Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-interaction error overbinds water clusters but cancels in structural energy differences

Significance Self-interaction error has long been identified as one of the limitations of practical density functional approximations. This error originates in the inability of approximate density functionals to exactly cancel self-Coulomb and self-exchange–correlation for all one-electron densities. Self-interaction error can be subtracted from an approximate functional on an orbital-by-orbital basis, improving the description of stretched bonds. In this work, we show that, by explicitly removing self-interaction error, the hydrogen bond binding energies of water are also significantly improved. In particular, the self-interaction correction to SCAN improves binding energies and the many-body analysis without altering the correct energy ordering for small water clusters. We gauge the importance of self-interaction errors in density functional approximations (DFAs) for the case of water clusters. To this end, we used the Fermi–Löwdin orbital self-interaction correction method (FLOSIC) to calculate the binding energy of clusters of up to eight water molecules. Three representative DFAs of the local, generalized gradient, and metageneralized gradient families [i.e., local density approximation (LDA), Perdew–Burke–Ernzerhof (PBE), and strongly constrained and appropriately normed (SCAN)] were used. We find that the overbinding of the water clusters in these approximations is not a density-driven error. We show that, while removing self-interaction error does not alter the energetic ordering of the different water isomers with respect to the uncorrected DFAs, the resulting binding energies are corrected toward accurate reference values from higher-level calculations. In particular, self-interaction–corrected SCAN not only retains the correct energetic ordering for water hexamers but also reduces the mean error in the hexamer binding energies to less than 14 meV/H2O from about 42 meV/H2O for SCAN. By decomposing the total binding energy into many-body components, we find that large errors in the two-body interaction in SCAN are significantly reduced by self-interaction corrections. Higher-order many-body errors are small in both SCAN and self-interaction–corrected SCAN. These results indicate that orbital-by-orbital removal of self-interaction combined with a proper DFA can lead to improved descriptions of water complexes.
A Novel Antipredator Mechanism in Salamanders: Rolling Escape in Hydromantes platycephalus

Antipredator mechanisms in salamanders involve behavioral responses that are usually combined with aposematic coloration and skin toxicity (Brodie, 1970, 1977, 1983; Dodd and Brodie, 1976). Behavioral responses range from immobility to active escape, including the adoption of stereotyped postures (Brodie, 1983). Escape mechanisms involve active responses like rapid coiling and uncoiling movements which flip or propel the animal, tail lashing, lateral writhing, and locomotion (Duellman and Trueb, 1986). Although escape responses are usually followed by immobility, no escape mechanism involving passive transport has been reported. Based on field observations, we document a novel antipredator mechanism in the salamander Hydromantes platycephalus that consists of body and tail coiling and limb tucking followed by passive rolling escape. Although coiling is widespread among salamanders, H. platycephalus performs it in the novel context of the steep slopes of the northern Sierra Nevada of California. This results in the peculiar antipredator mechanism of rolling escape. We observed Hydromantes platycephalus at two localities in California, in the vicinity of Sonora Pass: (1) the slopes of Blue Canyon in Stanislaus National Forest, Tuolumne County, and (2) near the Pacific Crest Trail in Toyabee National Forest, Mono County. We found 19 individuals at the first locality on 21 August and 11 September, 1993 and two at the second locality on 11 September, 1993. We observed defensive behavior of 10 individuals from the first locality and two from the second.
Associations between candidate SNPs in the calpain 1, calpastatin and leptin genes and meat tenderness among Swedish beef populations

Abstract The contribution of three candidate genes to the variation in meat tenderness was tested in muscle samples from 243 pure-bred, young, beef bulls of Angus, Charolais, Hereford, Limousin and Simmental breeds, raised in Swedish commercial herds. The animals were genotyped for single nucleotide polymorphisms (SNPs) in the calpain 1 (CAPN1), calpastatin (CAST) and leptin genes. The frequent calpain 1 CAPN1:c.947G>C G allele showed an unfavourable association with tenderness. The calpastatin CAST:c.155C>T T allele, which was the most common allele, showed a favourable association with Warner–Bratzler shear force (WBSF) and compression tests. An association was observed between the leptin UASMS2C>T SNP and compression tests.
External pH modulation during the growth of Vibrio tapetis, the aetiological agent of brown ring disease

Brown ring disease (BRD) is an infection of the Manila clam Ruditapes philippinarum due to the pathogen Vibrio tapetis. During BRD, clams are facing immunodepression and shell biomineralization alteration. In this paper, we studied the role of pH on the growth of the pathogen and formulated hypothesis on the establishment of BRD by V. tapetis.
miRNA‐21 deficiency impairs alveolar socket healing in mice

