Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissolved organic carbon fluxes in the Middle Atlantic Bight: An integrated approach based on satellite data and ocean model products

Continental margins play an important role in global carbon cycle, accounting for 15–21% of the global marine primary production. Since carbon fluxes across continental margins from land to the open ocean are not well constrained, we undertook a study to develop satellite algorithms to retrieve dissolved organic carbon (DOC) and combined these satellite data with physical circulation model products to quantify the shelf boundary fluxes of DOC for the U.S. Middle Atlantic Bight (MAB). Satellite DOC was computed through seasonal relationships of DOC with colored dissolved organic matter absorption coefficients, which were derived from an extensive set of in situ measurements. The multiyear time series of satellite‐derived DOC stocks (4.9 Teragrams C; Tg) shows that freshwater discharge influences the magnitude and seasonal variability of DOC on the continental shelf. For the 2010–2012 period studied, the average total estuarine export of DOC into the MAB shelf is 0.77 Tg C yr−1 (year). The integrated DOC tracer fluxes across the shelf boundaries are 12.1 Tg C yr−1 entering the MAB from the southwest alongshore boundary, 18.5 Tg C yr−1 entering the MAB from the northeast alongshore boundary, and 29.0 Tg C yr−1 flowing out of the MAB across the entire length of the 100 m isobath. The magnitude of the cross‐shelf DOC flux is quite variable in time (monthly) and space (north to south). The highly dynamic exchange of water along the shelf boundaries regulates the DOC budget of the MAB at subseasonal time scales.
Fast and incremental indexing in effective and efficient XML element retrieval systems

A method for fast and incremental indexing, with both effective and efficient query processing, is proposed for XML element retrieval. When frequent document updates occur on the Web, they must be handled to maintain the effectiveness of the search system. When new topics are added and document statistics change drastically, search accuracy is also reduced. We therefore consider a method not only for updating indices efficiently but also for processing queries effectively and efficiently. We construct indices for fast updating and propose a method for computing accurate term weights even under dynamically changing statistics. Experimental results show that our proposed system can handle document updates at low cost and search documents accurately even when their statistics change.
Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function

Glucocorticoid-induced TNF receptor ligand (GITRL), a recently identified member of the TNF family, binds to its receptor GITR on both effector and regulatory T cells and generates positive costimulatory signals implicated in a wide range of T cell functions. Structural analysis reveals that the human GITRL (hGITRL) ectodomain self-assembles into an atypical expanded homotrimer with sparse monomer–monomer interfaces. Consistent with the small intersubunit interfaces, hGITRL exhibits a relatively weak tendency to trimerize in solution and displays a monomer–trimer equilibrium not reported for other TNF family members. This unique assembly behavior has direct implications for hGITRL–GITR signaling, because enforced trimerization of soluble hGITRL ectodomain results in an ≈100-fold increase in its receptor binding affinity and also in enhanced costimulatory activity. The apparent reduction in affinity that is the consequence of this dynamic equilibrium may represent a mechanism to realize the biologically optimal level of signaling through the hGITRL–GITR pathway, as opposed to the maximal achievable level.
Discrepancies Between Randomized Controlled Trial Registry Entries and Content of Corresponding Manuscripts Reported in Anesthesiology Journals

