Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat stress causes dysfunctional autophagy in oxidative skeletal muscle

We have previously established that 24 h of environmental hyperthermia causes oxidative stress and have implicated mitochondria as likely contributors to this process. Given this, we hypothesized that heat stress would lead to increased autophagy/mitophagy and a reduction in mitochondrial content. To address this hypothesis pigs were housed in thermoneutral (TN; 20°C) or heat stress (35°C) conditions for 1‐ (HS1) or 3‐ (HS3) days and the red and white portions of the semitendinosus collected. We did not detect differences in glycolytic muscle. Counter to our hypothesis, upstream activation of autophagy was largely similar between groups as were markers of autophagosome nucleation and elongation. LC3A/B‐I increased 1.6‐fold in HS1 and HS3 compared to TN (P < 0.05), LC3A/B‐II was increased 4.1‐fold in HS1 and 4.8‐fold in HS3 relative to TN, (P < 0.05) and the LC3A/B‐II/I ratio was increased 3‐fold in HS1 and HS3 compared to TN suggesting an accumulation of autophagosomes. p62 was dramatically increased in HS1 and HS3 compared to TN. Heat stress decreased mitophagy markers PINK1 7.0‐fold in HS1 (P < 0.05) and numerically by 2.4‐fold in HS3 compared to TN and BNIP3L/NIX by 2.5‐fold (P < 0.05) in HS1 and HS3. Markers of mitochondrial content were largely increased without activation of PGC‐1α signaling. In total, these data suggest heat‐stress‐mediated suppression of activation of autophagy and autophagosomal degradation, which may enable the persistence of damaged mitochondria in muscle cells and promote a dysfunctional intracellular environment.
Influence of Race on Kidney Transplantation in the Department of Defense Healthcare System

Background: We report the influence of race on transplant outcomes in the Department of Defense (DOD) system. Methods: Retrospective cohort analysis of all kidney transplants performed at WRAMC from 1996 to 2005. Kaplan-Meier analysis was used to assess for differences in graft survival, and Cox regression was used to calculate adjusted hazard ratios for graft loss. For our analyses, we used the cutoff of 6 years (year 2000) when we introduced thymoglobulin induction; maintenance immunosuppression consisted of mycophenolate mofetil and tacrolimus, and rapid steroid taper (completed withdrawal at 6 weeks) was used for all patients. Results: There were 220 transplants (91 Blacks, 107 Caucasians and 22 Asians). Because the curve for graft survival for Blacks over time violated the proportional hazards assumption (at 6 years post-transplant), analysis was segregated into two segments. Through 6 years of follow-up, graft survival was 77% for Blacks and 81% for non-Blacks (p = 0.74 by log rank). Through 9 potential years of follow-up, graft survival for Blacks was 56% and 78% for Whites (p = 0.005). In Cox regression analysis, Black race, compared with non-Black race, was not significantly associated with graft loss at 6 years, but was significantly associated with graft loss occurring after 6 years. Conclusions: In the DOD health system, no significant differences were seen in graft survival among recipients of different races at 6 years. Black recipients who received a kidney transplant before the year 2000 showed decreased graft survival compared to non-Blacks. This was consistent with change in immunosuppressive regimen in our institution with the introduction of thymoglobulin induction and maintenance therapy with tacrolimus, mycophenolate mofetil and withdrawal of prednisone at 6 weeks.
Removing the mustard oil bomb from seeds: transgenic ablation of myrosin cells in oilseed rape (Brassica napus) produces MINELESS seeds