Abstract Background MicroRNAs (miRNAs) are small noncoding RNAs demonstrated as critical post‐transcriptional modulators in dental tissues and bone regeneration, particularly miR‐21‐5p. However, the role of miR‐21‐5p in the healing of alveolar sockets following tooth extraction remains unknown. In this study we evaluated the influence of miR‐21‐5p in the healing of alveolar socket after tooth extraction. Methods Eight miR‐21‐5p knockout mice and eight littermate controls underwent tooth extraction of the upper right incisor. After a healing period of 14 days microCT and histological analyses were performed. Results MicroCT analysis showed that the percentage of bone in the extraction socket was significantly higher in the control group than in the miR‐21 knockout mice; either in the coronal (39.0%, CI 31.8 to 48.0 versus 23.0%, CI 17.8 to 35.2, P = 0.03) or in the middle part of the alveolar socket (56.0%, CI 50.9 to 62.5 versus 43.5% CI 28.6 to 54.6, P = 0.03). These differences were not noted in the apical part of the extraction socket. Histological analysis supported the microCT findings. Newly bone volume per tissue volume (BV/TV) was significantly higher in the control group when compared to miR‐21 knockout mice, 27.4% (CI 20.6 to 32.9) versus 19.0% (CI 14.7 to 21.5, P < 0.05), respectively. Surprisingly, no evident signs of buccal bone resorption were observed in both groups. Conclusion Despite the limitation of one observation period, these findings suggest that miR‐21‐5p delays the early healing of alveolar socket following tooth extraction. Whether miR‐21‐5p is essential for healing of alveolar sockets remains to be elucidated.
Selection of Filamentous Fungi for Treatment of Synthetic Cassava Starch Processing Wastewater Containing Cyanide

Eight strains of filamentous fungi, which were known as producers of amylase and glucoamylase for digesting raw starch, were used for investigating treatment capacity of the synthetic cassava starch processing (SCSP) wastewater containing pure cassava starch. Among these strains, three strains of Aspergillus oryzae showed high efficiency in the removal of COD and TOC, starch hydrolysis and production of fungal biomass. With A. oryzae KCC F-0010, treatment efficiency obtained 72% (TOC), 81% (COD), 94% (starch) and 2.4 g/l of biomass after 14-day incubation. The presence of cyanide caused inhibition for the growth of fungi. The toleration of A. oryzae IFO 30113 to cyanide was associated with its ability to remove cyanide. Ammonia was indicated as the end product of biodegradation of cyanide. Volatilization and microbial metabolism were shown as the main mechanisms in the cyanide removal of the aerobic treatment process by fungi under the acidic condition.
Cumulative Burden of Financial Hardship From Medical Bills Across the Spectrum of Diabetes Mellitus and Atherosclerotic Cardiovascular Disease Among Non‐Elderly Adults in the United States

Background Atherosclerotic cardiovascular disease (ASCVD) has a strong association with diabetes mellitus (DM), accounting for approximately two thirds of deaths in this patient population. Many individuals with ASCVD and DM are vulnerable to financial hardship associated with treatment‐related expenses. Therefore, we examined the burden of financial hardship from medical bills across the spectrum of ASCVD status with and without DM. Methods and Results Using data from the National Health Interview Survey from 2013 to 2017, we used logistic regression analysis to examine the association of ASCVD and DM status with financial hardship and an inability to pay medical bills from a representative sample of non‐elderly adults in the United States. Our study population consisted of 121 672 individuals. Approximately 3.1% of the weighted population had ASCVD, 5.6% had DM, and 1.3% had both ASCVD and DM. Nearly 50% of individuals with ASCVD and DM reported financial hardship from medical bills (23% being unable to pay medical bills at all), whereas ≈28% of those with neither ASCVD nor DM reported financial hardship from medical bills (8% being unable to pay medical bills at all). Individuals with concurrent ASCVD and DM had the highest relative odds of expressing an inability to pay at all when compared with those with neither condition (odds ratio, 2.69; 95% CI, 2.21–3.28). Conclusions Individuals with concurrent ASCVD and DM are at a disproportionately high risk of being unable to pay their medical bills. The findings provide strong evidence for developing more effective public health policies that protect vulnerable populations from financial hardship.
Junctional rhythm with severe hypotension following infiltration of lidocaine containing epinephrine during dental surgery

We experienced an unusual case of accelerated junctional rhythm with severe hypotension after infiltration of lidocaine containing epinephrine during dental surgery under general anesthesia. The patient's electrocardiogram exhibited retrograde P-waves following the QRS complex, which could be misinterpreted as ST-segment depression. As a temporary measure, administration of ephedrine restored the patient's blood pressure to normal levels. The importance of this case lies in its demonstration of an unexpected and serious side effect of commonly used epinephrine infiltration. This case also highlights the need for accurate interpretation of the electrocardiogram and comprehensive understanding of best practices for patient management.
Changes in Peptaibol Production of Trichoderma Species during In Vitro Antagonistic Interactions with Fungal Plant Pathogens

Trichoderma species are widely used as biofungicides for the control of fungal plant pathogens. Several studies have been performed to identify the main genes and compounds involved in Trichoderma–plant–microbial pathogen cross-talks. However, there is not much information about the exact mechanism of this profitable interaction. Peptaibols secreted mainly by Trichoderma species are linear, 5–20 amino acid residue long, non-ribosomally synthesized peptides rich in α-amino isobutyric acid, which seem to be effective in Trichoderma–plant pathogenic fungus interactions. In the present study, reversed phase (RP) high-performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) mass spectrometry (MS) was used to detect peptaibol profiles of Trichoderma strains during interactions with fungal plant pathogens. MS investigations of the crude extracts deriving from in vitro confrontations of Trichoderma asperellum and T. longibrachiatum with different plant pathogenic fungi (Fusarium moniliforme, F. culmorum, F. graminearum, F. oxysporum species complex, Alternaria solani and Rhizoctonia solani) were performed to get a better insight into the role of these non-ribosomal antimicrobial peptides. The results revealed an increase in the total amount of peptaibols produced during the interactions, as well as some differences in the peptaibol profiles between the confrontational and control tests. Detection of the expression level of the peptaibol synthetase tex1 by qRT-PCR showed a significant increase in T. asperellum/R. solani interaction in comparison to the control. In conclusion, the interaction with plant pathogens highly influenced the peptaibol production of the examined Trichoderma strains.
Diversity of fungal isolates from fungus‐growing termite Macrotermes barneyi and characterization of bioactive compound from Xylaria escharoidea

Owing to their potential applications, as well as their structural diversity, the discovery of novel secondary metabolites from insect‐associated fungi has been of interest to researchers in recent years. The aim of this study was therefore to estimate the diversity of fungi associated with fungus‐growing termites and bioprospecting these for potential secondary metabolites. In total, 18 fungal species were isolated and described from the gut and comb of Macrotermes barneyi based on 18S ribosomal DNA gene sequence analysis. Antimicrobial activity assays were carried out on all the known fungi, and nine isolates were recorded as active against pathogenic fungi. Xylaria escharoidea, the best performing isolate, was grown at laboratory scale and 4,8‐dihydroxy‐3,4‐dihydronaphthalen‐1(2H) was isolated and characterized. The minimum inhibitory concentration of this isolated compound against tested pathogenic organisms was found to be 6.25 μg. In addition, molecular docking studies have revealed that 4,8‐dihydroxy‐3,4‐dihydronaphthalen‐1(2H) is a prominent antibacterial agent with a marked interaction with key residues on protein A (agrAC) that regulates the accessory gene. The findings of this study support the drug discovery of antimicrobial properties in insect‐associated fungi, which may lead to novel secondary metabolites.
Using patient‐reported outcomes (PROs) and patient‐reported outcome measures (PROMs) in routine head and neck cancer care: What do health professionals perceive as barriers and facilitators?

Patient‐reported outcomes (PROs) are direct reports from patients about their health status. Patient‐reported outcome measures (PROMs) are validated tools assessing PROs and completed by patients. Though commonly used in research, implementing PROMs into routine clinical care has been challenging. We aimed to examine health professionals’ (HPs’) perceptions of barriers and facilitators to PRO and PROM use in the routine care of head and neck cancer (HNC) patients.
Structure and pathogenic variability in Ascochyta rabiei populations on chickpea in the Canadian prairies

A population study of Ascochyta rabiei from the Canadian prairies was conducted to assess pathogenicity among isolates with the objectives to investigate the existence of a race or pathotype structure and to evaluate whether there had been a shift to higher aggressiveness between 1998 and 2002. Ninety-nine isolates collected in 1998, 2001 and 2002 were inoculated onto seven differential chickpea genotypes. Significant isolate × differential interactions occurred, but accounted for a small proportion of the total variability. It was found that very few interaction effects between all combinations of differentials and isolates were significant and frequency distributions of disease severity of isolates tested on the differentials revealed continuous distributions. These results suggest that no genotype-specific relationship existed between A. rabiei and its host and that Canadian populations of the pathogen cannot be objectively classified into races or pathotypes. Isolates from 2001 and 2002 caused significantly more disease than isolates from 1998, suggesting that disease epidemics encountered since 1999 were in part caused by a shift in the population to higher aggressiveness.
The effect of herbage allowance upon the herbage intake and performance of suckler cows and calves