BACKGROUND: Clinical trial registries have been created to reduce reporting bias. Study registration enables the examination of discrepancies between the original study design and the final results reported in the literature. The main objective of the current investigation is to compare the original clinical trial registrations and the corresponding published results in high-impact anesthesiology journals. Specifically, we examined the rates of major discrepancies (i.e., involving primary outcome, sample size calculation, or study intervention). METHODS: The 5 highest-impact factor anesthesiology journals (Anaesthesia, Anesthesia & Analgesia, Anesthesiology, British Journal of Anaesthesia, and Regional Anesthesia and Pain Medicine) were screened for randomized controlled trials published in 2013. A major discrepancy was defined as a difference in the content of the manuscript compared with the original entry in a clinical trial registry for at least one of the 3 areas: primary outcome, target sample size, and study intervention. The type of primary outcome discrepancy was further classified as adding/omitting measures or outcomes, downgrading/upgrading from primary to secondary outcomes, or changing the definition of the outcomes measured. RESULTS: Two hundred one articles were included in the final analysis. One hundred thirty of 201 (64%; 95% confidence interval [CI], 57%–71%) published clinical trials were not prospectively registered as recommended by the International Committee of Medical Journal Editors. Registration rates were significantly lower between studies performed in the United States, 15 of 40 (37%), compared with studies not performed in the United States, 92 of 161 (57%), P = 0.03. Fifty-two of 107 (48%; 95% CI, 39%–58%) registered trials had a major discrepancy when the published manuscript was compared with the clinical trial registration. Thirty-one of the 46 (67%; 95% CI, 51%–80%) primary outcome discrepancies had changes in the outcome with characteristics of reporting bias. CONCLUSIONS: We detected a high rate of major discrepancies between the published results and the original registered protocols for clinical trial manuscripts in high-impact anesthesiology journals. Future action to reduce the negative impact of reporting bias in the anesthesiology field is warranted.
Simultaneous valorization and biocatalytic upgrading of heavy vacuum gas oil by the biosurfactant‐producing Pseudomonas aeruginosa AK6U

Heavy vacuum gas oil (HVGO) is a complex and viscous hydrocarbon stream that is produced as the bottom side product from the vacuum distillation units in petroleum refineries. HVGO is conventionally treated with thermochemical process, which is costly and environmentally polluting. Here, we investigate two petroleum biotechnology applications, namely valorization and bioupgrading, as green approaches for valorization and upgrading of HVGO. The Pseudomonas aeruginosa AK6U strain grew on 20% v/v of HVGO as a sole carbon and sulfur source. It produced rhamnolipid biosurfactants in a growth‐associated mode with a maximum crude biosurfactants yield of 10.1 g l−1, which reduced the surface tension of the cell‐free culture supernatant to 30.6 mN m−1 within 1 week of incubation. The rarely occurring dirhamnolipid Rha–Rha–C12–C12 dominated the congeners’ profile of the biosurfactants produced from HVGO. Heavy vacuum gas oil was recovered from the cultures and abiotic controls and the maltene fraction was extracted for further analysis. Fractional distillation (SimDist) of the biotreated maltene fraction showed a relative decrease in the high‐boiling heavy fuel fraction (BP 426–565 °C) concomitant with increase in the lighter distillate diesel fraction (BP 315–426 °C). Analysis of the maltene fraction revealed compositional changes. The number‐average (Mn) and weight‐average (Mw) molecular weights, as well as the absolute number of hydrocarbons and sulfur heterocycles were higher in the biotreated maltene fraction of HVGO. These findings suggest that HVGO can be potentially exploited as a carbon‐rich substrate for production of the high‐value biosurfactants by P. aeruginosa AK6U and to concomitantly improve/upgrade its chemical composition.
Frequency Measurement Capability of a Fiber-Based Frequency Comb at 633 nm

A fiber-based frequency comb has been developed to measure the frequency of a 633-nm iodine-stabilized laser at the National Metrology Institute of Japan (NMIJ). The measured frequency was consistent with the previous results measured with a Ti:sapphire-based comb. The NMIJ comb was shipped to Australia for the validation of the measurement capability of the National Measurement Institute, Australia (NMIA) and NMIJ combs using a common microwave reference and a common optical frequency. Consequently, the frequency consistency of the two combs was approximately 8 times10-17. Furthermore, we demonstrate that an absolute mode number of the comb can easily and clearly be determined by using the two combs.
Fibulin-2 Is Dispensable for Mouse Development and Elastic Fiber Formation

