Model of a fluid at small and large length scales and the hydrophobic effect

We present a statistical field theory to describe large length scale effects induced by solutes in a cold and otherwise placid liquid. The theory divides space into a cubic grid of cells. The side length of each cell is of the order of the bulk correlation length of the bulk liquid. Large length scale states of the cells are specified with an Ising variable. Finer length scale effects are described with a Gaussian field, with mean and variance affected by both the large length scale field and by the constraints imposed by solutes. In the absence of solutes and corresponding constraints, integration over the Gaussian field yields an effective lattice gas Hamiltonian for the large length scale field. In the presence of solutes, the integration adds additional terms to this Hamiltonian. We identify these terms analytically. They can provoke large length scale effects, such as the formation of interfaces and depletion layers. We apply our theory to compute the reversible work to form a bubble in liquid water, as a function of the bubble radius. Comparison with molecular simulation results for the same function indicates that the theory is reasonably accurate. Importantly, simulating the large length scale field involves binary arithmetic only. It thus provides a computationally convenient scheme to incorporate explicit solvent dynamics and structure in simulation studies of large molecular assemblies

Metasql: A Generate-then-Rank Framework for Natural Language to SQL Translation

The Natural Language Interface to Databases (NLIDB) empowers non-technical users with database access through intuitive natural language (NL) interactions. Advanced approaches, utilizing neural sequence-to-sequence models or large-scale language models, typically employ auto-regressive decoding to generate unique SQL queries sequentially. While these translation models have greatly improved the overall translation accuracy, surpassing 70% on NLIDB benchmarks, the use of auto-regressive decoding to generate single SQL queries may result in sub-optimal outputs, potentially leading to erroneous translations. In this paper, we propose Metasql, a unified generate-then-rank framework that can be flexibly incorporated with existing NLIDBs to consistently improve their translation accuracy. Metasql introduces query metadata to control the generation of better SQL query candidates and uses learning-to-rank algorithms to retrieve globally optimized queries. Specifically, Metasql first breaks down the meaning of the given NL query into a set of possible query metadata, representing the basic concepts of the semantics. These metadata are then used as language constraints to steer the underlying translation model toward generating a set of candidate SQL queries. Finally, Metasql ranks the candidates to identify the best matching one for the given NL query. Extensive experiments are performed to study Metasql on two public NLIDB benchmarks. The results show that the performance of the translation models can be effectively improved using Metasql

Aniline hydrogenolysis on nickel: effects of surface hydrogen and surface structure

Fluorescence yield near-edge spectroscopy (FYNES) above the carbon K edge and temperature programmed reaction spectroscopy (TPRS) have been used as the methods for characterizing the reactivity and structure of adsorbed aniline and aniline derived species on the Ni(100) and Ni(111) surfaces over an extended range of temperatures and hydrogen pressures. The Ni(100) surface shows appreciably higher hydrogenolysis activity towards adsorbed aniline than the Ni(111) surface. Hydrogenolysis of aniline on the Ni(100) surface results in benzene formation at 470 K, both in reactive hydrogen atmospheres and in vacuum. External hydrogen significantly enhances the hydrogenolysis activity for aniline on the Ni(100) surface. Based on spectroscopic evidence, we believe that the dominant aniline hydrogenolysis reaction is preceded by partial hydrogenation of the aromatic ring of aniline in the presence of 0.001 Torr of external hydrogen on the (100) surface. In contrast, very little adsorbed aniline undergoes hydrogen induced C-N bond activation on the Ni(111) surface for hydrogen pressures as high as 10 −7 Torr below 500 K. Thermal dehydrogenation of aniline dominates with increasing temperature on the Ni(111) surface, resulting in the formation of a previously observed polymeric layer which is stable up to 820 K. Aniline is adsorbed at a smaller angle relative to the Ni(111) surface than the Ni(100) surface at temperatures below the hydrogenolysis temperature. We believe that the proximity and strong π-interaction between the aromatic ring of the aniline and the surface is one major factor which controls the competition between dehydrogenation and hydrogen addition. In this case the result is a substantial enhancement of aniline dehydrogenation relative to hydrogenation on the Ni(111) surface.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44251/1/10562_2004_Article_BF00806886.pd

PURPLE: Making a Large Language Model a Better SQL Writer

Large Language Model (LLM) techniques play an increasingly important role in Natural Language to SQL (NL2SQL) translation. LLMs trained by extensive corpora have strong natural language understanding and basic SQL generation abilities without additional tuning specific to NL2SQL tasks. Existing LLMs-based NL2SQL approaches try to improve the translation by enhancing the LLMs with an emphasis on user intention understanding. However, LLMs sometimes fail to generate appropriate SQL due to their lack of knowledge in organizing complex logical operator composition. A promising method is to input the LLMs with demonstrations, which include known NL2SQL translations from various databases. LLMs can learn to organize operator compositions from the input demonstrations for the given task. In this paper, we propose PURPLE (Pre-trained models Utilized to Retrieve Prompts for Logical Enhancement), which improves accuracy by retrieving demonstrations containing the requisite logical operator composition for the NL2SQL task on hand, thereby guiding LLMs to produce better SQL translation. PURPLE achieves a new state-of-the-art performance of 80.5% exact-set match accuracy and 87.8% execution match accuracy on the validation set of the popular NL2SQL benchmark Spider. PURPLE maintains high accuracy across diverse benchmarks, budgetary constraints, and various LLMs, showing robustness and cost-effectiveness.Comment: 12 pages, accepted by ICDE 2024 (40th IEEE International Conference on Data Engineering