Many plant phytochemicals constitute binary enzyme–glucoside systems and function in plant defence. In brassicas, the enzyme myrosinase is confined to specific myrosin cells that separate the enzyme from its substrate; the glucosinolates. The myrosinase-catalysed release of toxic and bioactive compounds such as isothiocyanates, upon activation or tissue damage, has been termed ‘the mustard oil bomb’ and characterized as a ‘toxic mine’ in plant defence. The removal of myrosin cells and the enzyme that triggers the release of phytochemicals have been investigated by genetically modifying Brassica napus plants to remove myrosinase-storing idioblasts. A construct with the seed myrosin cell-specific Myr1.Bn1 promoter was used to express a ribonuclease, barnase. Transgenic plants ectopically expressing barnase were embryo lethal. Co-expressing barnase under the control of the Myr1.Bn1 promoter with the barnase inhibitor, barstar, under the control of the cauliflower mosaic virus 35S promoter enabled a selective and controlled death of myrosin cells without affecting plant viability. Ablation of myrosin cells was confirmed with light and electron microscopy, with immunohistological analysis and immunogold-electron microscopy analysis showing empty holes where myrosin cells normally are localized. Further evidence for a successful myrosin cell ablation comes from immunoblots showing absence of myrosinase and negligible myrosinase activity, and autolysis experiments showing negligible production of glucosinolate hydrolysis products. The plants where the myrosin defence cells have been ablated and named ‘MINELESS plants’. The epithiospecifier protein profile and glucosinolate levels were changed in MINELESS plants, pointing to localization of myrosinases and a 35 kDa epithiospecifier protein in myrosin cells and a reduced turnover of glucosinolates in MINELESS plants.
Association of Irisin with Fat Mass, Resting Energy Expenditure, and Daily Activity in Conditions of Extreme Body Mass Index

FNDC5/irisin has been recently postulated as beneficial in the treatment of obesity and diabetes because it is induced in muscle by exercise, increasing energy expenditure. However, recent reports have shown that WAT also secretes irisin and that circulating irisin is elevated in obese subjects. The aim of this study was to evaluate irisin levels in conditions of extreme BMI and its correlation with basal metabolism and daily activity. The study involved 145 female patients, including 96 with extreme BMIs (30 anorexic (AN) and 66 obese (OB)) and 49 healthy normal weight (NW). The plasma irisin levels were significantly elevated in the OB patients compared with the AN and NW patients. Irisin also correlated positively with body weight, BMI, and fat mass. The OB patients exhibited the highest REE and higher daily physical activity compared with the AN patients but lower activity compared with the NW patients. The irisin levels were inversely correlated with daily physical activity and directly correlated with REE. Fat mass contributed to most of the variability of the irisin plasma levels independently of the other studied parameters. Conclusion. Irisin levels are influenced by energy expenditure independently of daily physical activity but fat mass is the main contributing factor.
Following experimental stroke, the recovering brain is vulnerable to lipoxygenase‐dependent semaphorin signaling

Recovery from stroke is limited, in part, by an inhibitory environment in the postischemic brain, but factors preventing successful remodeling are not well known. Using cultured cortical neurons from mice, brain endothelial cells, and a mouse model of ischemic stroke, we show that signaling from the axon guidance molecule Sema3A via eicosanoid second messengers can contribute to this inhibitory environment. Either 90 nM recombinant Sema3A, or the 12/15‐lipoxygenase (12/15‐LOX) metabolites 12‐HETE and 12‐HPETE at 300 nM, block axon extension in neurons compared to solvent controls, and decrease tube formation in endothelial cells. The Sema3A effect is reversed by inhibiting 12/15‐LOX, and neurons derived from 12/15‐LOX‐knockout mice are insensitive to Sema3A. Following middle cerebral artery occlusion to induce stroke in mice, immunohistochemistry shows both Sema3A and 12/15‐LOX are increased in the cortex up to 2 wk. To determine whether a Sema3A‐dependent damage pathway is activated following ischemia, we injected recombinant Sema3A into the striatum. Sema3A alone did not cause injury in normal brains. But when injected into postischemic brains, Sema3A increased cortical damage by 79%, and again, this effect was reversed by 12/15‐LOX inhibition. Our findings suggest that blocking the semaphorin pathway should be investigated as a therapeutic strategy to improve stroke recovery. —Pekcec, A. , Yigitkanli, K. , Jung, J. E. , Pallast, S. , Xing, C. , Antipenko, A. , Minchenko, M. , Nikolov, D. B. , Holman, T. R. , Lo, E. H. , van Leyen, K. Following experimental stroke, the recovering brain is vulnerable to lipoxygenase‐dependent semaphorin signaling. FASEB J. 27, 437–445 (2013). www.fasebj. org
Disbond monitoring in adhesive joints using shear stress optical fiber sensors