ABSTRACT Fibulin-2 is an extracellular matrix protein belonging to the five-member fibulin family, of which two members have been shown to play essential roles in elastic fiber formation during development. Fibulin-2 interacts with two major constituents of elastic fibers, tropoelastin and fibrillin-1, in vitro and localizes to elastic fibers in many tissues in vivo. The protein is prominently expressed during morphogenesis of the heart and aortic arch vessels and at early stages of cartilage development. To examine its role in vivo, we generated mice that do not express the fibulin-2 gene (Fbln2) through homologous recombination of embryonic stem cells. Unexpectedly, the fibulin-2-null mice were viable and fertile and did not display gross and anatomical abnormalities. Histological and ultrastructural analyses revealed that elastic fibers assembled normally in the absence of fibulin-2. No compensatory up-regulation of mRNAs for other fibulin members was detected in the aorta and skin tissue. However, in the fibulin-2 null aortae, fibulin-1 immunostaining was increased in the inner elastic lamina, where fibulin-2 preferentially localizes. The results demonstrate that fibulin-2 is not required for mouse development and elastic fiber formation and suggest possible functional redundancy between fibulin-1 and fibulin-2.
Minimization of Antenna Quality Factor

Optimal currents on arbitrarily shaped radiators with respect to the minimum quality factor are found using a simple and efficient procedure. The solution starts with a reformulation of the problem of minimizing quality factor <inline-formula> <tex-math notation="LaTeX">$Q$ </tex-math></inline-formula> as an alternative, so-called dual, problem. Taking advantage of modal decomposition and group theory, it is shown that the dual problem can easily be solved and always results in minimal quality factor <inline-formula> <tex-math notation="LaTeX">$Q$ </tex-math></inline-formula>. Moreover, the optimization procedure is generalized to minimize quality factor <inline-formula> <tex-math notation="LaTeX">$Q$ </tex-math></inline-formula> for embedded antennas, with respect to the arbitrarily weighted radiation patterns, or with prescribed magnitude of the electric and magnetic near fields. The obtained numerical results are compatible with previous results based on the composition of modal currents, convex optimization, and quasi-static approximations; however, using the methodology in this paper, the class of solvable problems is significantly extended.
Cloning, nucleotide sequence, and regulation of the Bacillus subtilis pbpF gene, which codes for a putative class A high-molecular-weight penicillin-binding protein

The partial nucleotide sequence of a gene encoding a Bacillus subtilis homolog to the Escherichia coli ponA gene, encoding penicillin-binding protein 1A, was previously reported. The remaining part of this gene, termed pbpF, was isolated, and its nucleotide sequence was completed. Deletion of this gene did not alter the profile of B. subtilis penicillin-binding proteins observed after gel electrophoresis and resulted in no observable phenotype. A transcriptional pbpF-lacZ fusion was weakly expressed during vegetative growth. Expression diminished during the first hours of sporulation but was slightly induced in the forespore compartment during late sporulation. This sporulation expression was dependent on spoIIIG, which encodes the forespore-specific transcription factor sigma G. A single transcription start site which was apparently directly dependent on E sigma A was detected in vegetative cells.
Equilibrium Labor Market Search and Health Insurance Reform

We present and empirically implement an equilibrium labor market search model where risk-averse workers facing medical expenditure shocks are matched with firms making health insurance coverage decisions. We use our estimated model to evaluate the equilibrium impact of many health care reform proposals, including the 2010 Affordable Care Act (ACA). We use the estimates of the early impact of the ACA as a model validation. We find that income-based subsidies for health insurance premiums are crucial for the sustainability of the ACA, while the ACA can still substantially reduce the uninsured rate without the individual or the employer mandate.
Nuclear Receptor DAX-1 Recruits Nuclear Receptor Corepressor N-CoR to Steroidogenic Factor 1

