Miracle-dz/UniFAR-FTUs huggingface dataset:
Sensitivity of modeled atmospheric nitrogen species and nitrogen deposition to variations in sea salt emissions in the North Sea and Baltic Sea regions

Abstract. Coarse sea salt particles are emitted ubiquitously from the ocean surface by wave-breaking and bubble-bursting processes. These particles impact the atmospheric chemistry by affecting the condensation of gas-phase species and, thus, indirectly the nucleation of new fine particles, particularly in regions with significant air pollution. In this study, atmospheric particle concentrations are modeled for the North Sea and Baltic Sea regions in northwestern Europe using the Community Multiscale Air Quality (CMAQ) modeling system and are compared to European Monitoring and Evaluation Programme (EMEP) measurement data. The sea salt emission module is extended by a salinity-dependent scaling of the sea salt emissions because the salinity in large parts of the Baltic Sea is very low, which leads to considerably lower sea salt mass emissions compared to other oceanic regions. The resulting improvement in predicted sea salt concentrations is assessed. The contribution of surf zone emissions is considered separately. Additionally, the impacts of sea salt particles on atmospheric nitrate and ammonium concentrations and on nitrogen deposition are evaluated. The comparisons with observational data show that sea salt concentrations are commonly overestimated at coastal stations and partly underestimated farther inland. The introduced salinity scaling improves the predicted Baltic Sea sea salt concentrations considerably. The dates of measured peak concentrations are appropriately reproduced by the model. The impact of surf zone emissions is negligible in both seas. Nevertheless, they might be relevant because surf zone emissions were cut at an upper threshold in this study. Deactivating sea salt leads to minor increases in NH3 + NH4+ and HNO3 + NO3− and a decrease in NO3− concentrations. However, the overall effect on NH3 + NH4+ and HNO3 + NO3− concentrations is smaller than the deviation from the measurements. Nitrogen wet deposition is underestimated by the model at most stations. In coastal regions, the total nitrogen deposition (wet and dry) is considerably affected by sea salt particles. Approximately 3–7 % of atmospheric nitrogen deposition into the North Sea is caused by sea salt particles. The contribution is lower in the Baltic Sea region. The stations in the EMEP network provide a solid basis for model evaluation and validation. However, for a more detailed analysis of the impact of sea salt particles on atmospheric nitrogen species, size-resolved measurements of Na+, NH4+, and NO3− are needed.
"Hot spot" in the PROP1 gene responsible for combined pituitary hormone deficiency.

As pituitary function depends on the integrity of the hypothalamic-pituitary axis, any defect in the development and organogenesis of this gland may account for a form of combined pituitary hormone deficiency (CPHD). Although pit-1 was 1 of the first factors identified as a cause of CPHD in mice, many other homeodomain and transcription factors have been characterized as being involved in different developmental stages of pituitary gland development, such as prophet of pit-1 (prop-1), P-Lim, ETS-1, and Brn 4. The aims of the present study were first to screen families and patients suffering from different forms of CPHD for PROP1 gene alterations, and second to define possible hot spots and the frequency of the different gene alterations found. Of 73 subjects (36 families) analyzed, we found 35 patients, belonging to 18 unrelated families, with CPHD caused by a PROP1 gene defect. The PROP1 gene alterations included 3 missense mutations, 2 frameshift mutations, and 1 splice site mutation. The 2 reported frameshift mutations could be caused by any 2-bp GA or AG deletion at either the 148-GGA-GGG-153 or 295-CGA-GAG-AGT-303 position. As any combination of a GA or AG deletion yields the same sequencing data, the frameshift mutations were called 149delGA and 296delGA, respectively. All but 1 mutation were located in the PROP1 gene encoding the homeodomain. Importantly, 3 tandem repeats of the dinucleotides GA at location 296-302 in the PROP1 gene represent a hot spot for CPHD. In conclusion, the PROP1 gene seems to be a major candidate gene for CPHD; however, further studies are needed to evaluate other genetic defects involved in pituitary development.
Black-box optimization of noisy functions with unknown smoothness

