Phase transition in the computational complexity of the shortest common superstring and genome assembly.

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle formulation. That is, the computing time is believed to grow exponentially with the problem size in the worst case. Despite this fact, high-throughput technologies and modern algorithms currently allow bioinformaticians to handle datasets of billions of reads. Using methods from statistical mechanics, we address this conundrum by demonstrating the existence of a phase transition in the computational complexity of the problem and showing that practical instances always fall in the "easy" phase (solvable by polynomial-time algorithms). In addition, we propose a Markov-chain Monte Carlo method that outperforms common deterministic algorithms in the hard regime.

Single nucleotide polymorphisms in ADAM17, IL23R and SLCO1C1 genes protect against infliximab failure in adults with Crohn's disease.

BACKGROUND: To predict primary failure of infliximab (IFX) therapy in Crohn's disease (CD) and to identify patients who maintain long-term effectiveness to IFX is currently not feasible. Some genetic variations are proposed as potential biomarkers. AIM: We assessed a set of single nucleotide polymorphisms (SNPs) in genes related to the IFX mechanism of action and the presence of HLA-DQA1 * 05 allele on the primary response and long-term durability in CD patients. METHODS: A multi-centre cross-sectional study of IFX-exposed adult patients with CD was undertaken. Treatment persistence and time to failure were co-primary endpoints. DNA from the 131 patients was genotyped. Association between SNPs and clinical variables with IFX persistence was assessed. RESULTS: Failure to IFX was documented in 65 (49.6%) out of 131 patients. IFX persistence was associated either with carrying the TT genotype in ADAM17 rs10929587 (ORa=0.2; 95%CI=0.1-0.8; p = 0.021), or the CC genotype in SLCO1C1 rs3794271 (ORa=0.2; 95%CI=0.1-0.7; p = 0.008), according to multivariate logistic regression. In contrast, previous bowel resection increased the risk of IFX failure (ORa=2.8; 95%CI=1.1-7.3; p = 0.025). Cox regression analysis confirmed these findings and also identified IL23R rs10489629-TT (HRa 0.41; 95%CI=0.22-0.75; p = 0.004) and concomitant immunosuppressants (HRa 0.46; 95%CI=0.27-0.77; p = 0.003) as protection from IFX failure. However, no association between HLA-DQA1 * 05 allele and persistence of IFX therapy was found, with similar failure rates among carriers and non-carriers (52.8% vs. 47.4%, respectively; p = 0.544). CONCLUSIONS: SNPs rs10929587-TT in ADAM17, rs10489629-TT in IL23R and rs3794271-CC in SLCO1C1, together with no previous bowel surgery and concomitant immunosuppression, were identified as protection from failure to IFX.

Erratum: Numerical test of the replica-symmetric Hamiltonian for correlations of the critical state of spin glasses in a field [Phys. Rev. E 105, 054106 (2022)].

This corrects the article DOI: 10.1103/PhysRevE.105.054106.

Numerical test of the replica-symmetric Hamiltonian for correlations of the critical state of spin glasses in a field.

A growing body of evidence indicates that the sluggish low-temperature dynamics of glass formers (e.g., supercooled liquids, colloids, or spin glasses) is due to a growing correlation length. Which is the effective field theory that describes these correlations? The natural field theory was drastically simplified by Bray and Roberts in 1980. More than 40 years later, we confirm the tenets of Bray and Roberts's theory by studying the Ising spin glass in an externally applied magnetic field, both in four spatial dimensions (data obtained from the Janus collaboration) and on the Bethe lattice.

Consensus of experts from the Spanish Pharmacogenetics and Pharmacogenomics Society and the Spanish Society of Medical Oncology for the genotyping of DPYD in cancer patients who are candidates for treatment with fluoropyrimidines.

