Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrification in Mono Lake, California: Activity and community composition during contrasting hydrological regimes

Rates of nitrification, geochemical variables, and the associated ammonia oxidizer microbial community were investigated in the water column of Mono Lake, California, between August 2002 and August 2003. Ammonia oxidation rates were measured using a 15N isotope tracer technique. 16S ribosomal deoxyribonucleic acid, functional gene, and fluorescence in situ hybridization (FISH) analyses were used to characterize the ammonia oxidizer population. Peak ammonia oxidation activity occurred consistently between 12 and 14 m; the maximum integrated rate was observed in November 2002. The ammonia‐oxidizing bacterial (AOB) community exhibited sequences most closely related to halo and/or alkaline tolerant Nitrosomonas‐like sequences. The observed phylogeny represented a significant shift from previously documented AOB community composition and was coincident with Mono Lake's transition from monomixis to meromixis. Samples were also analyzed for ammoniaoxidizing archaea (AOA). FISH analysis revealed a substantial population of Crenarchaeota, the phylum encompassing all known AOA; however, no archaeal ammonia monooxygenase (amoA) sequences were detected. Unrealistic AOB cell‐specific nitrification rates strongly indicate the possibility of a missing nitrification source, and correlations between nitrification rates, geochemical variables, and crenarchaeal and AOB abundance also indicate a significant AOA contribution to nitrification. However, the lack of verifiable archaeal amoA genes leaves open the question of whether AOA contribute to nitrification in Mono Lake.
Evaluating the effects of interactivity in a post-editing workbench

This paper describes the field trial and subsequent evaluation of a post-editing workbench which is currently under development in the EU-funded CasMaCat project. Based on user evaluations of the initial prototype of the workbench, this second prototype of the workbench includes a number of interactive features designed to improve productivity and user satisfaction. Using CasMaCat’s own facilities for logging keystrokes and eye tracking, data were collected from nine post-editors in a professional setting. These data were then used to investigate the effects of the interactive features on productivity, quality, user satisfaction and cognitive load as reflected in the post-editors gaze activity. These quantitative results are combined with the qualitative results derived from user questionnaires and interviews conducted with all the participants.
Serum homocysteine concentration as an indicator of survival in patients with acute coronary syndromes.

BACKGROUND Circulating homocysteine levels are predictive of survival in patients with stable coronary artery disease. The prognostic value of serum homocysteine levels, obtained in the acute phase in patients with myocardial infarction or unstable angina, is unknown. OBJECTIVES To test the hypothesis that circulating homocysteine levels, obtained during the first 24 hours following hospital admission in patients with acute coronary syndromes, are predictive of long-term mortality. METHODS To test this hypothesis we performed a prospective inception cohort study at a teaching hospital in Gothenburg, Sweden. A total of 579 patients (179 women and 400 men; median age, 67 years) were included (Q-wave myocardial infarction in 163 patients, non-Q-wave myocardial infarction in 210 patients, unstable angina pectoris in 206 patients). MAIN OUTCOME MEASURE All-cause mortality. RESULTS During a median follow-up of 628 days, 65 patients died. The serum homocysteine level (mean [SD]) was significantly lower in long-term survivors (n = 514) than in nonsurvivors (n=65) (12.3 [7.0] vs 14.3 [5.9] pmol/L; P=.003). The relative risk (all-cause mortality) for patients with homocysteine levels in the upper quartile was 2.4 (95% confidence interval, 1.5-4.0) compared with that of patients in the 3 lower quartiles. After adjustment for relevant confounders, the relative risk estimate remained significant (relative risk= 1.69; 95% confidence interval, 1.02-2.80). In a stepwise model the homocysteine level provided prognostic information additional to that of patient age, diabetes mellitus, and diuretic usage prior to hospital admission (P=.03). CONCLUSION The serum homocysteine level on hospital admission is an independent predictor of long-term survival in patients with acute coronary syndromes.
Neural retina identity is specified by lens-derived BMP signals