We study the problem of black-box optimization of a function f of any dimension, given function evaluations perturbed by noise. The function is assumed to be locally smooth around one of its global optima, but this smoothness is unknown. Our contribution is an adaptive optimization algorithm, POO or parallel optimistic optimization, that is able to deal with this setting. POO performs almost as well as the best known algorithms requiring the knowledge of the smoothness. Furthermore, POO works for a larger class of functions than what was previously considered, especially for functions that are difficult to optimize, in a very precise sense. We provide a finite-time analysis of POO's performance, which shows that its error after n evaluations is at most a factor of √ln n away from the error of the best known optimization algorithms using the knowledge of the smoothness.
DILATOMETER METHOD FOR DETERMINATION OF THERMAL COEFFICIENT OF EXPANSION OF FINE AND COARSE AGGREGATE

THE METHOD IS PARTICULARLY ADAPTABLE TO THE STUDY OF SANDS AND ALSO PROVIDES A MEANS OF OBTAINING AND TESTING A REPRESENTATIVE SAMPLE OF A HETEROGENEOUS COARSE AGGREGATE OR OF THE VARIOUS MINERALOGICAL PORTIONS COMPRISING THE COARSE AGGREGATE. IT DETERMINES THE CUBICAL THERMAL COEFFICIENT OF EXPANSION FROM WHICH THE MEAN LINEAR THERMAL EXPANSION MAY BE CALCULATED. WITH THE PRESENT APPARATUS, THE THERMAL COEFFICIENT IS MEASURED OVER A RANGE OF APPROXIMATELY 7 DEG. F. BOTH THE TEMPERATURE INCREMENT AND THE BASE TEMPERATURE USED IN THE DETERMINATION CAN BE EASILY MODIFIED. THE ACCURACY OF THE APPARATUS HAD BEEN VERIFIED BY THE COMPARISON OF RESULTS OBTAINED WITH MATERIALS OF KNOWN THERMAL COEFFICIENTS OF EXPANSION. THE THERMAL COEFFICIENTS OF EXPANSION OF VARIOUS FINE AND COARSE AGGREGATES ARE INCLUDED. /AUTHOR/
INSTRUMENTAL AND SENSORY CHARACTERIZATION OF COOKED POTATO TEXTURE

Uniaxial compression, Texture Profile Analysis (TPA) and chemical measurements were related to sensory texture evaluation of potato quality during storage. Principal component analysis grouped the varieties into three types of variation: mealiness versus firmness and springiness (PC1), moistness versus adhesiveness (PC2) and hardness versus adhesiveness and moistness (PC3). In uniaxial compression the variable ‘stress', ‘work up to fracture’ and ‘total work during compression’ described the same type of information in the data. These uniaxial data and most of the TPA data were highly correlated. Uniaxial compression data (stress, strain, modulus of deformability), starch structural data (area, roundness, aspect ratio), specific gravity and pectin methyl esterase activity discriminated between the varieties and harvest times. Partial Least Squares Regression showed stress, strain, modulus of deformability and specific gravity to be the most important variables in distinguishing between two groups of sensory texture attributes explaining 65% of the total variance in the sensory data. Coefficients of correlation between predicted and measured sensory attributes were in the range 0.36–0.79. The TPA data were not found to be relevant substitutions for the sensory attributes.
Fully dynamic algorithms for maintaining all-pairs shortest paths and transitive closure in digraphs

This paper presents the first fully dynamic algorithms for maintaining all-pairs shortest paths in digraphs with positive integer weights less than b. For approximate shortest paths with an error factor of (2+/spl epsiv/), for any positive constant /spl epsiv/, the amortized update time is O(n/sup 2/ log/sup 2/ n/log log n); for an error factor of (1+/spl epsiv/) the amortized update time is O(n/sup 2/ log/sup 3/ (bn)//spl epsiv//sup 2/). For exact shortest paths the amortized update time is O(n/sup 2.5/ /spl radic/(b log n)). Query time for exact and approximate shortest distances is O(1); exact time and approximate paths can be generated in time proportional to their lengths. Also presented is a fully dynamic transitive closure algorithm with update time O(n/sup 2/ log n) and query time O(1). The previously known fully dynamic transitive closure algorithm with fast query time has one-sided error and update time O(n/sup 2.28/). The algorithms use simple data structures, and are deterministic.
Properties of Co Substituted Bismuth Ferrite System by Rapid Liquid Phase Sintering