ABSTRACT The orphan nuclear receptor steroidogenic factor 1 (SF-1) is a critical developmental regulator in the urogenital ridge, because mice targeted for disruption of the SF-1 gene lack adrenal glands and gonads. SF-1 was recently shown to interact with DAX-1, another orphan receptor whose tissue distribution overlaps that of SF-1. Naturally occurring loss-of-function mutations of the DAX-1 gene cause the human disorder X-linked adrenal hypoplasia congenita (AHC), which resembles the phenotype of SF-1-deficient mice. Paradoxically, however, DAX-1 represses the transcriptional activity of SF-1, and AHC mutants of DAX-1 lose repression function. To further investigate these findings, we characterized the interaction between SF-1 and DAX-1 and found that their interaction indeed occurs through a repressive domain within the carboxy terminus of SF-1. Furthermore, we demonstrate that DAX-1 recruits the nuclear receptor corepressor N-CoR to SF-1, whereas naturally occurring AHC mutations of DAX-1 permit the SF-1–DAX-1 interaction, but markedly diminish corepressor recruitment. Finally, the interaction between DAX-1 and N-CoR shares similarities with that of the nuclear receptor RevErb and N-CoR, because the related corepressor SMRT was not efficiently recruited by DAX-1. Therefore, DAX-1 can serve as an adapter molecule that recruits nuclear receptor corepressors to DNA-bound nuclear receptors like SF-1, thereby extending the range of corepressor action.
Doppler Mode Pulse Sequences Mitigate Glomerular Capillary Hemorrhage in Contrast-Aided Diagnostic Ultrasound of Rat Kidney

Glomerular capillary hemorrhage (GCH) induced in rat kidney by diagnostic ultrasound involving contrast agent destruction was characterized for different modes to explore possible mitigation strategies. Anesthetized hairless rats were scanned at 2.5 MHz in a water bath with contrast agent infused at 10 mul/kg/minute via tail vein. B mode flash echo imaging (FEI), color Doppler (CD) FEI and realtime Doppler imaging at 1 frame per second were tested, which had image pulse sequences of approximately 0.53 ms, 15.8 ms, and 83.5 ms duration, respectively. Bioeffects endpoints included grossly observed blood-filled tubules, histological evaluation of GCH, and detection of hematuria. B mode FEI for 1 minute induced GCH in 38.6plusmn17. 1% of glomeruli in histology from the scan plane for a peak rarefactional pressure amplitude (RPA) of 2.6 MPa. The threshold for GCH was approximately 1.5 MPa, confirmed by 10-minute exposure with agent infusion. Paradoxically, CD mode FEI delivered many more pulses but produced less GCH (P < 0.02), and real-time Doppler mode induced only 5.3plusmn3. 8% (P < 0.005). Hematuria results followed the GCH trends. These findings indicate a promising strategy, which is to use relatively slow ramp-up of pulse RPAs in agent-destroying image pulse sequences, for mitigating potential bioeffects in contrast-aided diagnostic ultrasound.
Consequences of clonality for sexual fitness: Clonal expansion enhances fitness under spatially restricted dispersal

Clonality is a pervasive feature of sessile organisms, but this form of asexual reproduction is thought to interfere with sexual fitness via the movement of gametes among the modules that comprise the clone. This within-clone movement of gametes is expected to reduce sexual fitness via mate limitation of male reproductive success and, in some cases, via the production of highly inbred (i.e., self-fertilized) offspring. However, clonality also results in the spatial expansion of the genetic individual (i.e., genet), and this should decrease distances gametes and sexually produced offspring must travel to avoid competing with other gametes and offspring from the same clone. The extent to which any negative effects of clonality on mating success might be offset by the positive effects of spatial expansion is poorly understood. Here, we develop spatially explicit models in which fitness was determined by the success of genets through their male and female sex functions. Our results indicate that clonality serves to increase sexual fitness when it is associated with the outward expansion of the genet. Our models further reveal that the main fitness benefit of clonal expansion might occur through the dispersal of offspring over a wider area compared with nonclonal phenotypes. We conclude that, instead of interfering with sexual reproduction, clonal expansion should often serve to enhance sexual fitness.
Structured telephone support or non-invasive telemonitoring for patients with heart failure