Sarcoplasmic reticular Ca 2+ -ATPase inhibition paradoxically upregulates murine skeletal muscle Na v 1.4 function

Abstract: Skeletal muscle Na+ channels possess Ca2+- and calmodulin-binding sites implicated in Nav1.4 current (INa) downregulation following ryanodine receptor (RyR1) activation produced by exchange protein directly activated by cyclic AMP or caffeine challenge, effects abrogated by the RyR1-antagonist dantrolene which itself increased INa. These findings were attributed to actions of consequently altered cytosolic Ca2+, [Ca2+]i, on Nav1.4. We extend the latter hypothesis employing cyclopiazonic acid (CPA) challenge, which similarly increases [Ca2+]i, but through contrastingly inhibiting sarcoplasmic reticular (SR) Ca2+-ATPase. Loose patch clamping determined Na+ current (INa) families in intact native murine gastrocnemius skeletal myocytes, minimising artefactual [Ca2+]i perturbations. A bespoke flow system permitted continuous INa comparisons through graded depolarizing steps in identical stable membrane patches before and following solution change. In contrast to the previous studies modifying RyR1 activity, and imposing control solution changes, CPA (0.1 and 1 µM) produced persistent increases in INa within 1–4 min of introduction. CPA pre-treatment additionally abrogated previously reported reductions in INa produced by 0.5 mM caffeine. Plots of peak current against voltage excursion demonstrated that 1 µM CPA increased maximum INa by ~ 30%. It only slightly decreased half-maximal activating voltages (V0.5) and steepness factors (k), by 2 mV and 0.7, in contrast to the V0.5 and k shifts reported with direct RyR1 modification. These paradoxical findings complement previously reported downregulatory effects on Nav1.4 of RyR1-agonist mediated increases in bulk cytosolic [Ca2+]. They implicate possible local tubule-sarcoplasmic triadic domains containing reduced [Ca2+]TSR in the observed upregulation of Nav1.4 function following CPA-induced SR Ca2+ depletion

Sarcoplasmic reticular Ca 2+ -ATPase inhibition paradoxically upregulates murine skeletal muscle Na v 1.4 function

Abstract: Skeletal muscle Na+ channels possess Ca2+- and calmodulin-binding sites implicated in Nav1.4 current (INa) downregulation following ryanodine receptor (RyR1) activation produced by exchange protein directly activated by cyclic AMP or caffeine challenge, effects abrogated by the RyR1-antagonist dantrolene which itself increased INa. These findings were attributed to actions of consequently altered cytosolic Ca2+, [Ca2+]i, on Nav1.4. We extend the latter hypothesis employing cyclopiazonic acid (CPA) challenge, which similarly increases [Ca2+]i, but through contrastingly inhibiting sarcoplasmic reticular (SR) Ca2+-ATPase. Loose patch clamping determined Na+ current (INa) families in intact native murine gastrocnemius skeletal myocytes, minimising artefactual [Ca2+]i perturbations. A bespoke flow system permitted continuous INa comparisons through graded depolarizing steps in identical stable membrane patches before and following solution change. In contrast to the previous studies modifying RyR1 activity, and imposing control solution changes, CPA (0.1 and 1 µM) produced persistent increases in INa within 1–4 min of introduction. CPA pre-treatment additionally abrogated previously reported reductions in INa produced by 0.5 mM caffeine. Plots of peak current against voltage excursion demonstrated that 1 µM CPA increased maximum INa by ~ 30%. It only slightly decreased half-maximal activating voltages (V0.5) and steepness factors (k), by 2 mV and 0.7, in contrast to the V0.5 and k shifts reported with direct RyR1 modification. These paradoxical findings complement previously reported downregulatory effects on Nav1.4 of RyR1-agonist mediated increases in bulk cytosolic [Ca2+]. They implicate possible local tubule-sarcoplasmic triadic domains containing reduced [Ca2+]TSR in the observed upregulation of Nav1.4 function following CPA-induced SR Ca2+ depletion

Diimide formation on the Ni(100) surface

Diimide (N2H2), an extremely reactive species, is observed as a gas phase product from the Ni(100) surface in the 200 to 450 K range during hydrazine thermal decomposition and during thermal desorption of predissociated ammonia. These results suggest that the primary mechanism for diimide formation is recombination of an adsorbed NH surface intermediate. The observation that diimide can be formed from predissociated ammonia illustrates that a nitrogen-nitrogen bond in the precursor is not required for diimide formation. Diimide formation from predissociated ammonia is enhanced by coadsorbed hydrogen, which we believe stabilizes NH on the Ni(100) surface. In addition, the direct decomposition of adsorbed N2H4 contributes to the production of diimide at 230 K.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30742/1/0000392.pd

