Miracle-dz/UniFAR-FTUs huggingface dataset:
Organic nutrients and excess nitrogen in the North Atlantic subtropical gyre

Abstract. To enable an accurate estimate of total excess nitrogen (N) in the North Atlantic, a new tracer TNxs is defined, which includes the contribution of organic nutrients to the assessment of N:P stoichiometric anomalies. We measured the spatial distribution of TNxs within the subtropical North Atlantic using data from a trans-Atlantic section across 24.5° N occupied in 2004. We then employ three different approaches to infer rates of total excess nitrogen accumulation using pCFC-12 derived ventilation ages (a TNxs vertical integration, a one end-member and a two-end member mixing model). Despite some variability among the different methods the dissolved organic nutrient fraction always contributes to about half of the TNxs accumulation, which is in the order of 9.38±4.18×1011 mol N y−1. We suggest that neglecting organic nutrients in stoichiometric balances of the marine N and P inventories can lead to systematic errors when estimating deviations of nitrogen excess or deficit relative to the Redfield ratio in the oceans. For the North Atlantic the inclusion of the organic fraction to the excess nitrogen pool leads to an upward revision of the N supply by N2 fixation to 10.2±6.9×1011 mol N y−1.
Metagenomic Profile of the Bacterial Communities Associated with Ixodes ricinus Ticks

Assessment of the microbial diversity residing in arthropod vectors of medical importance is crucial for monitoring endemic infections, for surveillance of newly emerging zoonotic pathogens, and for unraveling the associated bacteria within its host. The tick Ixodes ricinus is recognized as the primary European vector of disease-causing bacteria in humans. Despite I. ricinus being of great public health relevance, its microbial communities remain largely unexplored to date. Here we evaluate the pathogen-load and the microbiome in single adult I. ricinus by using 454- and Illumina-based metagenomic approaches. Genomic DNA-derived sequences were taxonomically profiled using a computational approach based on the BWA algorithm, allowing for the identification of known tick-borne pathogens at the strain level and the putative tick core microbiome. Additionally, we assessed and compared the bacterial taxonomic profile in nymphal and adult I. ricinus pools collected from two distinct geographic regions in Northern Italy by means of V6-16S rRNA amplicon pyrosequencing and community based ecological analysis. A total of 108 genera belonging to representatives of all bacterial phyla were detected and a rapid qualitative assessment for pathogenic bacteria, such as Borrelia, Rickettsia and Candidatus Neoehrlichia, and for other bacteria with mutualistic relationship or undetermined function, such as Wolbachia and Rickettsiella, was possible. Interestingly, the ecological analysis revealed that the bacterial community structure differed between the examined geographic regions and tick life stages. This finding suggests that the environmental context (abiotic and biotic factors) and host-selection behaviors affect their microbiome. Our data provide the most complete picture to date of the bacterial communities present within I. ricinus under natural conditions by using high-throughput sequencing technologies. This study further demonstrates a novel detection strategy for the microbiomes of arthropod vectors in the context of epidemiological and ecological studies.
Rational points of quiver moduli spaces

For a perfect field $k$, we study actions of the absolute Galois group of $k$ on the $\overline{k}$-valued points of moduli spaces of quiver representations over $k$; the fixed locus is the set of $k$-rational points and we obtain a decomposition of this fixed locus indexed by elements in the Brauer group of $k$. We provide a modular interpretation of this decomposition using quiver representations over division algebras, and we reinterpret this description using twisted quiver representations. We also see that moduli spaces of twisted quiver representations give different forms of the moduli space of quiver representations.
Crude glycerine in growing and finishing pigs feeding

Two experiments were carried out aiming to determine the nutritional value and to evaluate performance, carcass traits and economic feasibility of growing-finishing pigs fed on two types of crude glycerine (CG) which were made from vegetable oil (CGS), and mixed of animal fat + soybean oil (CGA). In Experiment I, a digestibility assay were carried out using 32 (24 test diet and 8 basal diet) cross breed pig (45.08 ± 4.11 kg). The experimental unit consisted of one pig, with a total of four experimental units per diet. Glycerine levels used in the digestibility assay were 6, 12, and 18% of the basal diet (corn + soybean meal based). The values (as-fed-basis) of DE and ME (kcal/kg) obtained were: CGS= 5,040 and 4,481; CGA= 5,234 and 4,707, respectively. In the Experiment II, 63 pigs, were allotted in a completely randomized design in 2 x 4 factorial scheme, with two types of crude glycerine (CGS and CGA) and four inclusion levels (3, 6, 9, and 12%). Additionally, it was formulated a control diet containg no glycerine (0%). There was no interaction (P≥0.05) among levels of CG and types of glycerine sources, and the regression analysis indicates no effects (P≥0.05) of crude glycerine inclusion on performance and carcass traits (backfat thickness and loin depth). The results suggest that it is feasible to use up to 12% of both crude glycerine (made from soybean oil and mixed) on growing-finishing pigs diet, without impairing performance and carcass traits, besides providing a reduction of about 11% on feeding cost.
Whole-Inactivated Influenza Virus Is a Potent Adjuvant for Influenza Peptides Containing CD8+ T Cell Epitopes

Influenza peptide antigens coding for conserved T cell epitopes have the capacity to induce cross-protective influenza-specific immunity. Short peptide antigens used as a vaccine, however, often show poor immunogenicity. In this study, we demonstrate that whole-inactivated influenza virus (WIV) acts as an adjuvant for influenza peptide antigens, as shown by the induction of peptide-specific CD8+ T cells in HLA-A2.1 transgenic mice upon vaccination with the influenza-M1-derived GILGFVFTL peptide (GIL), formulated with WIV. By screening various concentrations of GIL and WIV, we found that both components contributed to the GIL-specific T cell response. Whereas co-localization of the peptide antigen and WIV adjuvant was found to be important, neither physical association between peptide and WIV nor fusogenic activity of WIV were relevant for the adjuvant effect of WIV. We furthermore show that WIV may adjuvate T cell responses to a variety of peptides, using pools of either conserved wild-type influenza peptides or chemically altered peptide ligands. This study shows the potential of WIV as an adjuvant for influenza peptides. The simple formulation process and the solid safety record of WIV make this an attractive adjuvant for T cell peptides, and may also be used for non-influenza antigens.
Recruitment Potential of a Green Alga Ulva flexuosa Wulfen Dark Preserved Zoospore and Its Development

The recruitment potential and the ability of Ulva flexuosa Wulfen zoospores to survive darkness were tested under different conditions in the present study. The dark preserved zoospore was cultured under a two-factor experimental design to test the effect of salinity and nitrate, effect of salinity and phosphate, effect of light and salinity, and effect of light and phosphate. The recruitment (germination and growth) of zoospores was significantly affected by light and salinity. The nitrate concentration of 20 µmol. l−1 was found to initiate the process of germination and its subsequent growth and, its effect appeared greatest under 25 psu condition. While nitrate enhances the growth of biomass more than phosphate, both show a positive interactive effect on biomass increase when crossed with salinity. The combined effect of 25 psu salinity and 8 µmol. l−1 phosphate exhibited higher biomass growth. There was a significant effect of light and salinity on the biomass of zoospore, though there was no significant interaction between the two factors. There was an increase in biomass of growing zoospores to increase in light intensity and 80 µmol. m−2.s−1 of light intensity was considered optimal. Similarly, high light intensity condition favored higher biomass growth and there was significant interaction between light (80 µmol. m−2. s−1) and phosphate (4 µmol. l−1) in high salinity (35 psu) condition. The result of this study showed that dark preserved zoospores of U. flexuosa have the potential for recruitment and it gives us an understanding how different factors play a role in the process of recruitment.
Massive MIMO downlink 1-bit precoding for frequency selective channels

Quantized massive multiple-input-multiple-output (MIMO) systems are gaining more interest due to their power efficiency. We present a new precoding technique in a quantized downlink multi-user (MU) multiple-input-single-output (MISO) system with frequency selective channels. This work is restricted to 1-bit quantization at the transmitter and receiving PSK modulation schemes. The transmit signal vector is optimized for every desired received vector taking into account the 1-bit quantization. The optimization is based on maximizing the safety margin to the decision thresholds of the PSK modulation. This optimization is applied for the following three cases: symbol-wise processing as well as block-wise processing without and with cyclic prefix. Simulation results show a significant gain in terms of the uncoded bit-error-ratio (BER) compared to existing linear precoding techniques.
Cause-specific mortality in a large population-based cohort of patients with rheumatoid arthritis in Italy.

OBJECTIVES The aim of our study was to investigate cause-specific mortality in rheumatoid arthritis (RA) subjects living in Italy. METHODS We identified in the electronic archive of the Veneto Region patients aged 20-89 years who were exempt from co-payment for RA in January 2010, and linked them with the archive of causes of deaths of the period 2010-2015. Causes of death were coded according to the International Classification of Diseases, 10th Edition. Standardised mortality ratios (SMRs) with 95% confidence intervals were computed as the ratios between deaths observed in the cohort, and those expected according to age- and gender-specific regional mortality rates. RESULTS Overall, 16,098 residents diagnosed with RA and aged 20-89 years were enrolled in the cohort. The overall follow-up amounted to 88,599 person-years, with 2,142 registered decedents. The most common causes of death were circulatory diseases (36.6%), neoplasms (24.2%), and respiratory diseases (8.3%). Overall mortality was increased in RA subjects (SMR=1.42, confidence interval 1.36-1.48). Mortality was significantly increased from circulatory (SMR=1.56, 1.45-1.67), respiratory (SMR=1.83, 1.57-2.12), digestive (SMR=1.93, 1.60-2.32), infectious (SMR=2.34, 1.88-2.89), haematological diseases (SMR=3.22, 2.04-4.83), and falls (SMR=1.95, 1.19-3.01). RA was the underlying cause of death in 6.1% of all deaths in the cohort and was mentioned in 25.4% of death certificates. CONCLUSIONS In our study, a 42% excess risk of death was observed among subjects with RA compared with the general population. Cardiovascular disease is the primary cause of premature death in RA. Adverse effects of therapy and comorbidities should be adequately monitored in RA subjects.
Neural correlates of subjective CS/UCS association in appetitive conditioning

Explicit knowledge of conditioned stimulus (CS)/unconditioned stimulus (UCS) associations is proposed as important factor in classical conditioning. However, while previous studies have focused on its roles in fear conditioning, it has been neglected in the context of appetitive conditioning. The present functional magnetic resonance study aimed to investigate neural activation and functional connectivity linked to subjective CS/UCS association in appetitive conditioning. In total, 85 subjects participated in an appetitive acquisition procedure in which a neutral stimulus (CS+) was paired with a monetary reward, while another neutral stimulus (CS‐) was never paired with the reward. Directly afterwards, subjective CS/UCS association was assessed by measuring the extent to which the CS+ was thought to be associated with the UCS compared to the CS‐. Close relationships were established between subjective CS/UCS association and activations in the primary visual cortex (V1) during the early phase of conditioning and in the striatum during the late conditioning phase. In addition, we observed inverse relationships between subjective CS/UCS association and both V1/ventromedial prefrontal cortex (vmPFC) and striatal/vmPFC connectivity. The results suggest the involvement of decoupling vmPFC connectivity in reward learning in general and the roles of attentional processes in the formation of the subjective CS/UCS association during the early phase and reward prediction during the late phase of appetitive conditioning.
Feature selection for automotive object detection tasks - A study

For object detection in monocular images, the Boosted Cascade [1] has become the standard approach for driver assistance systems. This paper studies the discriminative power of different features for common automotive object detection tasks: pedestrian and vehicle detection using infrared cameras at night, as well as pedestrian and vehicle detection in daylight conditions. It is shown that the use of intra-stage information propagation with Activation History Features (AHFs) [2] significantly speeds up the detection at the same detection rate. Thus, AHFs offer a speedup at no cost.
Interaction of the Anticancer Plant Alkaloid Sanguinarine with Bovine Serum Albumin

Background Interaction of the iminium and alkanolamine forms of sanguinarine with bovine serum albumin (BSA) was characterized by spectroscopic and calorimetric techniques. Methodology/Principal Findings Formation of strong complexes of BSA with both iminium and alkanolamine forms was revealed from fluorescence quenching of sanguinarine. Binding parameters calculated from Stern-Volmer quenching method revealed that the neutral alkanolamine had higher affinity to BSA compared to the charged iminium form. Specific binding distances of 3.37 and 2.38 nm between Trp 212 (donor) and iminium and alkanolamine forms (acceptor), respectively, were obtained from Forster resonance energy transfer studies. Competitive binding using the site markers warfarin and ibuprofen, having definite binding sites, demonstrated that both forms of sanguinarine bind to site I (subdomain IIA) on BSA. Sanguinarine binding alters protein conformation by reducing the α-helical organization and increasing the coiled structure, indicating a small but definitive partial unfolding of the protein. Thermodynamic parameters evaluated from isothermal titration calorimetry suggested that the binding was enthalpy driven for the iminium form but favoured by negative enthalpy and strong favourable entropy contributions for the alkanolamine form, revealing the involvement of different molecular forces in the complexation. Conclusions/Significance The results suggest that the neutral alkanolamine form binds to the protein more favourably compared to the charged iminium, in stark contrast to the reported DNA binding preference of sanguinarine.
Radiographic, computed tomographic, and arthroscopic diagnosis of radioulnar incongruence in dogs with medial coronoid disease

OBJECTIVE To characterize radioulnar incongruence (RUI) in large dogs with medial coronoid disease (MCD) and determine the agreement between radiography, computed tomography (CT), and arthroscopy. STUDY DESIGN Prospective observational case series. ANIMALS Twenty-four large-breed dogs under 3 years of age with confirmed MCD. METHODS MCD and incongruence were evaluated by radiographs and CT. RUI was measured along the ulnar commissure, mid-body, and apex of the medial coronoid process (MCP) by CT and arthroscopy. Joints with RUI ≥ 2 mm were considered incongruent. Variables recorded during arthroscopic treatment included type of MCD, RUI, and modified Outerbridge score. Agreement between the 3 diagnostic imaging techniques was evaluated, and the association between RUI and cartilage damage was analyzed. RESULTS Single fragmentation was the most common MCD according to CT and arthroscopy. RUI was associated with degenerative joint disease according to CT and with cartilage damage according to arthroscopy. RUI was diagnosed in 26% of elbows by radiography, in 35% of elbows by CT, in 78% of elbows according to CT measurements of RUI ≥ 2 mm, and in 57% of joints by arthroscopy. RUI was most commonly detected at the ulnar commissure with CT and at the apex of the MCP with arthroscopy. Imaging modalities were in poor to fair agreement with arthroscopy when evaluating RUI. CONCLUSION CT and arthroscopy provided similar detection of MCD and cartilage disease but disagreed in the assessment and localization of RUI. CLINICAL SIGNIFICANCE CT does not reliably predict arthroscopic assessment of RUI and associated treatment decisions for MCD.
Immunoglobulin heavy chain variable region gene repertoire and B-cell receptor stereotypes in Indian patients with chronic lymphocytic leukemia

Abstract In chronic lymphocytic leukemia (CLL), the geographical bias in immunoglobulin heavy-chain variable (IGHV) gene usage lead us to analyze IGHV gene usage and B-cell receptor stereotypy in 195 patients from India. IGHV3, IGHV4, and IGHV1 families were the most frequently used. 20.5% sequences had stereotyped BCR and were clustered in 12 pre-defined and 6 novel subsets. Unmutated IGHV was significantly associated with reduced time to first treatment (p < 0.033) and poor overall survival (OS; p = 0.01). We observed a significant difference in OS between IGHV1, IGHV3, and IGHV4 family cases (p = 0.045) in early stage patients. Regarding subfamily usage, only IGHV1-69 expression was found to have statistically significant poor outcome (p = 0.017). Our results from the analysis of various molecular and clinical features suggest that the expression of specific IGHV gene influences the outcome in early stage CLL, and hence its assessment may be added to the clinical leukemia laboratory armamentarium.
Clinicopathologic Characteristics of Microsatellite Instable Gastric Carcinomas Revisited: Urgent Need for Standardization

Microsatellite instable gastric cancer (MSI-GC) is a specific molecular subtype of GC. We studied the phenotypes, genotypes, and clinicopathologic characteristics of MSI-GC in a white GC cohort and compared our findings with an extended literature review. The study cohort consisted of 482 patients. Specimens were available from 452 cases and were used for immunostaining (MLH1, PMS2, MSH2, MSH6) and molecular biological analyses (BAT-25, BAT-26, NR-21, NR-24, NR-27; