Miracle-dz/UniFAR-FTUs huggingface dataset:
Presence of Trifolium repens Promotes Complementarity of Water Use and N Facilitation in Diverse Grass Mixtures

Legume species promote productivity and increase the digestibility of herbage in grasslands. Considerable experimental data also indicate that communities with legumes produce more above-ground biomass than is expected from monocultures. While it has been attributed to N facilitation, evidence to identify the mechanisms involved is still lacking and the role of complementarity in soil water acquisition by vertical root differentiation remains unclear. We used a 20-months mesocosm experiment to investigate the effects of species richness (single species, two- and five-species mixtures) and functional diversity (presence of the legume Trifolium repens) on a set of traits related to light, N and water use and measured at community level. We found a positive effect of Trifolium presence and abundance on biomass production and complementarity effects in the two-species mixtures from the second year. In addition the community traits related to water and N acquisition and use (leaf area, N, water-use efficiency, and deep root growth) were higher in the presence of Trifolium. With a multiple regression approach, we showed that the traits related to water acquisition and use were with N the main determinants of biomass production and complementarity effects in diverse mixtures. At shallow soil layers, lower root mass of Trifolium and higher soil moisture should increase soil water availability for the associated grass species. Conversely at deep soil layer, higher root growth and lower soil moisture mirror soil resource use increase of mixtures. Altogether, these results highlight N facilitation but almost soil vertical differentiation and thus complementarity for water acquisition and use in mixtures with Trifolium. Contrary to grass-Trifolium mixtures, no significant over-yielding was measured for grass mixtures even those having complementary traits (short and shallow vs. tall and deep). Thus, vertical complementarity for soil resources uptake in mixtures was not only dependant on the inherent root system architecture but also on root plasticity. We also observed a time-dependence for positive complementarity effects due to the slow development of Trifolium in mixtures, possibly induced by competition with grasses. Overall, our data underlined that soil water resource was an important driver of over-yielding and complementarity effects in Trifolium-grass mixtures.
A Specific Inorganic Triphosphatase from Nitrosomonas europaea

The CYTH superfamily of proteins is named after its two founding members, the CyaB adenylyl cyclase from Aeromonas hydrophila and the human 25-kDa thiamine triphosphatase. Because these proteins often form a closed β-barrel, they are also referred to as triphosphate tunnel metalloenzymes (TTM). Functionally, they are characterized by their ability to bind triphosphorylated substrates and divalent metal ions. These proteins exist in most organisms and catalyze different reactions depending on their origin. Here we investigate structural and catalytic properties of the recombinant TTM protein from Nitrosomonas europaea (NeuTTM), a 19-kDa protein. Crystallographic data show that it crystallizes as a dimer and that, in contrast to other TTM proteins, it has an open β-barrel structure. We demonstrate that NeuTTM is a highly specific inorganic triphosphatase, hydrolyzing tripolyphosphate (PPPi) with high catalytic efficiency in the presence of Mg2+. These data are supported by native mass spectrometry analysis showing that the enzyme binds PPPi (and Mg-PPPi) with high affinity (Kd < 1.5 μm), whereas it has a low affinity for ATP or thiamine triphosphate. In contrast to Aeromonas and Yersinia CyaB proteins, NeuTTM has no adenylyl cyclase activity, but it shares several properties with other enzymes of the CYTH superfamily, e.g. heat stability, alkaline pH optimum, and inhibition by Ca2+ and Zn2+ ions. We suggest a catalytic mechanism involving a catalytic dyad formed by Lys-52 and Tyr-28. The present data provide the first characterization of a new type of phosphohydrolase (unrelated to pyrophosphatases or exopolyphosphatases), able to hydrolyze inorganic triphosphate with high specificity.
Understanding Tradeoffs in Software Transactional Memory

There has been a flurry of recent work on the design of high performance software and hybrid hardware/software transactional memories (STMs and HyTMs). This paper re-examines the design decisions behind several of these state-of-the-art algorithms, adopting some ideas, rejecting others, all in an attempt to make STMs faster. We created the transactional locking (TL) framework of STM algorithms and used it to conduct a range of comparisons of the performance of non-blocking, lock-based, and Hybrid STM algorithms versus fine-grained hand-crafted ones. We were able to make several illuminating observations regarding lock acquisition order, the interaction of STMs with memory management schemes, and the role of overheads and abort rates in STM performance
Distributions of aspartate aminotransferase and malate dehydrogenase activities in rat retinal layers.