5-Fluorouracil (5-FU) and oral fluoropyrimidines, such as capecitabine, are widely used in the treatment of cancer, especially gastrointestinal tumors and breast cancer, but their administration can produce serious and even lethal toxicity. This toxicity is often related to the partial or complete deficiency of the dihydropyrimidine dehydrogenase (DPD) enzyme, which causes a reduction in clearance and a longer half-life of 5-FU. It is advisable to determine if a DPD deficiency exists before administering these drugs by genotyping DPYD gene polymorphisms. The objective of this consensus of experts, in which representatives from the Spanish Pharmacogenetics and Pharmacogenomics Society and the Spanish Society of Medical Oncology participated, is to establish clear recommendations for the implementation of genotype and/or phenotype testing for DPD deficiency in patients who are candidates to receive fluoropyrimidines. The genotyping of DPYD previous to treatment classifies individuals as normal, intermediate, or poor metabolizers. Normal metabolizers do not require changes in the initial dose, intermediate metabolizers should start treatment with fluoropyrimidines at doses reduced to 50%, and poor metabolizers are contraindicated for fluoropyrimidines.

Propolis extract and oregano essential oil as biofungicides for garlic seed cloves: in vitro assays and synergistic interaction against Penicillium allii.

AIMS: This study aimed to evaluate in vitro individual and combined antifungal activity of propolis extract (PE) and oregano essential oil (OEO) against Penicillium allii, causal agent of blue mould disease. The chemical characterization of both products was also included. METHODS AND RESULTS: Chromatographic analysis of PE and OEO confirmed the presence of bioactive compounds. The antifungal susceptibility assays showed that PE and OEO were highly active against the mycelial growth and conidial germination of P. allii. PE and OEO MICs were 12·5 and 1·5 µl ml-1 , respectively. The MFCs of these products were 50 and 3·1 µl ml-1 , respectively. PE acted mainly through diffusion, while OEO acted by a mixed contribution of vapour and diffusion. Synergism and additive effect between both products were found in some combination ratios. CONCLUSION: PE and OEO, both natural products with different chemical composition, have a strong antifungal activity against P. allii and show a favourable interaction causing synergism. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study indicated the potential use of PE combined with OEO as a non-conventional strategy towards the formulation of a biofungicide to control blue mould disease in garlic seed-cloves.

Scaling Law Describes the Spin-Glass Response in Theory, Experiments, and Simulations.

The correlation length ξ, a key quantity in glassy dynamics, can now be precisely measured for spin glasses both in experiments and in simulations. However, known analysis methods lead to discrepancies either for large external fields or close to the glass temperature. We solve this problem by introducing a scaling law that takes into account both the magnetic field and the time-dependent spin-glass correlation length. The scaling law is successfully tested against experimental measurements in a CuMn single crystal and against large-scale simulations on the Janus II dedicated computer.

Aging Rate of Spin Glasses from Simulations Matches Experiments.

Experiments on spin glasses can now make precise measurements of the exponent z(T) governing the growth of glassy domains, while our computational capabilities allow us to make quantitative predictions for experimental scales. However, experimental and numerical values for z(T) have differed. We use new simulations on the Janus II computer to resolve this discrepancy, finding a time-dependent z(T,t_{w}), which leads to the experimental value through mild extrapolations. Furthermore, theoretical insight is gained by studying a crossover between the T=T_{c} and T=0 fixed points.

Genes differentially expressed by methylprednisolone in vivo in CD4 T lymphocytes from multiple sclerosis patients: potential biomarkers.

