Miracle-dz/UniFAR-FTUs huggingface dataset:
The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes

Whilst adaptation and phenotypic plasticity might buffer species against habitat degradation associated with global climate change, few studies making such claims also possess the necessary and sufficient data to support them. Doing so requires demonstration of heritable variation in traits affecting fitness under new environmental conditions. We address this issue using an emerging aquatic system to study adaptation to climate change, the crimson‐spotted rainbowfish (Melanotaenia duboulayi), a freshwater species from a region of eastern Australia projected to be affected by marked temperature increases. Captive born M. duboulayi of known pedigree were used to assess the long‐term effects of contemporary and 2070‐projected summer temperatures on the expression of genes previously identified in a climate change transcriptomics (RNA‐Seq) experiment. Nearly all genes responded to increasing temperature. Significant additive genetic variance explained a moderate proportion of transcriptional variation for all genes. Most genes also showed broad‐sense genetic variation in transcriptional plasticity. Additionally, molecular pathways of candidate genes co‐occur with genes inferred to be under climate‐mediated selection in wild M. duboulayi populations. Together, these results indicate the presence of existing variation in important physiological traits, and the potential for adaptive responses to a changing thermal environment.
Reduced fitness of Atlantic salmon released in the wild after one generation of captive breeding

Salmonids rank among the most socioeconomically valuable fishes and the most targeted species by stocking with hatchery‐reared individuals. Here, we used molecular parentage analysis to assess the reproductive success of wild‐ and hatchery‐born Atlantic salmon over three consecutive years in a small river in Québec. Yearly restocking in this river follows a single generation of captive breeding. Among the adults returning to the river to spawn, between 11% and 41% each year were born in hatchery. Their relative reproductive success (RRS) was nearly half that of wild‐born fish (0.55). RRS varied with life stage, being 0.71 for fish released at the fry stage and 0.42 for fish released as smolt. The lower reproductive success of salmon released as smolt was partly mediated by the modification of the proportion of single‐sea‐winter/multi‐sea‐winter fish. Overall, our results suggest that modifications in survival and growth rates alter the life‐history strategies of these fish at the cost of their reproductive success. Our results underline the potential fitness decrease, warn on long‐term evolutionary consequences for the population of repeated stocking and support the adoption of more natural rearing conditions for captive juveniles and their release at a younger stage, such as unfed fry.
Walnuts lower serum cholesterol in Japanese men and women.

Recent studies have shown that incorporating moderate quantities of walnuts into the recommended cholesterol-lowering diet in the U.S. decreased serum concentrations of total cholesterol in normal American men. To explore whether walnut consumption would also prove effective as part of the Japanese diet, we studied the effects of walnut consumption on serum lipids and blood pressure in Japanese subjects. We randomly assigned 20 men and 20 women to two mixed natural diets, each to be consumed for 4 wk in a crossover design. Both diets conformed to the average Japanese diet (reference diet) and contained identical foods and macronutrients, except that 12.5% of the energy of the walnut diet was derived from walnuts (43-57 g/d) (offset by lesser amounts of fatty foods, meat and visible fat). Total cholesterol concentration was 0.16 mmol/L lower for men (P = 0.05) and 0.21 mmol/L lower for women (P<0.01) when they consumed the walnut diet than when they consumed the reference diet. The LDL cholesterol concentrations were 0.18 mmol/L lower for men (P = 0.13) and 0.22 mmol/L lower for women (P<0.01) when they consumed the walnut diet. The ratio of LDL cholesterol to HDL cholesterol and the apolipoprotein B concentration were also lowered by the walnut diet (P<0.05). Blood pressures did not differ between the walnut and reference diet periods. Incorporating moderate quantities of walnuts into the average Japanese diet while maintaining the intake of total dietary fat and energy decreases serum total cholesterol concentrations and favorably modifies the lipoprotein profile in Japanese, particularly in women.
Comparative Evaluation of the Antioxidant and Anti-Alzheimer’s Disease Potential of Coumestrol and Puerarol Isolated from Pueraria lobata Using Molecular Modeling Studies