The multiferroic ceramic samples of Co substituted Bi0.9Nd0. 1Fe1-xCoxO3 ( x = 0.00, 0.03, 0.05, 0.07, 0.09, 0.10, 0.20 and 0.30) were prepared by a rapid liquid phase sintering technique. As Co content increases, the Bi0.9Nd0. 1Fe1-xCoxO3 samples have a structural transformation from rhombohedral (space group R3c) to cubic structure (space group I23). A small amount of Co substitution maintains the ferroelectric properties while high doping content deteriorates the ferroelectric behavior due to the attendant high leakage current caused by the valence fluctuation of Co ions. It is found that the remnant magnetization (Mr) is enhanced greatly from a value of 4.87  10-6 emu/g at x = 0.00 to 0.054 emu/g at x = 0.30.
Emergence of Minor Drug-Resistant HIV-1 Variants after Triple Antiretroviral Prophylaxis for Prevention of Vertical HIV-1 Transmission

Background WHO-guidelines for prevention of mother-to-child transmission of HIV-1 in resource-limited settings recommend complex maternal antiretroviral prophylaxis comprising antenatal zidovudine (AZT), nevirapine single-dose (NVP-SD) at labor onset and AZT/lamivudine (3TC) during labor and one week postpartum. Data on resistance development selected by this regimen is not available. We therefore analyzed the emergence of minor drug-resistant HIV-1 variants in Tanzanian women following complex prophylaxis. Method 1395 pregnant women were tested for HIV-1 at Kyela District Hospital, Tanzania. 87/202 HIV-positive women started complex prophylaxis. Blood samples were collected before start of prophylaxis, at birth and 1–2, 4–6 and 12–16 weeks postpartum. Allele-specific real-time PCR assays specific for HIV-1 subtypes A, C and D were developed and applied on samples of mothers and their vertically infected infants to quantify key resistance mutations of AZT (K70R/T215Y/T215F), NVP (K103N/Y181C) and 3TC (M184V) at detection limits of <1%. Results 50/87 HIV-infected women having started complex prophylaxis were eligible for the study. All women took AZT with a median duration of 53 days (IQR 39–64); all women ingested NVP-SD, 86% took 3TC. HIV-1 resistance mutations were detected in 20/50 (40%) women, of which 70% displayed minority species. Variants with AZT-resistance mutations were found in 11/50 (22%), NVP-resistant variants in 9/50 (18%) and 3TC-resistant variants in 4/50 women (8%). Three women harbored resistant HIV-1 against more than one drug. 49/50 infants, including the seven vertically HIV-infected were breastfed, 3/7 infants exhibited drug-resistant virus. Conclusion Complex prophylaxis resulted in lower levels of NVP-selected resistance as compared to NVP-SD, but AZT-resistant HIV-1 emerged in a substantial proportion of women. Starting AZT in pregnancy week 14 instead of 28 as recommended by the current WHO-guidelines may further increase the frequency of AZT-resistance mutations. Given its impact on HIV-transmission rate and drug-resistance development, HAART for all HIV-positive pregnant women should be considered.
Microbial TLR Agonists and Humoral Immunopathogenesis in HIV Disease

Although T cells are the primary and most-studied targets of the Human Immunodeficiency Virus (HIV), B cells, especially memory B lymphocytes, are also chronically depleted in the course of HIV disease. Although the lack of CD4+ T cell help may explain these deficiencies, intrinsic defects in B lymphocytes appear to contribute to B cell depletion and reduced antibody (Ab) production in the setting of HIV, especially of some antigens eliciting T cell-independent responses. The gut mucosal barrier is disrupted in HIV disease, resulting in increased systemic exposure to microbial products such as Toll-Like Receptor (TLR) agonists. The association of enhanced systemic levels of TLR agonists and B cell dysfunction in HIV disease is not understood. This review discusses the potential role of microbial TLR agonists in the B cell depletion, enhanced autoantibody production and impaired responses to vaccination observed in HIV-infected hosts. Increased microbial translocation in HIV infection may drive B cells to produce autoantibodies and increase susceptibilities of B cells to apoptosis through activation-induced cell death. Determining the mechanisms of B cell perturbations in HIV disease will inform the design of novel strategies of improve immune responses to vaccines, reduce opportunistic infections and slow disease progression.
Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients

Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.
Rapamycin and CTLA4Ig Synergize to Induce Stable Mixed Chimerism Without the Need for CD40 Blockade

The mixed chimerism approach achieves donor‐specific tolerance in organ transplantation, but clinical use is inhibited by the toxicities of current bone marrow (BM) transplantation (BMT) protocols. Blocking the CD40:CD154 pathway with anti‐CD154 monoclonal antibodies (mAbs) is exceptionally potent in inducing mixed chimerism, but these mAbs are clinically not available. Defining the roles of donor and recipient CD40 in a murine allogeneic BMT model, we show that CD4 or CD8 activation through an intact direct or CD4 T cell activation through the indirect pathway is sufficient to trigger BM rejection despite CTLA4Ig treatment. In the absence of CD4 T cells, CD8 T cell activation via the direct pathway, in contrast, leads to a state of split tolerance. Interruption of the CD40 signals in both the direct and indirect pathway of allorecognition or lack of recipient CD154 is required for the induction of chimerism and tolerance. We developed a novel BMT protocol that induces mixed chimerism and donor‐specific tolerance to fully mismatched cardiac allografts relying on CD28 costimulation blockade and mTOR inhibition without targeting the CD40 pathway. Notably, MHC‐mismatched/minor antigen‐matched skin grafts survive indefinitely whereas fully mismatched grafts are rejected, suggesting that non‐MHC antigens cause graft rejection and split tolerance.
Hypercalcemia in cats: a retrospective study of 71 cases (1991-1997).

A retrospective study was conducted to characterize the diseases, clinical findings, and clinicopathologic and ultrasonographic findings associated with hypercalcemia (serum calcium concentration >11 mg/dL) in 71 cats presented to North Carolina State University Veterinary Teaching Hospital. The 3 most common diagnoses were neoplasia (n = 21), renal failure (n = 18), and urolithiasis (n = 11). Primary hyperparathyroidism was diagnosed in 4 cats. Lymphoma and squamous cell carcinoma were the most frequently diagnosed tumors. Calcium oxalate uroliths were diagnosed in 8 of 11 cats with urolithiasis. Cats with neoplasia had a higher serum calcium concentration (13.5 +/- 2.5 mg/dL) than cats with renal failure or urolithiasis and renal failure (11.5 +/- 0.4 mg/dL; P < .03). Serum phosphorus concentration was higher in cats with renal failure than in cats with neoplasia (P < .004). Despite the fact that the majority of cats with uroliths were azotemic, their serum urea nitrogen and creatinine concentrations and urine specific gravity differed from that of cats with renal failure. Additional studies are warranted to determine the underlying disease mechanism in the cats we identified with hypercalcemia and urolithiasis. We also identified a small number of cats with diseases that are not commonly reported with hypercalcemia. Further studies are needed to determine whether an association exists between these diseases and hypercalcemia, as well as to characterize the underlying pathophysiologic mechanism for each disease process.
Progressing from brief assessments to extended experimental analyses in the evaluation of aberrant behavior.

The role of experimental analyses in guiding treatment is well established. However, not all experimental analyses yield conclusive results. Outcomes may be inconclusive due to time limitations that preclude extended observation and detailed experimental manipulations, or may result from interactions across experimental conditions, multiple control, or other unknown factors. In this study, we describe an assessment sequence that moves through four phases beginning with relatively brief (1 to 2 hr) analyses and culminating in extended analyses that may control for experimental confounding effects (e.g., interaction effects). Data illustrating the model are presented for 20 individuals referred for severe behavior problems including self-injury, aggression, stereotypy, and tantrums. Analyses were considered to be complete only when clear and replicable response patterns emerged. Results showed that clear and replicable response patterns emerged for 85% of the participants.
AUTOGENOUS HEALING PROPERTIES OF CONCRETE UNDER FLEXURAL LOADING

Autogenous healing of concrete structure was studied as a part of measures for reduction of the total life cycle cost. This study presents the measurement for autogenous healing ability by using the stiffness through three-point bending test. It shows the relation between autogenous healing ability and the initial loading age for three kinds of concrete, such as normal concrete, fly ash concrete and fly ash concrete with fiber. Furthermore, the size effect of specimens on autogenous healing is examined.
Lambertian reflectance and linear subspaces