MUC1-associated proliferation signature predicts outcomes in lung adenocarcinoma patients

Background: MUC1 protein is highly expressed in lung cancer. The cytoplasmic domain of MUC1 (MUC1-CD) induces tumorigenesis and resistance to DNA-damaging agents. We characterized MUC1-CD-induced transcriptional changes and examined their significance in lung cancer patients. Methods: Using DNA microarrays, we identified 254 genes that were differentially expressed in cell lines transformed by MUC1-CD compared to control cell lines. We then examined expression of these genes in 441 lung adenocarcinomas from a publicly available database. We employed statistical analyses independent of clinical outcomes, including hierarchical clustering, Student's t-tests and receiver operating characteristic (ROC) analysis, to select a seven-gene MUC1-associated proliferation signature (MAPS). We demonstrated the prognostic value of MAPS in this database using Kaplan-Meier survival analysis, log-rank tests and Cox models. The MAPS was further validated for prognostic significance in 84 lung adenocarcinoma patients from an independent database. Results: MAPS genes were found to be associated with proliferation and cell cycle regulation and included CCNB1, CDC2, CDC20, CDKN3, MAD2L1, PRC1 and RRM2. MAPS expressors (MAPS+) had inferior survival compared to non-expressors (MAPS-). In the initial data set, 5-year survival was 65% (MAPS-) vs. 45% (MAPS+, p < 0.0001). Similarly, in the validation data set, 5-year survival was 57% (MAPS-) vs. 28% (MAPS+, p = 0.005). Conclusions: The MAPS signature, comprised of MUC1-CD-dependent genes involved in the control of cell cycle and proliferation, is associated with poor outcomes in patients with adenocarcinoma of the lung. These data provide potential new prognostic biomarkers and treatment targets for lung adenocarcinoma

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

<p>Abstract</p> <p>Background</p> <p>Analysis of microarray experiments often involves testing for the overrepresentation of pre-defined sets of genes among lists of genes deemed individually significant. Most popular gene set testing methods assume the independence of genes within each set, an assumption that is seriously violated, as extensive correlation between genes is a well-documented phenomenon.</p> <p>Results</p> <p>We conducted a meta-analysis of over 200 datasets from the Gene Expression Omnibus in order to demonstrate the practical impact of strong gene correlation patterns that are highly consistent across experiments. We show that a common independence assumption-based gene set testing procedure produces very high false positive rates when applied to data sets for which treatment groups have been randomized, and that gene sets with high internal correlation are more likely to be declared significant. A reanalysis of the same datasets using an array resampling approach properly controls false positive rates, leading to more parsimonious and high-confidence gene set findings, which should facilitate pathway-based interpretation of the microarray data.</p> <p>Conclusions</p> <p>These findings call into question many of the gene set testing results in the literature and argue strongly for the adoption of resampling based gene set testing criteria in the peer reviewed biomedical literature.</p

Real-Time Imaging of HIF-1α Stabilization and Degradation

HIF-1α is overexpressed in many human cancers compared to normal tissues due to the interaction of a multiplicity of factors and pathways that reflect specific genetic alterations and extracellular stimuli. We developed two HIF-1α chimeric reporter systems, HIF-1α/FLuc and HIF-1α(ΔODDD)/FLuc, to investigate the tightly controlled level of HIF-1α protein in normal (NIH3T3 and HEK293) and glioma (U87) cells. These reporter systems provided an opportunity to investigate the degradation of HIF-1α in different cell lines, both in culture and in xenografts. Using immunofluorescence microscopy, we observed different patterns of subcellular localization of HIF-1α/FLuc fusion protein between normal cells and cancer cells; similar differences were observed for HIF-1α in non-transduced, wild-type cells. A dynamic cytoplasmic-nuclear exchange of the fusion protein and HIF-1α was observed in NIH3T3 and HEK293 cells under different conditions (normoxia, CoCl2 treatment and hypoxia). In contrast, U87 cells showed a more persistent nuclear localization pattern that was less affected by different growing conditions. Employing a kinetic model for protein degradation, we were able to distinguish two components of HIF-1α/FLuc protein degradation and quantify the half-life of HIF-1α fusion proteins. The rapid clearance component (t1/2 ∼4–6 min) was abolished by the hypoxia-mimetic CoCl2, MG132 treatment and deletion of ODD domain, and reflects the oxygen/VHL-dependent degradation pathway. The slow clearance component (t1/2 ∼200 min) is consistent with other unidentified non-oxygen/VHL-dependent degradation pathways. Overall, the continuous bioluminescence readout of HIF-1α/FLuc stabilization in vitro and in vivo will facilitate the development and validation of therapeutics that affect the stability and accumulation of HIF-1α