Aspartate aminotransferase (AAT), an enzyme interconverting glutamate and aspartate, has been suggested to be a marker for glutamatergic and/or aspartatergic neurons. However, AAT, glutamate, and aspartate are also involved in cellular metabolism, e.g., the malate-aspartate shuttle. To investigate the extent to which AAT might be involved in these several functions in retina, the distribution of AAT activity in rat retinal layers was compared to that of malate dehydrogenase (MDH), an enzyme of aerobic metabolism proposed to be physically complexed with AAT in the malate-aspartate shuttle mechanism. The distribution of AAT activity in retinal layers closely paralleled that of MDH (correlation coefficient AAT versus MDH = 0.93). AAT activity was proportionately higher than MDH in the photoreceptor inner segments, containing a high density of mitochondria, and in the outer plexiform layer (OPL), containing photoreceptor terminals and bipolar and horizontal cell processes. The amount of total AAT activity in the inner segments related to the mitochondrial isoenzyme is almost twice that in the other layers tested, including the OPL. The correlation between AAT and MDH activities is consistent with AAT involvement in retinal energy metabolism, although other functions, such as neurotransmission, are possible.
A coupled schema of probabilistic atlas and statistical shape and appearance model for 3D prostate segmentation in MR images

A hybrid framework of probabilistic atlas and statistical shape and appearance model (SSAM) is proposed to achieve 3D prostate segmentation. An initial 3D segmentation of the prostate is obtained by registering the probabilistic atlas to the test dataset with deformable Demons registration. The initial results obtained are used to initialize multiple SSAMs corresponding to the apex, central and base regions of the prostate gland to incorporate local variabilities. Multiple mean parametric models of shape and appearance are derived from principal component analysis of prior shape and intensity information of the prostate from the training data. The parameters are then modified with the prior knowledge of the optimization space to achieve 2D segmentation. The 2D labels are registered to the 3D labels generated using probabilistic atlas to constrain the pose variation and generate valid 3D shapes. The proposed method achieves a mean Dice similarity coefficient value of 0.89±0.11 and mean Hausdorff distance of 3.05±2.25 mm when validated with 15 prostate volumes of a public dataset in a leave-one-out validation framework.
Magnetospheric Emissions from the Planet Orbiting τ Bootis: A Multiepoch Search

All of the solar system gas giants produce electron cyclotron masers driven by the solar wind impinging on their magnetospheres. Extrapolating to the planet orbiting τ Boo, various authors have predicted that it may be within the detection limits of the 4 m wavelength (74 MHz) system on the Very Large Array. This paper reports three epochs of observations of τ Boo. In no epoch do we detect the planet; various means of determining the upper limit to the emission yield single-epoch limits ranging from 135 to 300 mJy. We develop a likelihood method for multiepoch observations and use it to constrain various radiation properties of the planet. If we assume that the planet does radiate at our observation wavelength, its typical luminosity must be less than about 1016 W, unless its radiation is highly beamed into a solid angle of Ω ≪ 1 sr. While this value is within the range of luminosities predicted by various authors for this planet, it is lower than recent estimates that attempt to take into account the stellar wind of τ Boo using the known properties of the star itself. Electron cyclotron maser emission from solar system planets is beamed, but with characteristic solid angles of approximately 1 sr illuminated. Future long-wavelength instruments (e.g., the Long Wavelength Array and the Low Frequency Array) must be able to make typical flux density measurements of approximately 25 mJy on short timescales (≈15 minutes) in order to improve these constraints significantly.
Muscle expression of a local Igf-1 isoform protects motor neurons in an ALS mouse model