We prove that the set of all reflectance functions (the mapping from surface normals to intensities) produced by Lambertian objects under distant, isotropic lighting lies close to a 9D linear subspace. This implies that the images of a convex Lambertian object obtained under a wide variety of lighting conditions can be approximated accurately with a low-dimensional linear subspace, explaining prior empirical results. We also provide a simple analytic characterization of this linear space. We obtain these results by representing lighting using spherical harmonics and describing the effects of Lambertian materials as the analog of a convolution. These results allow us to construct algorithms for object recognition based on linear methods as well as algorithms that use convex optimization to enforce non-negative lighting functions.
Phosphorylation-Dependent Regulation of G-Protein Cycle during Nodule Formation in Soybean[OPEN]

Components of heterotrimeric G-proteins directly interact with the soybean Nod factor receptors, which phosphorylate the regulatory RGS protein, thereby affecting G-protein cycle-dependent nodulation. Signaling pathways mediated by heterotrimeric G-protein complexes comprising Gα, Gβ, and Gγ subunits and their regulatory RGS (Regulator of G-protein Signaling) protein are conserved in all eukaryotes. We have shown that the specific Gβ and Gγ proteins of a soybean (Glycine max) heterotrimeric G-protein complex are involved in regulation of nodulation. We now demonstrate the role of Nod factor receptor 1 (NFR1)-mediated phosphorylation in regulation of the G-protein cycle during nodulation in soybean. We also show that during nodulation, the G-protein cycle is regulated by the activity of RGS proteins. Lower or higher expression of RGS proteins results in fewer or more nodules, respectively. NFR1 interacts with RGS proteins and phosphorylates them. Analysis of phosphorylated RGS protein identifies specific amino acids that, when phosphorylated, result in significantly higher GTPase accelerating activity. These data point to phosphorylation-based regulation of G-protein signaling during nodule development. We propose that active NFR1 receptors phosphorylate and activate RGS proteins, which help maintain the Gα proteins in their inactive, trimeric conformation, resulting in successful nodule development. Alternatively, RGS proteins might also have a direct role in regulating nodulation because overexpression of their phospho-mimic version leads to partial restoration of nodule formation in nod49 mutants.
Histological Subtypes of Lung Adenocarcinoma Have Differential 18F-Fluorodeoxyglucose Uptakes on the Positron Emission Tomography/Computed Tomography Scan

Introduction: Previous studies have shown that lung squamous cell carcinoma has higher 18F-fluorodeoxyglucose (FDG) uptake on positron emission tomography (PET) than adenocarcinoma. We hypothesized that histological subtypes of lung adenocarcinoma were also different in 18F-FDG uptake. Methods: Patients who had preoperative PET/computed tomography (CT) scan and had undergone complete resection for lung adenocarcinoma between April 2007 and December 2009 were enrolled in this study. Because of the limitation of spatial resolution on PET/CT, tumors less than 1 cm were excluded for analysis. Two independent classification systems were used to categorize histological subtypes of adenocarcinoma; one was modified from the current World Health Organization classification and the other used the morphological features of the terminal respiratory unit (TRU). The maximal standardized uptake value (SUVmax) on PET/CT and the glucose transporter type 1 (GLUT-1) expression of the tumors were measured and correlated to the histology of lung adenocarcinoma. Results: One hundred fifty-two patients with 153 primary lung adenocarcinomas were included. There was a significant difference in SUVmax among different histological subtypes. Namely, solid predominant adenocarcinomas had significantly higher SUVmax than those with other predominant histology (p < 0.001), and TRU-type adenocarcinomas had significantly lower SUVmax than non-TRU-type adenocarcinomas (p < 0.001). Consistently, GLUT-1 expression was higher in tumors with a solid growth pattern than those without (p < 0.001) and in tumors with non-TRU type than TRU type (p < 0.001). Conclusions: The histological subtypes of lung adenocarcinomas differ in GLUT-1 expression and 18F-FDG uptake on the PET/CT scan, suggesting that histological subtyping not only has morphological but also biological implications.