Experimental Compilation and Computation of Hydration Free Energies for Ionic Solutes.

Although charged solutes are common in many chemical systems, traditional solvation models perform poorly in calculating solvation energies of ions. One major obstacle is the scarcity of experimental data for solvated ions. In this study, we release an experiment-based aqueous ionic solvation energy data set, IonSolv-Aq, that contains hydration free energies for 118 anions and 155 cations, more than 2 times larger than the set of hydration free energies for singly charged ions contained in the 2012 Minnesota Solvation Database commonly used in benchmarking studies. We discuss sources of systematic uncertainty in the data set and use the data to examine the accuracy of popular implicit solvation models COSMO-RS and SMD for predicting solvation free energies of singly charged ionic solutes in water. Our results indicate that most SMD and COSMO-RS modeling errors for ionic solutes are systematic and correctable with empirical parameters. We discuss two systematic offsets: one across all ions and one that depends on the functional group of the ionization site. After correcting for these offsets, solvation energies of singly charged ions are predicted using COSMO-RS to 3.1 kcal mol-1 MAE against a challenging test set and 1.7 kcal mol-1 MAE (about 3% relative error) with a filtered test set. The performance of SMD is similar, with MAE against those same test sets of 2.7 and 1.7 kcal mol-1. These results underscore the importance of compiling larger experimental data sets to improve solvation model parametrization and fairly assess performance.

Health and nutrition claims for infant formula: international cross sectional survey.

OBJECTIVES: To review available health and nutrition claims for infant formula products in multiple countries and to evaluate the validity of the evidence used for substantiation of claims. DESIGN: International cross sectional survey. SETTING: Public facing and healthcare professional facing company owned or company managed formula industry websites providing information about products marketed for healthy infants delivered at full term in 15 countries: Australia, Canada, Germany, India, Italy, Japan, Nigeria, Norway, Pakistan, Russia, Saudi Arabia, South Africa, Spain, the United Kingdom, and the United States in 2020-22. MAIN OUTCOME MEASURES: Number and type of claims made for each product and ingredient. References cited were reviewed and risk of bias was assessed for registered clinical trials using the Cochrane risk of bias tool, and for systematic reviews using the Risk Of Bias in Systematic reviews tool. RESULTS: 757 infant formula products were identified, each with a median of two claims (range from 1 (Australia) to 4 (US)), and 31 types of claims across all products. Of 608 products with ≥1 claims, the most common claim types were "helps/supports development of brain and/or eyes and/or nervous system" (323 (53%) products, 13 ingredients), "strengthens/supports a healthy immune system" (239 (39%) products, 12 ingredients), and "helps/supports growth and development" (224 (37%) products, 20 ingredients). 41 groups of ingredients were associated with ≥1claims, but many claims were made without reference to a specific ingredient (307 (50%) products). The most common groups of ingredients cited in claims were long chain polyunsaturated fatty acids (278 (46%) products, 9 different claims); prebiotics, probiotics, or synbiotics (225 (37%) products, 19 claims); and hydrolysed protein (120 (20%) products, 9 claims). 161/608 (26%) products with ≥1 claims provided a scientific reference to support the claim-266 unique references were cited for 24 different claim types for 161 products. The reference types most frequently cited were clinical trials (50%, 134/266) and reviews (20%, 52/266). 28% (38/134) of referenced clinical trials were registered, 14% (19/134) prospectively. 58 claims referred to 32 registered clinical trials, of which 51 claims (27 trials) related to a randomised comparison. 46 of 51 claims (90%) referenced registered clinical trial outcomes at high risk of bias, and all cited systematic reviews and pooled analyses, carried a high risk of bias. CONCLUSIONS: Most infant formula products had at least one health and nutrition claim. Multiple ingredients were claimed to achieve similar health or nutrition effects, multiple claims were made for the same ingredient type, most products did not provide scientific references to support claims, and referenced claims were not supported by robust clinical trial evidence.

A PDZ Protein GIPC3 Positively Modulates Hedgehog Signaling and Melanoma Growth.

The hedgehog (Hh) pathway is essential for animal development, but aberrant activation promotes cancer growth. In this study, we show that GIPC3, a PDZ domain-containing protein with putative adaptor protein function, positively modulates Hh target gene expression in normal fibroblasts and melanoma cells and supports melanoma tumor growth. Using overexpression and epistasis studies, we show that Gipc3 potentiates Hh transcriptional output and that it modulates GLI-dependent transcription independently of Sufu. Whereas we find that GIPC3 protein does not interact with Hh pathway components, Ingenuity Pathway Analyses of GIPC3-interacting proteins identified by coimmunoprecipitation and mass spectrometry show an association with cancer pathogenesis. Subsequent interrogation of The Cancer Genome Atlas and the Human Protein Atlas databases reveals GIPC3 upregulation in many cancers. Using expression screens in selected groups of GIPC3-upregulated cancers with reported Hh pathway activation, we find a significant positive correlation of GIPC3 expression with Hh pathway components GLI1, GLI2, and GPR161 in melanoma lines. Consistently, GIPC3 knockdown in melanoma lines significantly reduces GLI1 and GLI2 expression, cell viability, colony formation, and allograft tumor growth. Our findings highlight previously unidentified roles of GIPC3 in potentiating Hh response and melanoma tumorigenesis and suggest that GIPC3 modulation on Hh signaling may be targeted to reduce melanoma growth.

Clinical factors and mortality rates for non-traumatic upper extremity amputations.