The eye has served as a classical model to study cell specification and tissue induction for over a century. Nevertheless, the molecular mechanisms that regulate the induction and maintenance of eye-field cells, and the specification of neural retina cells are poorly understood. Moreover, within the developing anterior forebrain, how prospective eye and telencephalic cells are differentially specified is not well defined. In the present study, we have analyzed these issues by manipulating signaling pathways in intact chick embryo and explant assays. Our results provide evidence that at blastula stages, BMP signals inhibit the acquisition of eye-field character, but from neural tube/optic vesicle stages, BMP signals from the lens are crucial for the maintenance of eye-field character, inhibition of dorsal telencephalic cell identity and specification of neural retina cells. Subsequently, our results provide evidence that a Rax2-positive eye-field state is not sufficient for the progress to a neural retina identity, but requires BMP signals. In addition, our results argue against any essential role of Wnt or FGF signals during the specification of neural retina cells, but provide evidence that Wnt signals together with BMP activity are sufficient to induce cells of retinal pigment epithelial character. We conclude that BMP activity emanating from the lens ectoderm maintains eye-field identity, inhibits telencephalic character and induces neural retina cells. Our findings link the requirement of the lens ectoderm for neural retina specification with the molecular mechanism by which cells in the forebrain become specified as neural retina by BMP activity. SUMMARY: BMP signals from the lens are crucial to maintain eye-field character, inhibit dorsal telencephalic cell identity, and specificy neural retina cells in chick embryos.
Supersymmetry of Green-Schwarz superstring and matrix string theory

We study the dynamics of a Green-Schwarz superstring on the gravitational wave background corresponding to the matrix string theory and the supersymmetry transformation rules of the superstring. The dynamics is obtained in the light-cone formulation and is shown to agree with that derived from matrix string theory. The supersymmetry structure has corrections due to the effect of the background and is identified with that of the low-energy one-loop effective action of matrix string theory in a two superstring background in the weak string coupling limit.
Primary Biliary Cirrhosis Is Reversible Rabbits to the Mitochondrial Autoantigen of Xenobiotic-Induced Loss of Tolerance in

Eric GershwinA. Ansari, Kit S. Lam, Mikio Zeniya, Ross L. Coppel and M.Marik, Chao Quan, Mark J. Kurth, Michael H. Nantz, Aftab Katsushi Amano, Patrick S. C. Leung, Qingchai Xu, Janhttp://www.jimmunol.org/content/172/10/6444J Immunol€2004; 172:6444-6452; ;Referenceshttp://www.jimmunol.org/content/172/10/6444.full#ref-list-1This article cites 59 articles, 16 of which you can access for free at: Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai. org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:
Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds

Phenotypic diversity is not evenly distributed across lineages. Here, we describe and apply a maximum-likelihood phylogenetic comparative method to test for different rates of phenotypic evolution between groups of the avian order Charadriiformes (shorebirds, gulls and alcids) to test the influence of a binary trait (offspring demand; semi-precocial or precocial) on rates of evolution of parental care, mating systems and secondary sexual traits. In semi-precocial species, chicks are reliant on the parents for feeding, but in precocial species the chicks feed themselves. Thus, where the parents are emancipated from feeding the young, we predict that there is an increased potential for brood desertion, and consequently for the divergence of mating systems. In addition, secondary sexual traits are predicted to evolve faster in groups with less demanding young. We found that precocial development not only allows rapid divergence of parental care and mating behaviours, but also promotes the rapid diversification of secondary sexual characters, most notably sexual size dimorphism (SSD) in body mass. Thus, less demanding offspring appear to facilitate rapid evolution of breeding systems and some sexually selected traits.
Efficacy of Tomato Powder as Antioxidant in Cooked Pork Patties

This study was carried out to determine the effects of tomato powder (TP) on cooked pork patties during storage at 10±1°C in the dark. The total phenolic and flavonoid contents of TP extract were 26.22 mg gallic acid/100 g and 3.52 mg quercetin/100 g, respectively. The extract of TP showed a potential antioxidant activity in the DPPH radical-scavenging assay (EC50 = 16.76 μg/mL). Pork patties were manufactured with 0.25% (T1), 0.5% (T2), 0.75% (T3) and 1.0% (T4) TP in a basic formula (C). The pH and volatile basic nitrogen (VBN) values of T2, T3 and T4 patties were lower (p<0.05) than the C patties during storage. Increased concentration of TP in meat patties decreased (p<0.05) the 2-thiobarbituric acid reactive substances (TBARS) and total plate count (TPC) values at d 7 of storage. Tomato treated-patties had lower (p<0.05) values for lightness (L*), but higher (p<0.05) values for redness (a*) and yellowness (b*) at d 3 and 7 of storage compared with the C. In the case of sensory evaluation, the scores of colour, flavour and overall acceptability of T3 and T4 patties were higher (p<0.05) than those of the C patty after 3 or 7 days of storage.
Effects of interleukin‐1 on fibroblast extracellular matrix, using a 3‐dimensional culture system

This study describes the alterations induced by Interleukin‐1α and ‐β (IL‐1α and IL‐1β) on fibroblast‐synthesized extracellular matrix. Fibroblasts were grown between pieces of dentin or in collagen‐coated Terasaki wells for 3 or 6–9 weeks to create 3‐dimensional cell‐containing matrices constituted primarily of proteoglycans and collagens, respectively. Following incubation with IL‐1α or IL‐1β (10−9 M) at 37°C for 24 or 72 hr, samples were prepared for light and electron microscopy. Both IL‐1α and IL‐1β induced collapse of the extracellular matrix by 72 hr, as manifested by a decrease of the cross‐sectional area and an increased density of the matrices. Three‐week matrices were reduced 26% and 45% by using IL‐1α and IL‐1β, respectively. Comparable values obtained by using 6‐week matrices were 14% and 30%. Cells within the matrix, normally stellate in shape with numerous extended processes, attained a more rounded or spindle shape with few and reduced processes and showed apparent alterations at cell matrix attachment sites and rearrangement of the cytoskeleton. Elongated cells at the top of the matrix appeared more compressed. The alterations were more pronounced in cultures incubated with IL‐β than with IL‐1α. Immunocytochemistry of extracellular matrix components revealed a decrease in staining intensity of chondroitin and dermatan sulfate in the 3‐week matrix following IL‐1β incubation. There was also a decrease in collagen type I staining of 9‐week matrices treated with IL‐1α or IL‐1β. These studies show that IL‐1 has an effect on fibroblast‐synthesized extracellular matrix and indicate that the effects of IL‐1α and IL‐1β may differ. The resulting collapse of the matrix appears at least in part to be due to changes in proteoglycans and collagens.
Maternal Transfer of Photoperiodic Information Regulates the Postnatal Reproductive System Development of the Mongolian Gerbil (Meriones unguiculatus)

We investigated whether photoperiodic information is transferred from mother to young and whether the pineal gland and its hormone, melatonin, are involved in this transfer in Mongolian gerbils. Adult female gerbils were paired with males and housed in photoperiods of 12L:12D or 8L:16D. Three groups of pregnant gerbils in each photoperiod were prepared: one group was the sham-operated control, one group consisted of pinealectomized gerbils, and one group consisted of pinealectomized gerbils that were treated with melatonin. Pinealectomy was performed before pairing the animals and melatonin injections were applied to the pinealectomized group from day 8 of gestation until parturition. On the day of parturition, the mother and young were transferred to an intermediate photoperiod (10L:14D). After weaning, body weight gain and gonadal development of the male young were measured every week over 8 weeks. Animals gestated and born to control and pinealectomized + melatonin injected mothers exposed to 12L:12D responded to 10L:14D as a short day; they had significantly (P 0.05). These results are the first evidence that the photoperiod to which the mother is exposed during gestation affects the postnatal gonadal development of the young and the pineal gland and melatonin play an important role in the transmission of photoperiodic information in the Mongolian gerbil.
Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates

14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.
Temperature monitoring of narrow bandgap semiconductors

An integrated spectral pyrometry (ISP) technique particularly well suited to monitor the temperature of small bandgap semiconductors during molecular beam epitaxial growth is proposed. The technique relies on integrating the thermal radiation power emitted by the wafer over a spectral range where it is fully opaque, so as to avoid contribution from radiation transmitted from the substrate heater. In the present work, a 900–1700 nm array InGaAs spectrometer normally employed for band-edge thermometry was used. The temperature dependence of the integrated signal can be expressed by an Arrhenius-type exponential relation. The calibration procedure and the method employed to compensate for the background radiation from other hot objects in the reactor is discussed. The ISP performance is then demonstrated by monitoring the temperature during the growths of a Si doped InAs layer on InAs substrate and of an InSb/AlInSb quantum well structure on GaAs substrate. The ISP technique allows reproducible wafer tempera.
Lookit (Part 2): Assessing the Viability of Online Developmental Research, Results From Three Case Studies

To help address the participant bottleneck in developmental research, we developed a new platform called “Lookit,” introduced in an accompanying article (Scott & Schulz, 2017), that allows families to participate in behavioral studies online via webcam. To evaluate the viability of the platform, we administered online versions of three previously published studies involving different age groups, methods, and research questions: an infant (M = 14.0 months, N = 49) study of novel event probabilities using violation of expectation, a study of two-year-olds’ (M = 29.2 months, N = 67) syntactic bootstrapping using preferential looking, and a study of preschoolers’ (M = 48.6 months, N = 148) sensitivity to the accuracy of informants using verbal responses. Our goal was to evaluate the overall feasibility of moving developmental methods online, including our ability to host the research protocols, securely collect data, and reliably code the dependent measures, and parents’ ability to self-administer the studies. Due to procedural differences, these experiments should be regarded as user case studies rather than true replications. Encouragingly, however, all studies with all age groups suggested the feasibility of collecting developmental data online and the results of two of three studies were directly comparable to laboratory results.
Capacitated Metric Labeling