The current study assesses the antioxidant effects of two similar isoflavonoids isolated from Pueraria lobata, coumestrol and puerarol, along with the cholinergic and amyloid-cascade pathways to mitigate Alzheimer’s disease (AD). Antioxidant activity was evaluated via 1,1-diphenyl-2-picryhydrazyl (DPPH) and peroxynitrite (ONOO−) scavenging ability further screened via ONOO−-mediated nitrotyrosine. Similarly, acetyl- and butyrylcholinesterase (AChE/BChE) and β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitory activities were assessed together with docking and kinetic studies. Considering DPPH and ONOO− scavenging activity, coumestrol (EC50 values of 53.98 and 1.17 µM) was found to be more potent than puerarol (EC50 values of 82.55 and 6.99 µM) followed by dose dependent inhibition of ONOO−-mediated nitrotyrosine. Coumestrol showed pronounced AChE and BChE activity with IC50 values of 42.33 and 24.64 µM, respectively, acting as a dual cholinesterase (ChE) inhibitor. Despite having weak ChE inhibitory activity, puerarol showed potent BACE1 inhibition (28.17 µM). Kinetic studies of coumestrol showed AChE and BChE inhibition in a competitive and mixed fashion, whereas puerarol showed mixed inhibition for BACE1. In addition, docking simulations demonstrated high affinity and tight binding capacity towards the active site of the enzymes. In summary, we undertook a comparative study of two similar isoflavonoids differing only by a single aliphatic side chain and demonstrated that antioxidant agents coumestrol and puerarol are promising, potentially complementary therapeutics for AD.
Meeting calcium recommendations during middle childhood reflects mother-daughter beverage choices and predicts bone mineral status.

BACKGROUND Longitudinal data regarding the influence of beverage intakes on calcium adequacy are lacking. OBJECTIVE This study evaluated calcium intake from ages 5 to 9 y as a function of mother-daughter beverage choices and as a predictor of bone mineral status. DESIGN Intakes of energy, calcium, milk, sweetened beverages, fruit juices, and non-energy-containing beverages were measured with the use of three 24-h dietary recalls in 192 non-Hispanic white girls aged 5, 7, and 9 y and their mothers. Calcium intakes from ages 5 to 9 y were categorized as either meeting or falling below recommended adequate intakes (AIs). The girls' bone mineral status was assessed with dual-energy X-ray absorptiometry at age 9 y. RESULTS The mean 5-y calcium intake was related to bone mineral density at age 9 y (beta = 0.27, P < 0.001). The girls who met the AI for calcium were not heavier (P = 0.83) but had higher energy intakes (P < 0.0001) than did the girls who consumed less than the AI. Compared with the girls who consumed less than the AI, the girls who met the AI consumed, on average, almost twice as much milk (P < 0.0001), had smaller decreases in milk intake (P < 0.01), and consumed 18% less sweetened beverages (P < 0.01) from ages 5 to 9 y; the 2 groups did not differ significantly in juice and non-energy-containing beverage intakes. The girls who met the AI were also served milk more frequently than were the girls who consumed less than the AI (P < 0.0001) and had mothers who drank milk more frequently (P < 0.01) than did the mothers of the girls who consumed less than the AI. CONCLUSIONS These findings provide new longitudinal evidence that calcium intake predicts bone mineral status during middle childhood and reflects mother-daughter beverage choice patterns that are established well before the rapid growth and bone mineralization observed in adolescence.
Fabrication of birefringent nanocylinders for single-molecule force and torque measurement

Optically anisotropic subwavelength scale dielectric particles have been shown to enable studies of the mechanical properties of bio-molecules via optical trapping and manipulation. However, techniques emphasized to date for fabrication of such particles generally suffer from limited uniformity and control over particle dimensions, or low throughput and high cost. Here, an approach for rapid, low-cost, fabrication of large quantities of birefringent quartz nanocylinders with dimensions optimized for optical torque wrench experiments is described. For a typical process, 108 or more quartz cylinders with diameters of 500 nm and heights of 800 nm, with uniformity of ±5% in each dimension, can be fabricated over ∼10 cm2 areas, for binding to a single bio-molecule, and harvested for use in optical trapping experiments. Use of these structures to measure extensional and torsional dynamics of single DNA molecules is demonstrated with measured forces and torques shown to be in very good agreement with previously reported results.
Micro- and Nanostructured Surface Morphology on Electrospun Polymer Fibers