Heart failure is a common and growing problem, worldwide, often leading to repeated hospitalisations, reduced quality of life, disability, loss of independence and shortened life expectancy. Managing heart failure is costly and complex for individual patients, their families and healthcare systems. A range of pharmacological agents, devices and disease management programmes have proven to be effective but are not available to all patients. Non-invasive telemonitoring and structured telephone support for patients with heart failure have been researched for almost two decades; however the jury still appears to be out for the use of this intervention in clinical practice.1 The effectiveness of structured telephone support and non-invasive telemonitoring to reduce hospitalisations and mortality in patients with heart failure was assessed by a recent Cochrane review.2 This review was undertaken as an update to a previously published version. Randomised controlled trials (RCTs) that compared structured telephone support or non-invasive telemonitoring to standard practice were included. Studies were excluded if the telemonitoring intervention included other interventions such as home visits or frequent clinic visits or implanted monitoring devices. Compared with the previously published Cochrane review, 17 new studies were identified and 24 had been included in the previous review (total of 41 studies). Two studies were multiarm and included both structured telephone support and telemonitoring; hence there were 43 comparisons in the review. The primary outcomes included all-cause mortality and all-cause and heart failure related hospitalisations which were analysed using fixed-effects models. The review demonstrated that both non-invasive telemonitoring and structured telephone support offer statistically and clinically meaningful benefits to people with heart failure.2 For non-invasive telemonitoring, a 20% reduction in the risk of all-cause mortality was observed (Relative Risk (RR) 0.80, 95% Confidence Interval (CI) 0.68 to 0.94; participants=3740; studies=17; I2=24%; Grading of Recommendations Assessment, Development and …
SVCCA: Singular Vector Canonical Correlation Analysis for Deep Understanding and Improvement

With the continuing empirical successes of deep networks, it becomes increasingly important to develop better methods for understanding training of models and the representations learned within. In this paper we propose Singular Vector Canonical Correlation Analysis (SVCCA), a tool for quickly comparing two representations in a way that is both invariant to affine transform (allowing comparison between different layers and networks) and fast to compute (allowing more comparisons to be calculated than with previous methods). We deploy this tool to measure the intrinsic dimensionality of layers, showing in some cases needless over-parameterization; to probe learning dynamics throughout training, finding that networks converge to final representations from the bottom up; to show where class-specific information in networks is formed; and to suggest new training regimes that simultaneously save computation and overfit less.
Inclusion levels and modes of whole grain incorporation into wheat-based rations differentially influence the performance of broiler chickens

ABSTRACT 1. The objective was to compare three whole grain (WG) inclusion levels (7.5, 15 and 30%) offered to broiler chickens by three modes of WG incorporation: (i) pre-pellet WG inclusion, (ii) post-pellet WG inclusion as a blend of WG and pelleted concentrate and (iii) post-pellet WG inclusion where WG and pelleted concentrate were provided in separate feed trays against a ground-grain, wheat-based control diet. 2. Ten dietary treatments were offered to 6 replicate cages (6 birds per cage) of male Ross 308 chickens from 7 to 28 d post-hatch. The effects of treatment on relative gizzard weights, gizzard contents, pancreatic weights and pH of gizzard digesta were monitored. Parameters of growth performance, nutrient utilisation (apparent metabolisable energy [AME], metabolisable to gross energy [ME:GE] ratios, nitrogen [N] retention and N-corrected AME [AMEn]), apparent starch and protein (N) digestibility coefficients and disappearance rates in for small intestinal segments and concentrations of free amino acids in plasma taken from the anterior mesenteric vein were determined. 3. Whole grain feeding (WGF) did not influence weight gain, but 30% post-pellet blended and 15 and 30% post-pellet separated treatments significantly depressed (P < 0.05) feed intakes while the 30% post-pellet separated treatment improved (P < 0.01) feed conversion ratios (FCR). WGF regimes significantly increased relative gizzard weights. 4. Overall, WGF generated profound responses in AME, ME:GE ratios, N retention and AMEn that were highly correlated with relative gizzard weights. In general, WGF improved starch and protein (N) digestibilities and again there were some correlations with these outcomes and relative gizzard weights. 5. Post-pellet WG inclusions where WG and pelleted concentrate were offered separately provided chickens with the opportunity to choice feed. Birds showed a preference for the relatively high-protein pelleted concentrate and at 30% WG, this resulted in an improvement in FCR of 7.69% (1.260 versus 1.365; P < 0.001) relative to the ground-grain control diet.