Intravenous methylprednisolone (IVMP) is the gold standard treatment in acute relapses of multiple sclerosis. Knowing the response to IVMP in advance could facilitate earlier selection of patients for subsequent courses of therapy. However, molecular mechanisms and changes in gene expression induced by methylprednisolone remain unknown. The aim of the study was to identify in vivo differentially expressed genes in relapsing-remitting multiple sclerosis patients after 3-6 days of treatment with IVMP. For this purpose, whole-genome transcription profiling of CD4+ T lymphocytes was performed before and after treatment with IVMP in 8 relapsing-remitting multiple sclerosis patients during relapse using Human GE 4x44K v2 microarrays. Differentially expressed genes were identified using a paired t test on GeneSpring v13.0 software. A P-value <0.001 and a twofold change were considered significant. Microarray data were confirmed using real-time PCR. Microarray revealed changes in gene expression: four genes were downregulated (B3GNT3, ZNF683, IFNG and TNF) and seven upregulated (DEFA4, CTSG, DEFA8P, AZU1, MPO, ELANE and PRTN3). Pathway analysis revealed the transforming growth factor-ß signaling pathway to be affected. Comparison with previously published data on in vitro methylprednisolone-regulated genes showed that SMAD7, TNF and CHI3L1 were also downregulated in vivo in relapsing-remitting multiple sclerosis patients. In summary, we performed the first in vivo transcriptome analysis in CD4+ T lymphocytes before and after the treatment with IVMP in patients with multiple sclerosis. Identification of differentially expressed genes in patients receiving IVMP could improve our understanding of the molecular mechanisms underlying the therapeutic effects of IVMP and highlight potential biomarkers of the response to IVMP.

Numerical Construction of the Aizenman-Wehr Metastate.

Chaotic size dependence makes it extremely difficult to take the thermodynamic limit in disordered systems. Instead, the metastate, which is a distribution over thermodynamic states, might have a smooth limit. So far, studies of the metastate have been mostly mathematical. We present a numerical construction of the metastate for the d=3 Ising spin glass. We work in equilibrium, below the critical temperature. Leveraging recent rigorous results, our numerical analysis gives evidence for a dispersed metastate, supported on many thermodynamic states.

Matching Microscopic and Macroscopic Responses in Glasses.

We first reproduce on the Janus and Janus II computers a milestone experiment that measures the spin-glass coherence length through the lowering of free-energy barriers induced by the Zeeman effect. Secondly, we determine the scaling behavior that allows a quantitative analysis of a new experiment reported in the companion Letter [S. Guchhait and R. Orbach, Phys. Rev. Lett. 118, 157203 (2017)].PRLTAO0031-900710.1103/PhysRevLett.118.157203 The value of the coherence length estimated through the analysis of microscopic correlation functions turns out to be quantitatively consistent with its measurement through macroscopic response functions. Further, nonlinear susceptibilities, recently measured in glass-forming liquids, scale as powers of the same microscopic length.

Does DCD Donor Time-to-Death Affect Recipient Outcomes? Implications of Time-to-Death at a High-Volume Center in the United States.

For donation after circulatory death (DCD), many centers allow 1 h after treatment withdrawal to donor death for kidneys. Our center has consistently allowed 2 h. We hypothesized that waiting longer would be associated with worse outcome. A single-center, retrospective analysis of DCD kidneys transplanted between 2008 and 2013 as well as a nationwide survey of organ procurement organization DCD practices were conducted. We identified 296 DCD kidneys, of which 247 (83.4%) were transplanted and 49 (16.6%) were discarded. Of the 247 recipients, 225 (group 1; 91.1%) received kidneys with a time to death (TTD) of 0-1 h; 22 (group 2; 8.9%) received grafts with a TTD of 1-2 h. Five-year patient survival was 88.8% for group 1, and 83.9% for group 2 (p = 0.667); Graft survival was also similar, with 5-year survival of 74.1% for group 1, and 83.9% for group 2 (p = 0.507). The delayed graft function rate was the same in both groups (50.2% vs. 50.0%, p = 0.984). TTD was not predictive of graft failure. Nationally, the average maximum wait-time for DCD kidneys was 77.2 min. By waiting 2 h for DCD kidneys, we performed 9.8% more transplants without worse outcomes. Nationally, this practice would allow for hundreds of additional kidney transplants, annually.

Predicting Donor Death: Early Changes in Oxygen Saturation After Withdrawal of Support Predict Successful Donation During Donation After Circulatory Death.