Electrospun fibers were produced using a variety of solvents to investigate the influence of polymer/solvent properties on the fiber surface morphology. Electrospinning is a novel processing technique for the production of fibers with diameters in the range of a few nanometers to tens of micrometers. We have been able to produce polymeric fibers with a high surface area through the introduction of a micro- and nanostructured surface structure, which we refer to as a “porous” morphology. These features could be introduced in several different polymeric fibers increasing their range of application significantly. The pores vary from densely packed, well-formed nanopores with diameters in the range 20−350 nm to larger flat pores of about 1 μm. The increased surface area of polymeric fibers was correlated with high volatility solvents used in the electrospinning process. The effect of processing parameters on the fiber surface morphology was also investigated using optical microscopy, field emission scanning e.
Effects of dietary fat and fiber on plasma and urine androgens and estrogens in men: a controlled feeding study.

We conducted a controlled feeding study to evaluate the effects of fat and fiber consumption on plasma and urine sex hormones in men. The study had a crossover design and included 43 healthy men aged 19-56 y. Men were initially randomly assigned to either a low-fat, high-fiber or high-fat, low-fiber diet for 10 wk and after a 2-wk washout period crossed over to the other diet. The energy content of diets was varied to maintain constant body weight but averaged approximately 13.3 MJ (3170 kcal)/d on both diets. The low-fat diet provided 18.8% of energy from fat with a ratio of polyunsaturated to saturated fat (P:S) of 1.3, whereas the high-fat diet provided 41.0% of energy from fat with a P:S of 0.6. Total dietary fiber consumption from the low- and high-fat diets averaged 4.6 and 2.0 g.MJ-1.d-1, respectively. Mean plasma concentrations of total and sex-hormone-binding-globulin (SHBG)-bound testosterone were 13% and 15% higher, respectively, on the high-fat, low-fiber diet and the difference from the low-fat, high-fiber diet was significant for the SHBG-bound fraction (P = 0.04). Men's daily urinary excretion of testosterone also was 13% higher with the high-fat, low-fiber diet than with the low-fat, high-fiber diet (P = 0.01). Conversely, their urinary excretion of estradiol and estrone and their 2-hydroxy metabolites were 12-28% lower with the high-fat, low-fiber diet (P < or = 0.01). Results of this study suggest that diet may alter endogenous sex hormone metabolism in men.
Radiographic evaluation of osteotomized ulnar segments following arthroscopic treatment for canine medial coronoid disease

Summary Objective: To assess movement of ulnar segments radiographically, following proximal and midshaft ulnar osteotomy or ostectomy after arthroscopic treatment for dogs diagnosed with medial coronoid disease. Methods: Fragmentation and cartilage wear were treated arthroscopically and the presence of incongruity confirmed. Osteotomies were performed at the mid-point or proximal third of the length of the ulna. The distance of separation between the ulnar segments and the adjacent radius were measured and followed by serial radiographs postoperatively until healing had occurred. Results: Proximal oblique osteotomies located at one-third the length of the ulna were associated with the most movement of the ulnar segments, most notably of the proximal segment. Osteotomies or ostectomies performed in the middle demonstrated less segmental movement and on average, slightly longer time to heal. Movement of the ulnar segments in both groups occurred immediately, and then peaked at two to four weeks postoperatively, tending to plateau thereafter. Clinical significance: Radioulnar incongruity is considered a facet of the aetiopatho-genesis of canine medial coronoid disease. This creates abnormal loads and focal wear along the medial coronoid process. Performing an oblique osteotomy at a location measured at the proximal third of the length of the ulna allows increased movement of the proximal segment, which may result in unloading of the medial compartment. Performing an osteotomy or ostectomy distally dampens segmental movement due to constraint of the interosseous ligament. These findings suggest that a proximal oblique osteotomy at this location creates immediate favourable movement with low morbidity.
Rock glaciers in crystalline catchments: Hidden permafrost‐related threats to alpine headwater lakes