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by a selective degeneration of motor neurons, atrophy, and paralysis of skeletal muscle. Although a significant proportion of familial ALS results from a toxic gain of function associated with dominant SOD1 mutations, the etiology of the disease and its specific cellular origins have remained difficult to define. Here, we show that muscle-restricted expression of a localized insulin-like growth factor (Igf) -1 isoform maintained muscle integrity and enhanced satellite cell activity in SOD1G93A transgenic mice, inducing calcineurin-mediated regenerative pathways. Muscle-specific expression of local Igf-1 (mIgf-1) isoform also stabilized neuromuscular junctions, reduced inflammation in the spinal cord, and enhanced motor neuronal survival in SOD1G93A mice, delaying the onset and progression of the disease. These studies establish skeletal muscle as a primary target for the dominant action of inherited SOD1 mutation and suggest that muscle fibers provide appropriate factors, such as mIgf-1, for neuron survival.
Association between Acculturation and Breastfeeding among Hispanic Women

Background: Breastfeeding rates are typically higher among Hispanic women; however, they vary by acculturation status in that those more acculturated are less likely to breastfeed than those who are less acculturated. This study examined the association between acculturation and breastfeeding behaviors using population-based data. Methods: Data (N = 8942) from the Pregnancy Risk Assessment Monitoring System (PRAMS) were used for analysis. Acculturation status was determined using self-reported Hispanic ethnicity and the language in which the women responded to the PRAMS survey, either English or Spanish. Hispanic women who responded to the survey in Spanish were categorized as less acculturated than those who responded in English. Breastfeeding indicators used were: initiation, duration to ≥ 10 weeks, and exclusive breastfeeding to ≥ 10 weeks. Results: The prevalence rates of breastfeeding initiation, duration, and exclusive breastfeeding to ≥ 10 weeks were significantly higher among less acculturated than among highly acculturated. More acculturated were less likely to initiate breastfeeding (prevalence ratio [PR] = 0.88; 95% CI, 0.86-0.90), less likely to breastfeed ≥ 10 weeks (PR = 0.77; 95% CI, 0.72-0.82), and less likely to report exclusive breastfeeding to ≥ 10 weeks (PR =,0.70; 95% CI, 0.58-0.85). The relationship between breastfeeding continuation and acculturation persisted after adjusting for covariates in that more acculturated were less likely to breastfeed to ≥ 10 weeks (adjusted prevalence ratio [APR] = 0.81; 95% CI, 0.75-0.87), as did the relationship between exclusivity and acculturation; more acculturated were less likely to report exclusive breastfeeding (APR = 0.69; 95% CI, 0.55-0.87). Conclusions: Breastfeeding promotion efforts must include culturally/linguistically supportive services to assure that women are able to make optimal infant feeding decisions.
Patient and provider attitudes to emergency department-based HIV counselling and testing in South Africa

Background The national South African HIV Counselling and Testing (HCT) guidelines mandate that voluntary counselling and testing (VCT) should be offered in all healthcare facilities. Emergency departments (EDs) are at the forefront of many healthcare facilities, yet VCT is not routinely implemented in this setting. Methods We conducted a cross-sectional study that surveyed patients and healthcare providers at a tertiary care ED in the spring and summer of 2016 to ascertain their attitudes to VCT in the ED. We also used two previously validated survey instruments to gather data on patients’ HIV knowledge and providers’ stigma against patients living with HIV, as we anticipated that these may have an impact on providers’ and patients’ attitudes to the provision of HIV testing within the ED, and may offer insights for future intervention development. Results A total of 104 patients and 26 providers were enrolled in the study. Overall, patients responded more favourably to ED-based HIV testing (92.3%) compared to providers (only 40% responded favourably). When asked about potential barriers to receiving or providing HIV testing, 16.4% of patients and 24% of providers felt that the subject of HIV was too sensitive and 58.7% of patients and 80% of providers indicated that privacy and confidentiality issues would pose major barriers to implementing ED-based HIV testing. Conclusion This study shows that while ED-based HIV testing is overall highly acceptable to patients, providers seem less willing to provide this service. The survey data also suggest that future development of ED-based testing strategies should take into consideration privacy and confidentiality concerns that may arise within a busy emergency care setting. Furthermore, every effort should be made to tackle HIV stigma among providers to improve overall attitudes towards HIV-positive individuals that present for care in the ED.
Effectiveness of Spinosad on Four Classes of Wheat Against Five Stored-Product Insects