We present dedicated shear stress optical fiber sensors for in situ disbond monitoring of adhesive bonds. The shear stress sensitivity of these sensors is about 60 pm MPa−1, which corresponds to a shear strain sensing resolution of 50 μϵ. By integrating a combination of three such sensors in the adhesive bond line of a single lap joint, we can assess the internal shear stress distribution when the joint is tensile loaded. Disbonding of this joint was initiated by cyclic tensile loading, and the sensor responses were monitored during this process. Our results show that this sensing system can detect disbonds as small as 100 μm.
Association of individual hnRNP proteins and snRNPs with nascent transcripts

As they are transcribed, RNA polymerase II transcripts (hnRNAs or pre- mRNAs) associate with hnRNP proteins and snRNP particles, and the processing of pre-mRNA occurs within these ribonucleoprotein complexes. To better understand the relationship between hnRNP proteins and snRNP particles and their roles in mRNA formation, we have visualized them as they associate with nascent transcripts on the polytene chromosomes of Drosophila melanogaster salivary glands. Simultaneous pairwise detection of the abundant hnRNP proteins hrp36, hrp40, and hrp48 by direct double-label immunofluorescence microscopy reveals all of these proteins are bound to most transcripts, but their relative amounts on different transcripts are not fixed. Numerous differences in the relative amounts of snRNP particles and hnRNP proteins on nascent transcripts are also observed. These observations directly demonstrate that individual hnRNP proteins and snRNP particles are differentially associated with nascent transcripts and suggest that different pre- mRNAs bind different combinations of these factors to form transcript- specific, rather than a single type of, hnRNA-hnRNP-snRNP complexes. The distinct and specific constellation of hnRNP proteins and snRNP particles that assembles on different pre-mRNAs is likely to affect the fate and pathway of processing of these transcripts.
Application of grey-Taguchi method to optimise drilling of aluminium alloy 6061 with multiple performance characteristics

Abstract An approach to optimisation of the drilling of aluminium alloy 6061 with multiple performance characteristics, based on grey relational analysis associated with the Taguchi method, has been studied. Coated deposition, spindle speed and feed rate are optimised drilling parameters when the performance characteristics, which include tool life, surface roughness and burr height, are taken into consideration. Optimal drilling parameters for multiple performance characteristics have been derived. It is shown that the multiple performance characteristics are together improved by using this method.
Degradation of native and exotic riparian plant leaf litter in a floodplain pond

1. A litter-bag experiment was undertaken in a pond on the margins of a large temperate floodplain in south-western France to assess the potential influence of the replacement of native by exotic riparian species on organic matter degradation. We determined initial litter chemical composition, breakdown rates and the invertebrate assemblages associated with the litter for five pairs of native dominant and exotic invasive species co-occurring at different stages along a successional gradient. 2. Litter chemical composition, breakdown rates and abundance and diversity of detritivorous invertebrates were similar for the exotic and native species overall. No overall changes in organic matter degradation can thus be predicted from the replacement of dominant natives by exotic invasives. Breakdown rates were primarily driven by the C⁄N ratio. 3. One invasive species (Buddleja davidii) showed significantly higher breakdown rates than its native counterpart (Populus nigra), resulting in the disappearance of leaf litter 6 months prior to the next litterfall. In some cases, therefore, invasion by exotic species may result in discontinuity of resource supply for decomposers.
A functional polymorphic variant in the interleukin-6 gene promoter associated with low bone resorption in postmenopausal women.

