intel Optane DC Persistent Memory, for the first time, this paper provides a comprehensive evaluation of recent persistent index structures. We focus on B + -Tree-based range indexes and carefully choose four representative index structures for evaluation: wBTree, NV-Tree, BzTree and FPTree. These four tree structures cover a wide, representative range of techniques that are essential building blocks of PM-based index structures. For fair comparison, we used an unified programming model for all trees and developed PiBench , a benchmarking framework which targets PM-based indexes. Through empirical evaluation using representative workloads, we identify key, effective techniques, insights and caveats to guide the making of future PM-based index structures.
APPLICATION OF BOND WATER DYNAMIC THEORY TO SOIL SUBMERGENCE IN ANKANG CITY AND SURROUNDING AREAS ADJACENT XUNYANG HYDROPOWER STATION

Ankang City and the surrounding areas adjacent to Xunyang Hydropower Station reservoir tail zone locate on the terrace and the high-and low floodplain of the left bank of the Hanjiang River.The ground has the typical dualistic-structure characteristics.The surface layer of the high floodplain generally distributes relatively thick artificial fill.The bond water dynamic theory and the infiltration flow characteristics of the clay soil are applied to determine the relations among the pressure water level and the aquifer belt of clay layer water level.In this research,different submergence critical depths are defined by foundation types,depths of burial,fill layer thickness of different buildings and the type of crops of suburbs,etc.the paper calculates the groundwater Backwater Value and the burial depth of clay layer water-bearing zone in seven different normal impounded level conditions to investigate the submergence area and degree.As a result,a reasonable normal impounded level is determined ultimately.This result can provide a reliable geological basis for the migration resettlement work of this project reservoir area.
The LDBC Social Network Benchmark

The Linked Data Benchmark Council's Social Network Benchmark (LDBC SNB) is an effort intended to test various functionalities of systems used for graph-like data management. For this, LDBC SNB uses the recognizable scenario of operating a social network, characterized by its graph-shaped data. LDBC SNB consists of two workloads that focus on different functionalities: the Interactive workload (interactive transactional queries) and the Business Intelligence workload (analytical queries). This document contains the definition of the Interactive Workload and the first draft of the Business Intelligence Workload. This includes a detailed explanation of the data used in the LDBC SNB benchmark, a detailed description for all queries, and instructions on how to generate the data and run the benchmark with the provided software.
Design and selection of materialized views in a data warehousing environment: a case study

In this paper, we describe the design of a data warehousing system for an engineering company 'R'. A cost model was developed for this system to enable the evaluation of the total costs and benefits involved in selecting each materialized view. Using the cost analysis methodology for evaluation, an adapted greedy algorithm has been implemented for the selection of materialized views. The algorithm and cost model were applied to a set of real-life database items extracted from company 'R'. By selecting the most cost effective set of materialized summary views, the total of the maintenance, storage and query costs of the system is optimized, thereby resulting in an efficient data warehousing system.
Household Debt and Monetary Policy: Revealing the Cash-Flow Channel

We examine the effect of monetary policy on household spending when households are indebted and interest rates on outstanding loans are linked to short-term interest rates. Using administrative data on balance sheets and consumption expenditure of Swedish households, we reveal the cash-flow transmission channel of monetary policy. On average, indebted households reduce consumption spending by an additional 0.23–0.55 percentage points in response to a one-percentage-point increase in the policy rate, relative to a household with no debt. We show that these responses are driven by households that have some or a large share of their debt in contracts where interest rates vary with short-term interest rates, such as adjustable-rate mortgages (ARMs), which implies that monetary policy shocks are quickly passed through to interest expenses.
Volatilização de amônia do solo após doses de ureia com inibidores de urease e nitrificação na cultura do abacaxi