Abstract Spinosad is a commercial reduced-risk pesticide that is naturally derived. Spinosad’s performance was evaluated on four classes of wheat (hard red winter, hard red spring, soft red winter, and durum wheats) against adults of the lesser grain borer, Rhyzopertha dominica (F.); rice weevil, Sitophilus oryzae (L.); sawtoothed grain beetle, Oryzaephilus surinamensis (L.); red flour beetle, Tribolium castaneum (Herbst); and larvae of the Indianmeal moth, Plodia interpunctella (Hübner). Beetle adults (25) or P. interpunctella eggs (50) were exposed to untreated wheat and wheat treated with spinosad at 0.1 and 1 mg (AI)/kg of grain. On all untreated wheat classes, adult beetle mortality ranged from 0 to 6%, and P. interpunctella larval mortality ranged from 10 to 19%. The effects of spinosad on R. dominica and P. interpunctella were consistent across all wheat classes. Spinosad killed all exposed R. dominica adults and significantly suppressed progeny production (84–100%) and kernel damage (66–100%) at both rates compared with untreated wheat. Spinosad was extremely effective against P. interpunctella on all wheat classes at 1 mg/kg, based on larval mortality (97.6–99.6%), suppression of egg-to-adult emergence (93–100%), and kernel damage (95–100%), relative to similar effects on untreated wheats. The effects of spinosad on S. oryzae varied among wheat classes and between spinosad rates. Spinosad was effective against S. oryzae, O. surinamensis and T. castaneum only on durum wheat at 1 mg/kg. Our results suggest spinosad to be a potential grain protectant for R. dominica and P. interpunctella management in stored wheat.
Plant Essential Oils Synergize and Antagonize Toxicity of Different Conventional Insecticides against Myzus persicae (Hemiptera: Aphididae)

Plant-derived products can play an important role in pest management programs. Essential oils from Lavandula angustifolia (lavender) and Thymus vulgaris (thyme) and their main constituents, linalool and thymol, respectively, were evaluated for insecticidal activity and synergistic action in combination with insecticides against green peach aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae). The essential oils and their main constituents exerted similar insecticidal activity when aphids were exposed by direct sprays, but were non-toxic by exposure to treated leaf discs. In synergism experiments, the toxicity of imidacloprid was synergized 16- to 20-fold by L. angustifolia and T. vulgaris essential oils, but far less synergism occurred with linalool and thymol, indicating that secondary constituents of the oils were probably responsible for the observed synergism. In contrast to results with imidacloprid, the insecticidal activity of spirotetramat was antagonized by L. angustifolia and T. vulgaris essential oils, and linalool and thymol. Our results demonstrate the potential of plant essential oils as synergists of insecticides, but show that antagonistic action against certain insecticides may occur.
Interactions between pregnancy, obstructive sleep apnea, and gestational diabetes mellitus.

CONTEXT Questionnaire studies linked symptoms of obstructive sleep apnea (OSA) to the risk of gestational diabetes mellitus (GDM). Whether this association is present when OSA is assessed objectively by polysomnography is not known. OBJECTIVE The objective of the study was to assess the relationship between pregnancy, OSA, and GDM. DESIGN, SETTING, AND PARTICIPANTS We conducted observational case-control studies using polysomnography in 15 nonpregnant, nondiabetic women (NP-NGT), 15 pregnant women with normal glucose tolerance (P-NGT), and 15 pregnant women with GDM (P-GDM). The groups were frequency matched for age and race/ethnicity. Pregnant women were studied during the late second to early third trimester. MAIN OUTCOME MEASURES Comparisons of OSA diagnosis and sleep parameters between NP-NGT and P-NGT to assess the impact of pregnancy and between P-NGT and P-GDM to explore the association between GDM and OSA were measured. RESULTS Compared with NP-NGT, P-NGT women had a higher apnea hypopnea index (AHI) (median 2.0 vs 0.5, P = .03) and more disrupted sleep as reflected by a higher wake time after sleep onset (median 66 vs 21 min, P < .01) and a higher microarousal index (median 16.4 vs 10.6, P = .01). Among the pregnant women, P-GDM had markedly lower total sleep time (median 397 vs 464 min, P = .02) and a higher AHI (median 8.2 vs 2.0, P = .05) than P-NGT women. OSA was more prevalent in P-GDM than in P-NGT women (73% vs 27%, P = .01). After adjustment for prepregnancy body mass index, the diagnosis of GDM was associated with a diagnosis of OSA [odds ratio 6.60 (95% confidence interval 1.15-37.96)]. In pregnancy, after adjusting for prepregnancy body mass index, higher microarousal index significantly associated with higher hemoglobin A1c and fasting glucose levels. Higher oxygen desaturation index was associated with higher fasting glucose levels. CONCLUSION Pregnancy is associated with sleep disturbances. Sleep is more disturbed in GDM than in P-NGT women. There is a strong association between GDM and OSA.
Transactional conflict decoupling and value prediction