A global warming‐induced transition from glacial to periglacial processes has been identified in mountainous regions around the world. Degrading permafrost in pristine periglacial environments can produce acid rock drainage (ARD) and cause severe ecological damage in areas underlain by sulfide‐bearing bedrock. Limnological and paleolimnological approaches were used to assess and compare ARDs generated by rock glaciers, a typical landform of the mountain permafrost domain, and their effects on alpine headwater lakes with similar morphometric features and underlying bedrock geology, but characterized by different intensities of frost action in their catchments during the year. We argue that ARD and its effects on lakes are more severe in the alpine periglacial belt with mean annual air temperatures (MAAT) between −2°C and +3°C, where groundwater persists in the liquid phase for most of the year, in contrast to ARD in the periglacial belt where frost action dominates (MAAT < −2°C). The findings clearly suggest that the ambient air temperature is an important factor affecting the ARD production in alpine periglacial environments. Applying the paleoecological analysis of morphological abnormalities in chironomids through the past millennium, we tested and rejected the hypothesis that unfavorable conditions for aquatic life in the ARD‐stressed lakes are largely related to the temperature increase over recent decades, responsible for the enhanced release of ARD contaminants. Our results indicate that the ARDs generated in the catchments are of a long‐lasting nature and the frequency of chironomid morphological deformities was significantly higher during the Little Ice Age (LIA) than during pre‐ or post‐LIA periods, suggesting that lower water temperatures may increase the adverse impacts of ARD on aquatic invertebrates. This highlights that temperature‐mediated modulations of the metabolism and life cycle of aquatic organisms should be considered when reconstructing long‐term trends in the ecotoxicological state of lakes.
Whole-grain intake and insulin sensitivity: the Insulin Resistance Atherosclerosis Study.

BACKGROUND Increased intake of whole-grain foods has been related to a reduced risk of developing diabetes and heart disease. One underlying pathway for this relation may be increased insulin sensitivity. OBJECTIVE We assessed the relation between dietary intake of whole grain-containing foods and insulin sensitivity (S(I)). DESIGN We evaluated data from the Insulin Resistance Atherosclerosis Study (IRAS Exam I, 1992-1994). Usual dietary intakes in 978 middle-aged adults with normal (67%) or impaired (33%) glucose tolerance were ascertained by using an interviewer-administered, validated food-frequency questionnaire. Whole-grain intake (servings per day) was derived from dark breads and high-fiber and cooked cereals. S(I) was assessed by minimal model analyses of the frequently sampled intravenous-glucose-tolerance test. Fasting insulin was measured by using a radioimmunoassay. We modeled the relation of whole-grain intake to log(S(I) + 1) and to log(insulin) by using multivariable linear regression. RESULTS On average, IRAS participants consumed 0.8 servings of whole grains/d. Whole-grain intake was significantly associated with S(I) (beta = 0.082, P = 0.0005) and insulin (beta = -0.0646, P = 0.019) after adjustment for demographics, total energy intake and expenditure, smoking, and family history of diabetes. The addition of body mass index and waist circumference attenuated but did not explain the association with S(I). The addition of fiber and magnesium resulted in a nonsignificant association that is consistent with the hypothesis that these constituents account for some of the effect of whole grains on S(I). CONCLUSION Higher intakes of whole grains were associated with increases in insulin sensitivity.
Quantitative Imaging Flow Cytometry of Legionella-Infected Dictyostelium Amoebae Reveals the Impact of Retrograde Trafficking on Pathogen Vacuole Composition