Non-traumatic upper extremity amputations are an increasing concern with the rising prevalence of diabetes mellitus. To ascertain the risk factors and mortality rates for these amputations, the demographic information, amputation history, comorbidities and clinical outcomes of 140 patients who underwent non-traumatic upper extremity amputations between 1 January 2004 and 31 October 2017 were studied. Correlations were assessed using Cochran-Armitage chi-squared tests, odds ratios and multivariate binomial logistic regression as appropriate. Diabetes mellitus, coronary artery disease, end-stage renal failure, peripheral arterial disease and prior lower extremity amputation were significant risk factors for multiple upper extremity amputations. One-year, 2-year and 5-year mortality rates were 12%, 15% and 38%, respectively, following first upper extremity amputation. The risk factors for upper extremity amputations correspond with those for lower extremity amputations, comprising mainly diabetes mellitus and its related comorbidities. The mortality rates for non-traumatic upper extremity amputations highlight their significant burden on patients.Level of evidence: III.

Further Towards Unambiguous Edge Bundling: Investigating Power-Confluent Drawings for Network Visualization.

Bach et al. [1] recently presented an algorithm for constructing confluent drawings, by leveraging power graph decomposition to generate an auxiliary routing graph. We identify two issues with their method which we call the node split and short-circuit problems, and solve both by modifying the routing graph to retain the hierarchical structure of power groups. We also classify the exact type of confluent drawings that the algorithm can produce as 'power-confluent', and prove that it is a subclass of the previously studied 'strict confluent' drawing. A description and source code of our implementation is also provided, which additionally includes an improved method for power graph construction.

Platelets from HIV-infected individuals on antiretroviral drug therapy with poor CD4+ T cell recovery can harbor replication-competent HIV despite viral suppression.

In addition to hemostasis, human platelets have several immune functions and interact with infectious pathogens including HIV in vitro. Here, we report that platelets from HIV-infected individuals on combined antiretroviral drug therapy (ART) with low blood CD4+ T cell counts (<350 cells/µl) contained replication-competent HIV despite viral suppression. In vitro, human platelets harboring HIV propagated the virus to macrophages, a process that could be prevented with the biologic abciximab, an anti-integrin αIIb/ß3 Fab. Furthermore, in our cohort, 88% of HIV-infected individuals on ART with viral suppression and with platelets containing HIV were poor immunological responders with CD4+ T cell counts remaining below <350 cells/µl for more than one year. Our study suggests that platelets may be transient carriers of HIV and may provide an alternative pathway for HIV dissemination in HIV-infected individuals on ART with viral suppression and poor CD4+ T cell recovery.

Predation risk influences food-web structure by constraining species diet choice.

The foraging behaviour of species determines their diet and, therefore, also emergent food-web structure. Optimal foraging theory (OFT) has previously been applied to understand the emergence of food-web structure through a consumer-centric consideration of diet choice. However, the resource-centric viewpoint, where species adjust their behaviour to reduce the risk of predation, has not been considered. We develop a mechanistic model that merges metabolic theory with OFT to incorporate the effect of predation risk on diet choice to assemble food webs. This 'predation-risk-compromise' (PR) model better captures the nestedness and modularity of empirical food webs relative to the classical optimal foraging model. Specifically, compared with optimal foraging alone, risk-mitigated foraging leads to more-nested but less-modular webs by broadening the diet of consumers at intermediate trophic levels. Thus, predation risk significantly affects food-web structure by constraining species' ability to forage optimally, and needs to be considered in future work.

Graph Drawing by Stochastic Gradient Descent.

A popular method of force-directed graph drawing is multidimensional scaling using graph-theoretic distances as input. We present an algorithm to minimize its energy function, known as stress, by using stochastic gradient descent (SGD) to move a single pair of vertices at a time. Our results show that SGD can reach lower stress levels faster and more consistently than majorization, without needing help from a good initialization. We then show how the unique properties of SGD make it easier to produce constrained layouts than previous approaches. We also show how SGD can be directly applied within the sparse stress approximation of Ortmann et al. [1], making the algorithm scalable up to large graphs.

A dual substrate-accessing mechanism of a major facilitator superfamily protein facilitates lysophospholipid flipping across the cell membrane.

Lysophospholipid transporter (LplT) is a member of the major facilitator superfamily present in many Gram-negative bacteria. LplT catalyzes flipping of lysophospholipids (LPLs) across the bacterial inner membrane, playing an important role in bacterial membrane homeostasis. We previously reported that LplT promotes both uptake of exogenous LPLs and intramembranous LPL flipping across the bilayer. To gain mechanistic insight into this dual LPL-flipping activity, here we implemented a combination of computational approaches and LPL transport analyses to study LPL binding of and translocation by LplT. Our results suggest that LplT translocates LPLs through an elongated cavity exhibiting an extremely asymmetric polarity. We found that two D(E)N motifs form a head group-binding site, in which the carboxylate group of Asp-30 is important for LPL head group recognition. Substitutions of residues in the head group-binding site disrupted both LPL uptake and flipping activities. However, alteration of hydrophobic residues on the interface between the N- and C-terminal domains impaired LPL flipping specifically, resulting in LPLs accumulation in the membrane, but LPL uptake remained active. These results suggest a dual substrate-accessing mechanism, in which LplT recruits LPLs to its substrate-binding site via two routes, either from its extracellular entry or through a membrane-embedded groove between transmembrane helices, and then moves them toward the inner membrane leaflet. This LPL-flipping mechanism is likely conserved in many bacterial species, and our findings illustrate how LplT adjusts the major facilitator superfamily translocation pathway to perform its versatile lipid homeostatic functions.