This paper explores data speculation for improving the performance of Hardware Transactional Memory (HTM). We attempt to reduce transactional conflicts by decoupling them from cache coherence conflicts; many HTMs do not distinguish between transactional conflicts and coherence conflicts, leading to false transactional conflicts. We also attempt to mitigate the effects of coherence conflicts by using value prediction in transactions. We show that coherence decoupling and value prediction in transactions complement each other, because they both speculate on data in ways that are infeasible in the absence of HTM support. As a demonstration of how data speculation can improve performance, we introduce DPTM, a best-effort HTM that mitigates the effects of false sharing at the cache line level. DPTM does not alter the underlying cache coherence protocol, and requires only minor, processor-local, modifications. We evaluate DPTM against a baseline best-effort HTM, and compare it with data restructuring by padding, the most commonly used method to avoid false sharing. Our experiments show that DPTM can dramatically improve performance in the presence of false sharing without degrading performance in its absence, and consistently performs better than restructuring by padding.
Practical yet universally composable two-server password-authenticated secret sharing

Password-authenticated secret sharing (PASS) schemes, first introduced by Bagherzandi et al. at CCS 2011, allow users to distribute data among several servers so that the data can be recovered using a single human-memorizable password, but no single server (or even no collusion of servers up to a certain size) can mount an off-line dictionary attack on the password or learn anything about the data. We propose a new, universally composable (UC) security definition for the two-server case (2PASS) in the public-key setting that addresses a number of relevant limitations of the previous, non-UC definition. For example, our definition makes no prior assumptions on the distribution of passwords, preserves security when honest users mistype their passwords, and guarantees secure composition with other protocols in spite of the unavoidable non-negligible success rate of online dictionary attacks. We further present a concrete 2PASS protocol and prove that it meets our definition. Given the strong security guarantees, our protocol is surprisingly efficient: in its most efficient instantiation under the DDH assumption in the random-oracle model, it requires fewer than twenty elliptic-curve exponentiations on the user's device. We achieve our results by careful protocol design and by exclusively focusing on the two-server public-key setting.
Characterization of Defects in AlGaN/GaN HEMTs Based on Nonlinear Microwave Current Transient Spectroscopy

This paper presents a new nonlinear microwave-based characterization methodology for the study of the deep levels proprieties in gallium nitride (GaN)-based high electron mobility transistors (HEMTs). Currently, it is unique measurement method allowing the extraction of time constants of HEMTs operating under large signal RF conditions. This method improves the conventional dc techniques, since it employs RF excitation during the filling condition to investigate the impact of “real-life” RF excitation on the trapping mechanisms. The experimental results demonstrate that, beyond the presence of Poole–Frenkel effect, the slow detrapping time constant is accelerated by the power dissipation of the trapping bias point. Moreover, it is possible to distinguish the impact of dc and RF conditions on the trapping phenomena. The temperature measurements allow identifying the 0.75-eV deep level, attributed to extended defects in GaN, when ionized under dc excitation. This deep level trap is probably located in the buffer layer and contributes to the RF trapping phenomenon.