Os inibidores de urease N-(n-butil) tiofosforicotriamida (NBPT) e nitrificacao dicianodiamida (DCD) minimizam as perdas de nitrogenio (N) pela volatilizacao da amonia (NH3), por reducao da velocidade de hidrolise da ureia e conversao de amonio em nitrato, respectivamente. O objetivo deste estudo foi avaliar as perdas de N do solo por volatilizacao, apos a adicao de doses de N, na forma de ureia combinada com inibidores de urease e de nitrificacao, no semiarido mineiro. Utilizou-se o delineamento em blocos casualizados, com tres repeticoes, em esquema fatorial 4 x 5 x 7, constituidos por: quatro combinacoes de ureia com inibidores (ureia comum; ureia + NBPT; ureia + DCD e, ureia + NBPT + DCD), cinco doses de N (0,0; 3,7; 7,4; 11,1 e 14,8 g/planta) e sete tempos de avaliacao (3, 6, 9, 12, 15, 18 e 21 dias) apos a aplicacao, em cobertura, no cultivo de abacaxi irrigado. Foram avaliadas as perdas de amonia e o pH em torno do grânulo de ureia. O inibidor de urease (ureia + NBPT) foi mais eficiente nas menores doses de nitrogenio, alem de reduzir e atrasar os periodos de volatilizacao de N-NH3 e tambem diminuir o pH do solo, por causa, provavelmente da maior nitrificacao e, ou, do aumento da taxa de decomposicao da materia orgânica do solo (MOS), pela maior disponibilidade de N em comparacao aos tratamentos com ureia e ureia + DCD. O aumento das doses de nitrogenio reduziu as perdas relativas de N por volatilizacao, gracas a maior saturacao dos sitios de acao da enzima urease.
Hierarchical Bayesian Inversion of Marine CSEM Data Over the Scarborough Gas Field - A Lesson in Correlated Noise

Uncertainty in the transmitter position, theory error and insufficient model parameterization amongst various other factors can lead to significant correlated error in observed controlled source electromagnetic data. These errors come to light by an examination of the residuals after performing inversion. Since correlated error violates the assumption of independent data noise it can manifest in spurious structure in inverted models. We demonstrate this using both synthetic data and real data from Scarborough gas field, North West Australia. In this work we propose a method which uses a hierarchical Bayesian framework and reversible jump Markov chain Monte Carlo to account for correlated error. We find that this removes suspect structure from the inverted models and within reasonable prior bounds, provides information on the resolution of resistivity at depth.
ex-Fall-grown oat to extend the fall grazing season for replacement dairy heifers 1

Our objective was to assess the pasture productivity and forage characteristics of 2 fall-grown oat ( Avena sativa L.) cultivars, specifically for extending the grazing season and reducing reliance on harvested forages by replacement dairy heifers. A total of 160 gravid Holstein heifers (80 heifers/yr) were stratified by weight, and assigned to 1 of 10 identical research pens (8 heifers/pen). Initial body weights were 480 ± 43.5 kg in 2011 and 509 ± 39.4 kg in 2012. During both years of the trial, four 1.0-ha pasture replicates were seeded in August with Ogle oat (Schumitsch Seed Inc., Antigo, WI), and 4 separate, but similarly configured, pasture replicates were seeded with Forage Plus oat (Kratz Farms, Slinger, WI). Heifer groups were maintained as units, assigned to specific pastures, and then allowed to graze fall-oat pastures for 6 h daily before returning to the barn, where they were offered a forage-based basal total mixed ration. Two heifer groups were retained in confinement (without grazing) as controls and offered the identical total mixed ration as pasture groups. During 2011, available forage mass increased with strong linear and quadratic effects for both cultivars, peaking at almost 9 Mg/ha on October 31. In contrast, forage mass was not affected by evaluation date in 2012, remaining ≤2,639 kg/ha across all dates because of droughty climatic conditions. During 2012, Ogle exhibited greater forage mass than Forage Plus across all sampling dates (2,678 vs. 1,856 kg/ha), largely because of its more rapid maturation rate and greater canopy height. Estimates of energy density for oat forage ranged from 59.6 to 69.1% during 2011, and ranged narrowly from 68.4 to 70.4% during 2012. For 2011, responses for both cultivars had strong quadratic character, in which the most energy-dense forages oc-curred in mid November, largely due to accumulation of water-soluble carbohydrates that reached maximum concentrations of 18.2 and 15.1% for Forage Plus and Ogle, respectively. Across the 2-yr trial, average daily gain for grazing heifer groups tended to be greater than heifers remaining in confinement (0.85 vs. 0.74 kg/d), but both management strategies produced weight gains within reasonable proximity to normal targets for heifers in this weight range. Fall-grown oat should be managed as stockpiled forage for deferred grazing, and good utilization of fall-oat forage can be accomplished by a one-time removal of standing forage, facilitated by a single lead wire advanced daily to prevent waste.