BACKGROUND: We have previously shown that approximately 27% of patients do not progress to death in time to donate organs after attempted donation after circulatory death (DCD). As such, nearly 1000 transplants per year are not possible. One way to convert unsuccessful donations to successful donations is to increase procurement team "stand-down" times; however, increased stand-down times may predispose transplantable organs to increased ischemic damage. METHODS: Hemodynamics for successful and unsuccessful donations, occurring between 2011 and 2014, were characterized to determine if some unsuccessful DCDs could have donated successfully, had procurement teams waited longer. RESULTS: Analysis of 169 DCDs demonstrated statistically significant differences in hemodynamic profiles after withdrawal of support (WOS) between successful and unsuccessful donations. Early decreases in oxygen saturation were predictive of successful organ donation. We observed that for unsuccessful DCDs, patients who died in more than 2 hours but less than 12 hours were agonal within 10 minutes of WOS, suggesting that increasing stand-down times would result in prohibitive warm ischemia time. CONCLUSIONS: Early changes in oxygen saturation after withdrawal of support predict donor death. Alternative approaches that convert unsuccessful DCDs to successful DCDs but that do not result in low-quality organs should be explored.

Uptake of perfluorooctanoic acid, perfluorooctane sulfonate and perfluorooctane sulfonamide by carrot and lettuce from compost amended soil.

Sewage sludge, which acts like a sink for many pollutants, including metals, pathogens and organic pollutants, that are not completely removed in waste water treatment plants (WWTPs), is applied as a nutrient rich organic fertilizer in many agricultural applications. In the present work, carrot and lettuce crops were grown in two different compost amended soils fortified with perfluorooctanoic acid (PFOA), perfluorosulfonate acid (PFOS) and perfluorosulfonamide (FOSA) and cultivated in a greenhouse. The plants were harvested and divided into root core, root peel and leaves in the case of carrots and into heart and leaves for lettuces. Concentrations for all the different compartments were determined to assess the bioconcentration factors (BCFs) and the plant distribution of the target analytes. The highest carrot BCFs for PFOA and PFOS were determined in the leaves (0.6-3.4), while lower values were calculated in the core (0.05-0.6) and the peel (0.05-1.9) compartments. However, PFOA was taken up in the translocation stream and accumulated more than PFOS in the edible part of lettuce. FOSA was totally degraded in the presence of carrot; however, a lower FOSA degradation was observed in presence of the lettuce, which was dependent on the total organic carbon (TOC) content of the soil. The higher the TOC value, the higher the FOSA degradation observed. No degradation was observed in the crop absence. In the case of the carrot experiments, different polymeric materials (polyethersulfone, PES, polyoxymethylene, and silicone rod) were tested to predict the concentration in the cultivation media. A high correlation (r(2)>0.63) was observed for the BCFs in the PES and in the carrot core and peel for PFOA and PFOS. It could be, concluded that the PES can be used as a first approach for the determination of the uptake of compounds such as PFOS and PFOA in carrot.

Uptake of 8:2 perfluoroalkyl phosphate diester and its degradation products by carrot and lettuce from compost-amended soil.