OBJECTIVE To examine functional interleukin-6 (IL-6) -174 G-->C allelic variants in relation to bone turnover and bone mineral density (BMD) in postmenopausal women. METHODS Four hundred thirty-four healthy women living in the community (mean +/- SD age 71.7 +/- 5.7 years) were genotyped for the IL-6 -174 G-->C polymorphism. Serum levels of C-telopeptide of type I collagen (CTx), a marker of bone resorption, and osteocalcin (OC), a marker of bone formation, were determined. BMD at the hip and forearm was measured by dual-energy x-ray absorptiometry. RESULTS CTx levels differed significantly (P = 0.006) among IL-6 genotypes (mean +/- SEM 0.275 +/- 0.02 ng/ml, 0.325 +/- 0.01 ng/ml, and 0.356 +/- 0.02 ng/ml in women with the CC genotype [n = 68], the GC genotype [n = 204], and the GG genotype [n = 162], respectively). Compared with the GG group, age-adjusted odds ratios for high bone resorption were 0.65 (95% confidence interval [95% CI] 0.41-1.0, P = 0.06) and 0.37 (95% CI 0.18-0.73, P = 0.0047) in GC and CC subjects, respectively. In contrast, OC levels did not differ by genotype. BMD at the hip and forearm was 1.5-5% higher in CC subjects compared with GG subjects (P not significant). When the cohort was divided according to the median age (70.5 years), BMD was significantly decreased in older compared with younger postmenopausal women with the GG and GC genotypes (-9.6% on average; P < 0.01), but not in those with the CC genotype (-5.1% on average; P not significant). CONCLUSION Compared with the GC and GG IL-6 -174 G-->C genotypes, the CC genotype is associated with lower bone resorption and lesser decrease in bone mass in older postmenopausal women. These results suggest that IL-6 -174 G-->C alleles may be significant determinants of the risk for osteoporosis in elderly subjects.
Gate sizing using a statistical delay model

This paper is about gate sizing under a statistical delay model. It shows we can solve the gate sizing problem exactly for a given statistical delay model. The formulation used allows many different forms of objective functions, which could for example directly optimize the delay uncertainty at the circuit outputs. We formulate the gate sizing problem as a nonlinear programming problem, and show that if we do this carefully, we can solve these problems exactly for circuits up to a few thousand gates using the publicly available large scale nonlinear programming solver LANCELOT.
The Measurement of the Velocity Outside the High Pressure Water Jet and Abrasive Water Jet Nozzle Based on the Energy Transfer Method

The energy transfer method is used to measure the flow velocity of the outside the high pressure water jet (WJ) and Abrasive water jet (AWJ) nozzle. The impact forces of the flow measured by the piezoelectricity ergometer will be transformed to the velocity value, the average velocity of the flow outside the nozzle will be obtained. The result indicates the velocity will reduce along the direction of the flow, and the velocity of the AWJ flow will reduced greatly than the WJ flow, which indicates that the length of the core part of the AWJ flow is shorter than the WJ Flow, the stand-off should be within the 0mm-15mm ranges to gain the most effective machining.
Effect of a two-stage heat treatment process on the mechanical properties of full construction timber

Abstract This study investigated the impact of an industrially used two-stage heat-treatment method on the mechanical properties of full construction timber. Bending tests of full-size Norway spruce posts demonstrated changes due to heat treatment, such as a decrease in the density and bending strength, as well as an increase in the modulus of elasticity (MOE). The variability in bending strength and MOE appeared to be higher for treated posts and as a result the 5% values decreased, especially for the bending strength. The MOE was dependent on density for both treated and untreated posts, but this was not so for the bending strength. There appeared to be a relationship between the bending strength and the MOE, although it was rather weak, especially for treated posts. It was difficult to correlate the occurrence of natural defects in treated Norway spruce posts with an effect on the mechanical properties. Only a combination of several defects, such as large knots, enclosed pith and a deviating slope of grain, appeared to decrease the bending strength and MOE of treated posts, at least more than for untreated posts. The effect of a three year period of outdoor exposure on the strength properties of heat-treated terrace planking was limited. In particular, for the 5% value low strength range, where wood defects strongly determine the mechanical properties of wood, a three-year outdoor exposure did not change the bending strength or MOE of heat-treated wood.
Effects of 5-Amyno-4-(1,3-benzothyazol-2-yn)-1-(3-methoxyphenyl)-1,2-dihydro-3H-pyrrol-3-one Intake on Digestive System in a Rat Model of Colon Cancer