We introduce Capacitated Metric Labeling. As in Metric Labeling, we are given a weighted graph <i>G</i> = (<i>V, E</i>), a label set <i>L</i>, a semimetric <i>d</i><sub><i>l</i></sub> on this label set, and an assignment cost function &phis;: <i>V</i> x <i>L</i> → R<sup>+</sup>. The goal in Metric Labeling is to find an assignment <i>f</i>: <i>V</i> → <i>L</i> that minimizes a particular two-cost function. Here we add the additional restriction that each label <i>t</i><sub><i>i</i></sub> receive at most <i>l</i><sub><i>i</i></sub> nodes, and we refer to this problem as Capacitated Metric Labeling. Allowing the problem to specify capacities on each label allows the problem to more faithfully represent the classification problems that Metric Labeling is intended to model. Our main positive result is a polynomial-time, <i>O</i>(log |<i>V</i>|)-approximation algorithm when the number of labels is fixed, which is the most natural parameter range for classification problems. We also prove that it is impossible to approximate the value of an instance of Capacitated Metric Labeling to within any finite factor, if <i>P</i> ≠ <i>NP</i>. Yet this does not address the more interesting question of how hard Capacitated Metric Labeling is to approximate when we are allowed to violate capacities. To study this question, we introduce the notion of the "congestion" of an instance of Capacitated Metric Labeling. We prove that (under certain complexity assumptions) there is no polynomial-time approximation algorithm that can approximate the congestion to within <i>O</i>((log|<i>L</i>|)<sup>1/2−∈</sup>) (for any ∈ > 0) and this implies as a corollary that any polynomial-time approximation algorithm that achieves a finite approximation ratio must multiplicatively violate the label capacities by Ω((log |<i>L</i>|)<sup>1/2−∈</sup>). We also give a <i>O</i>(log |<i>L</i>|)-approximation algorithm for congestion.
Extending the transaction level modeling approach for fast communication architecture exploration

System-on-chip (SoC) designs are increasingly becoming more complex. Efficient on chip communication architectures are critical for achieving desired performance in these systems. System designers typically use Bus Cycle Accurate (BCA) models written in high level languages such as C/C++ to explore the communication design space. These models capture all of the bus signals and strictly maintain cycle accuracy, which is useful for reliable performance exploration but results in slow simulation speeds for complex designs, even when they are modeled using high level languages. Recently there have been several efforts to use the Transaction Level Modeling (TLM) paradigm for improving simulation performance of BCA models. However these BCA models capture a lot of details that can be eliminated when exploring communications architectures.
Texture Preserving Variational Denoising Using an Adaptive Fidelity Term

Denoising algorithms based on gradient dependent energy functionals, such as Perona-Malik and total variation denoising, modify images towards piecewise constant functions. Although edge sharpness and location is well preserved, important information, encoded in image features like textures or certain details, is often compromised in the process of denoising. We propose a mechanism that better preserves fine scale features in such denoising processes. This is accomplished by adding a spatially varying fidelity term that locally controls the extent of denoising over image regions according to their content. Local variance measures of the oscillatory part of the signal are used to compute the adaptive fidelity term. Our results show improvement in the signal-tonoise ratio over scalar fidelity term processes, and they are more appealing visually. This type of processing is relatively simple, can be used for a variety of tasks in PDE-based image processing and computer vision, and is stable and meaningful from a mathematical viewpoint.
A revised taxonomy of patients with chronic pain.

OBJECTIVE To examine the taxonomic categories derived from a reorganization of the popular and useful Multidimensional Pain Inventory (MPI)/Multiaxial Assessment of Pain (MAP) system. DESIGN Cluster-analytic procedures were utilized to analyze data from 976 pain patients who presented for treatment at a pain clinic. Ward's method was utilized followed by seeded and unseeded k-means procedures and a discriminant function analysis. RESULTS Three clusters were interpreted as: Interpersonally Focused, Stoic, and Adaptively Focused. Discriminant analyses followed by internal and external classification analyses provide evidence for the stability and replicability of the new clusters. Fisher's linear discriminant classification function coefficients were produced for clinical use. CONCLUSIONS Meaningful differences exist between the new MPI clusters and those previously reported. The results provide a contribution toward improvements on the original and popular MPI/MAP system.