ABSTRACT The ubiquitous environmental bacterium Legionella pneumophila survives and replicates within amoebae and human macrophages by forming a Legionella-containing vacuole (LCV). In an intricate process governed by the bacterial Icm/Dot type IV secretion system and a plethora of effector proteins, the nascent LCV interferes with a number of intracellular trafficking pathways, including retrograde transport from endosomes to the Golgi apparatus. Conserved retrograde trafficking components, such as the retromer coat complex or the phosphoinositide (PI) 5-phosphatase D. discoideum 5-phosphatase 4 (Dd5P4)/oculocerebrorenal syndrome of Lowe (OCRL), restrict intracellular replication of L. pneumophila by an unknown mechanism. Here, we established an imaging flow cytometry (IFC) approach to assess in a rapid, unbiased, and large-scale quantitative manner the role of retrograde-linked PI metabolism and actin dynamics in the LCV composition. Exploiting Dictyostelium discoideum genetics, we found that Dd5P4 modulates the acquisition of fluorescently labeled LCV markers, such as calnexin, the small GTPase Rab1 (but not Rab7 and Rab8), and retrograde trafficking components (Vps5, Vps26, Vps35). The actin-nucleating protein and retromer interactor WASH (Wiskott-Aldrich syndrome protein [WASP] and suppressor of cAMP receptor [SCAR] homologue) promotes the accumulation of Rab1 and Rab8 on LCVs. Collectively, our findings validate IFC for the quantitative and unbiased analysis of the pathogen vacuole composition and reveal the impact of retrograde-linked PI metabolism and actin dynamics on the LCV composition. The IFC approach employed here can be adapted for a molecular analysis of the pathogen vacuole composition of other amoeba-resistant pathogens. IMPORTANCE Legionella pneumophila is an amoeba-resistant environmental bacterium which can cause a life-threatening pneumonia termed Legionnaires' disease. In order to replicate intracellularly, the opportunistic pathogen forms a protective compartment, the Legionella-containing vacuole (LCV). An in-depth analysis of the LCV composition and the complex process of pathogen vacuole formation is crucial for understanding the virulence of L. pneumophila. Here, we established an imaging flow cytometry (IFC) approach to assess in a rapid, unbiased, and quantitative manner the accumulation of fluorescently labeled markers and probes on LCVs. Using IFC and L. pneumophila-infected Dictyostelium discoideum or defined mutant amoebae, a role for phosphoinositide (PI) metabolism, retrograde trafficking, and the actin cytoskeleton in the LCV composition was revealed. In principle, the powerful IFC approach can be used to analyze the molecular composition of any cellular compartment harboring bacterial pathogens.
Analysis of leakage current mechanisms in Schottky contacts to GaN and Al0.25Ga0.75N∕GaN grown by molecular-beam epitaxy

Temperature-dependent current-voltage measurements combined with conductive atomic force microscopy and analytical modeling have been used to assess possible mechanisms of reverse-bias leakage current flow in Schottky diodes fabricated from GaN and Al0.25Ga0. 75N∕GaN structures grown by molecular-beam epitaxy. Below 150K, leakage current is nearly independent of temperature, indicating that conduction is dominated by tunneling transport. At higher temperatures, leakage current in both GaN and Al0.25Ga0. 75N∕GaN diode structures is well described by a Frenkel-Poole emission model. Based on the inferred emission barrier heights and the observation that room-temperature leakage current is dominated by the presence of highly conductive dislocations, it is suggested that the key carrier transport process is emission of electrons from a trap state near the metal-semiconductor interface into a continuum of states associated with each conductive dislocation. In this model for leakage current flow, the emission barr.
Alterations of polyunsaturated fatty acid metabolism in ovarian tissues of polycystic ovary syndrome rats

The metabolism of polyunsaturated fatty acids (PUFAs) remains poorly characterized in ovarian tissues of patients with polycystic ovary syndrome (PCOS). This study aimed to explore alterations in the levels of PUFAs and their metabolites in serum and ovarian tissues in a PCOS rat model treated with a high‐fat diet and andronate. Levels of PUFAs and their metabolites were measured using gas/liquid chromatography‐mass spectrometry after the establishment of a PCOS rat model. Only 3 kinds of PUFAs [linoleic acid, arachidonic acid (AA) and docosahexaenoic acid] were detected in both the circulation and ovarian tissues of the rats, and their concentrations were lower in ovarian tissues than in serum. Moreover, significant differences in the ovarian levels of AA were observed between control, high‐fat diet‐fed and PCOS rats. The levels of prostaglandins, AA metabolites via the cyclooxygenase (COX) pathway, in ovarian tissues of the PCOS group were significantly increased compared to those in the controls. Further studies on the mechanism underlying this phenomenon showed a correlation between decreased expression of phosphorylated cytosolic phospholipase A2 (p‐cPLA2) and increased mRNA and protein expression of COX2, potentially leading to a deeper understanding of altered AA and prostaglandin levels in ovarian tissues of PCOS rats.