Introduction. Pyrrol derivate 5-amyno-4-(1,3-benzothyazol-2-yn)-1-(3-methoxyphenyl)-1,2-dihydro-3H-pyrrol-3-one (D1) has shown antiproliferative activities in vitro, so investigation of the impact of D1 intake on gut organs in rats that experienced colon cancer seems to be necessary. Materials and Methods. D1 at the dose of 2.3 mg/kg was administered per os daily for 27 (from the 1st day of experiment) or 7 (from the 21st week of experiment) weeks to rats that experienced 1,2-dimethylhydrazine (DMH)-induced colon cancer for 20 weeks. 5-Fluorouracil (5FU) was chosen as reference drug and was administered intraperitoneally weekly for 7 weeks (from the 21st week of experiment) at the dose of 45 mg/kg. Results. Antitumor activity of D1 comparable with the 5FU one against DMH-induced colon cancer in rats was observed (decrease of tumor number and tumor total area up to 46%). D1 attenuated the inflammation of colon, gastric and jejunal mucosa, and the liver, caused by DMH, unlike 5FU, aggravating the latter. In addition, D1 partially normalized mucosa morphometric parameters suggesting its functional restore. Conclusions. D1 possesses, comparable with 5-fluorouracil antitumor efficacy, less damaging effects on the tissues beyond cancerous areas and contributes to partial morphological and functional gut organs recovery.
Unsupervised Search for the Optimal Segmentation for Statistical Machine Translation

We tackle the previously unaddressed problem of unsupervised determination of the optimal morphological segmentation for statistical machine translation (SMT) and propose a segmentation metric that takes into account both sides of the SMT training corpus. We formulate the objective function as the posterior probability of the training corpus according to a generative segmentation-translation model. We describe how the IBM Model-1 translation likelihood can be computed incrementally between adjacent segmentation states for efficient computation. Submerging the proposed segmentation method in a SMT task from morphologically-rich Turkish to English does not exhibit the expected improvement in translation BLEU scores and confirms the robustness of phrase-based SMT to translation unit combinatorics. A positive outcome of this work is the described modification to the sequential search algorithm of Morfessor (Creutz and Lagus, 2007) that enables arbitrary-fold parallelization of the computation, which unexpectedly improves the translation performance as measured by BLEU.
Intensity-based framework and penalty formulation of optimal stopping problems

Financial derivatives commonly contain pre-mature termination clauses, which are embedded rights held by the holder or writer. Well known examples of these stopping rights include the early exercise right in American options, the callable right in callable securities and the prepayment right in mortgage loans. In this paper, we show how to model the mortgagor’s prepayment in mortgage loans and the issuer’s call in the American warrant as an event risk using the intensity based approach, where the propensity of prepayment or calling is modeled by the intensity of a Poisson process. We illustrate that the corresponding pricing formulation resembles the penalty approximation approach commonly used in the solution of the linear complementarity formulation of an optimal stopping problem. We obtain several theoretical results on the prepayment strategies of mortgage loans and calling polices of American warrants. We also propose robust second order accurate numerical schemes for solving the penalty formulation of an optimal stopping problem.
Climate, vocal folds, and tonal languages: Connecting the physiological and geographic dots

Significance The sound systems of human languages are not generally thought to be ecologically adaptive. We offer the most extensive evidence to date that such systems are in fact adaptive and can be influenced, at least in some respects, by climatic factors. Based on a survey of laryngology data demonstrating the deleterious effects of aridity on vocal cord movement, we predict that complex tone patterns should be relatively unlikely to evolve in arid climates. This prediction is supported by careful statistical sampling of climatic and phonological data pertaining to over half of the world’s languages. We conclude that human sound systems, like those of some other species, are influenced by environmental variables. We summarize a number of findings in laryngology demonstrating that perturbations of phonation, including increased jitter and shimmer, are associated with desiccated ambient air. We predict that, given the relative imprecision of vocal fold vibration in desiccated versus humid contexts, arid and cold ecologies should be less amenable, when contrasted to warm and humid ecologies, to the development of languages with phonemic tone, especially complex tone. This prediction is supported by data from two large independently coded databases representing 3,700+ languages. Languages with complex tonality have generally not developed in very cold or otherwise desiccated climates, in accordance with the physiologically based predictions. The predicted global geographic–linguistic association is shown to operate within continents, within major language families, and across language isolates. Our results offer evidence that human sound systems are influenced by environmental factors.