The present work studied the uptake of 8:2 perfluoroalkyl phosphate diester (diPAP) by two different crops (lettuce and carrot) and two different amended soils. Firstly, the possible degradation of 8:2 diPAP in the absence of crop was studied and 8:2 monoPAP (monophosphate), 8:2 FTCA (saturated fluorotelomer carboxylate), 8:2 FTUCA (unsaturated fluorotelomer carboxylate), 7:3 FTCA (saturated fluorotelomer carboxylate), PFHpA (perfluoroheptanoic acid), PFHxA (perfluorohexanoic acid) and PFOA (perfluorooctanoic acid) were detected. In the presence of crops, different degradation products were detected in the soil and, while PFNA (perfluorononanoic acid), PFHpA, PFHxA, PFPeA (perfluoropentacoic acid), PFBA (perfluorobutanoic acid), 7:3 FTCA and PFOA were determined in the cultivation media when carrot was grown, PFOA was the only degradation product detected in the case of lettuce experiments. Regarding the uptake in carrot, all the degradation products except 7:3 FTCA were translocated from the soil to the carrot. Carrot core, peel and leaves bioconcentration factors, BCFs, were determined for 8:2 diPAP and its degradation products. Values lower than method detection limits for core and low BCFs in peel (0.025-0.042) and leaves (0.028-0.049) were achieved for 8:2 diPAP. Regarding to the degradation products, the higher their water solubility, the higher the plant translocation. In this sense, the lower the carbon chain length of PFCAs, the higher the BCFs determined (PFBA > PFHxA > PFHpA > PFOA > PFNA). In general, lower total BCFs were achieved when the total organic carbon of the soils increased. For lettuce experiments, 8:2 diPAP (0.04-0.18) and PFOA (0.28-1.57) were only determined in lettuce heart.

Uptake of polybrominated diphenyl ethers by carrot and lettuce crops grown in compost-amended soils.

The uptake of polybrominated diphenyl ethers (PBDEs) by carrot and lettuce was investigated. Degradation of PBDEs in soil in the absence of the plants was discarded. Different carrot (Nantesa and Chantenay) and lettuce (Batavia Golden Spring and Summer Queen) varieties were grown in fortified or contaminated compost-amended soil mixtures under greenhouse conditions. After plant harvesting, roots (core and peel) and leaves were analyzed separately for carrot, while for lettuce, leaves and hearts were analyzed together. The corresponding bioconcentration factors (BCFs) were calculated. In carrots, a concentration gradient of 2,2',3,4,4',5'-hexabromodiphenyl ether (BDE-138) became evident that decreased from the root peel via root core to the leaves. For decabromodiphenyl ether (BDE-209) at the low concentration level (7 and 20 ng g(-1)), the leaves incorporated the highest concentration of the target substance. For lettuce, a decrease in the BCF value (from 0.24 to 0.02) was observed the higher the octanol-water partition coefficient, except in the case of BDE-183 (BCF = 0.51) and BDE-209 (BCF values from 0.41 to 0.74). Significant influence of the soils and crop varieties on the uptake could not be supported. Metabolic debromination, hydroxylation or methylation of the target PBDEs in the soil-plant system was not observed.

Spatial distribution, temporal variation and specificity of microhabitat of Tropisternus species (Coleoptera: Hydrophilidae) in permanent ponds.

The spatial distribution and temporal variation of 11 species of Tropisternus were analyzed in two permanent ponds located in the province of Corrientes, Argentina. Samples were collected every 15 days, between October 2010 and March 2011. The species recorded were Tropisternus collaris (Fabricius), Tropisternus ovalis Castelnau, Tropisternus laevis (Sturm), Tropisternus lateralis limbatus (Brullé), Tropisternus longispina Fernández & Bachmann, Tropisternus carinispina Orchymont, Tropisternus bourmeisteri Fernández & Bachmann, Tropisternus apicipalpis (Chevrolat), Tropisternus dilatatus Bruch, Tropisternus obesus Bruch, and Tropisternus ignoratus Knisch. The first four were present in higher proportions than the remaining during most of the study period. The spatial distribution of individuals was mostly related to the homogeneity or heterogeneity of the ecosystem in relation to microhabitats with aquatic vegetation: In ponds with different microhabitats, individuals were mainly aggregated, whereas in ponds with homogenous features, individuals were randomly distributed. However, when species were analyzed individually, the spatial distribution and the use of microhabitat by each species were different with respect to preference and behavior.

Simultaneous determination of a variety of endocrine disrupting compounds in carrot, lettuce and amended soil by means of focused ultrasonic solid-liquid extraction and dispersive solid-phase extraction as simplified clean-up strategy.

The present study is focused on the development of an analytical method based on focused ultrasonic solid-liquid extraction (FUSLE) followed by dispersive solid-phase extraction (dSPE) clean-up and liquid chromatography-triple quadrupole tandem mass spectrometry (LC-MS/MS) optimised for the simultaneous analysis of certain endocrine disrupting compounds (EDCs), including alkylphenols (APs), bisphenol A (BPA), triclosan (TCS) and several hormones and sterols in vegetables (lettuce and carrot) and amended soil samples. Different variables affecting the chromatographic separation, the electrospray ionisation and mass spectrometric detection were optimised in order to improve the sensitivity of the separation and detection steps. Under the optimised extraction conditions (sonication of 5min at 33% of power with pulse times on of 0.8s and pulse times off of 0.2s in 10mL of n-hexane:acetone (30:70, v:v) mixture using an ice bath), different dSPE clean-up sorbents, such as Florisil, Envi-Carb, primary-secondary amine bonded silica (PSA) and C18, or combinations of them were evaluated for FUSLE extracts before LC-MS/MS. Apparent recoveries and precision in terms of relative standard deviation (RSDs %) of the method were determined at two different fortification levels (according to the matrix and the analyte) and values in the 70-130% and 2-27% ranges, respectively, were obtained for most of the target analytes and matrices. Matrix-matched calibration approach and the use of labelled standards as surrogates were needed for the properly quantification of most analytes and matrices. Method detection limits (MDLs), estimated with fortified samples, in the ranges of 0.1-100ng/g for carrot, 0.2-152ng/g for lettuce and 0.9-31ng/g for amended soil were obtained. The developed methodology was applied to the analysis of 11 EDCs in both real vegetable bought in a local market and in compost (from a local wastewater treatment plant, WWTP) amended soil samples.

Simultaneous determination of perfluorinated compounds and their potential precursors in mussel tissue and fish muscle tissue and liver samples by liquid chromatography-electrospray-tandem mass spectrometry.

An analytical method for the simultaneous determination in fish liver and muscle tissue and mussel samples of 14 perfluorinated compounds (PFCs), including three perfluoroalkylsulfonates (PFSAs), seven perfluorocarboxylic acids (PFCAs), three perfluorophosphonic acids (PFPAs) and perfluorooctanesulfonamide (PFOSA), and 10 potential precursors, including four polyfluoroalkyl phosphates (PAPs), four fluorotelomer saturated acids (FTCAs) and two fluorotelomer unsaturated acids (FTUCAs), was developed in the present work. Different clean-up strategies by means of solid-phase extraction (SPE) using a mix-mode weak anion exchanger (WAX), reverse phase Envi-Carb or a combination of them was optimized and evaluated for the clean-up of focused ultrasonic solid-liquid (FUSLE) extracts before the analysis by liquid chromatography-triple quadrupole tandem mass spectrometry (LC-MS/MS). Mix-mode WAX coupled in-line to Envi-Carb was finally selected since it rendered the cleanest extracts and minimum matrix effect. The FUSLE-SPE-LC-MS/MS methodology was validated in terms of recovery, precision and method detection limits (MDLs). Apparent recovery values in the 65-116%, 59-119% and 67-126% range and MDLs in the 0.1-2.7 ng/g, 0.1-3.8 ng/g and 0.2-3.1ng/g range were obtained for liver, mussel and fish muscle tissue samples, respectively. The method developed was applied to the analysis of grey mullet liver (Chelon labrosus) and mussel (Mytilus galloprovincialis) samples from the Basque Coast (North of Spain) and Yellowfin tuna muscle tissue (Thunnus albacares) samples from the Indian Ocean. To the best of our knowledge this is the first method that describes the simultaneous determination of 14 PFCs and 10 potential precursors in fish liver, fish muscle tissue and mussel samples. Besides, this is the first time that 8:2 monosubstituted polyfluorodecyl phosphate (8:2 monoPAP) and 8:2 disubstituted polyfluorodecyl phosphate (8:2 diPAP) were detected in mussel and tuna samples, respectively.