Twenty-four Hereford × Friesian cows and their South Devon cross calves were allocated to three herbage allowances allotted daily for three periods of 8 weeks in a Latin square design. The daily allowances were 17, 34 and 51 g dry matter per kg cow plus calf live weight. Milk production was depressed by 0·2 and 1·2 kg d-1 at the medium and low allowances. The corresponding falls in liveweight gain were for cows 0·26 and 0·25, and for calves 0·27 and 0·24 kg d-1. Residual sward height after grazing gave a better indication of the animals' reaction to sward conditions and the management imposed than actual herbage allowance. The quantity per unit area and the composition of material present were important factors influencing intake. Calves were unable to compete with their dams to maintain herbage intake at the lower allowances and therefore are likely to benefit from additional feeding or creep grazing when residual sward height falls below 6cm for periods in excess of 1–2 weeks.
Effect of different amino acids density diets on lysine, methionine and protein efficiency in Arian broiler

The advantages provided by amino acid (AA) densities to broiler performance have been well documented, but little research has been reported on comparing the effect of different densities, i.e. high, medium, standard and low amino acid levels (HAA, MAA, SAA, and LAA), on protein and energy efficiency in broiler. This study evaluated the effects of the four different amino acid densities in a completely randomized experimental design on 800 male (10 replicates per treatment) broilers. All diets were isocaloric and isonitrogenous. In broilers receiving HAA, there had been a significant increase in body weight at Day 42. Feeding broilers with HAA diets significantly increased protein and energy intake in the grower period and during the overall study period (0–42 days of age) (P<0.05). There was a significant difference in efficiency of lysine and methionine during all time periods (P<0.05) and HAA levels were significantly higher than SAA. Protein efficiency ratio (PER) and energy efficiency ratio (EER) were not affected by an increase in AA density. AA levels had a significant effect on production efficiency factor (PEF). The results of this study suggest that additional lysine and methionine at 120% and other AA at 110% of National Research Council recommendations in starter and grower diets significantly improved body weight and PEF.
High nitrate, muddy estuaries as nitrogen sinks: the nitrogen budget of the River Colne estuary (United Kingdom)

The muddy estuary of the River Colne, east coast UK, is hypernutrified, with strong gradients of N 0 3 a n d NH,+up the estuary due to inputs from the river and sewage treatment works. There were no significant transformations of nitrogen detected in the water colun~n. In the sandy sediment at the mouth of the estuary nitrification occurred with N0,export from the sediment, but the muddy sedi m e n t ~ higher up the estuary were large sinks for NO3and major sites of denitrification. The flux of NO3into the sediment at these sites was correlated with the water column NOoconcentration, and there was a large capacity for the sediments to respond to increases in the water column N O , concentration. A seasonal cycle occurred with maximum denitrification during early winter, when water column NO< was greatest and low temperatures favoured denitrification over NO3ainmonihcation. Highest unit area rates of denitrificatlon were measured by acetylene inhibit~on at the uppermost site in the estuary, but when allowance was made for the area of sediment surface in each sector the middle reaches of the estuary were more significant to the estuarine nitrogen budget. Approximately 50% of the NO3flux through the estuary was denitrified during 1993-1994. In addition, measurements of denitrification by the '5N03' isotope pairing technique suggested that coupled nitrification-denitrification within the sediment was also important, and when this was also allowed for the sediments removed by denitrification between 18 and 27% of the total nitrogen flux through the estuary. There was some question, however, of whether the coupled nitrification-denitrification was overestimated if the anammox reaction was occurring in the highly organic, high NO3sediments at the river end of the estuary. It is concluded that in these turbid, muddy estuaries the sediments are not only major attenuators of the flux of NO;, but are also very effective traps for organically bound nitrogen. This suggests that the loads of nitrogen through these estuaries to the North Sea, which are usually derived from river gauging above the high tide mark, significantly overestimate the real load as they do not take into account attenuation of nitrogen flux within the estuary. While this attenuation may decrease the nitrogen loads, it implies that any environmental impact in coastal waters may be the result of much lower loads of nitrogen than hitherto assumed.
Geographical variation of barricade-building behaviour in the intertidal brachyuran crab Ilyoplax pusilla

The small dotillid crab Ilyoplax pusilla builds an earthen structure, termed barricade, close to its neighbour's burrow. Barricades function for territorial defence by deterring invasion by neighbours. Comparison of the frequency of barricade building in the breeding season among 5 localities across the geographical range of I. pusilla, showed higher values at more northern localities. In two localities differing in the frequency of barricade building, the response of crabs to artificial barricades placed near their burrows was examined. The artificial barricade was less often broken and more often avoided in the locality with the higher frequency of barricades. These results suggest that the local difference in frequency of barricade building is correlated with a difference in how crabs respond to this earthen barrier.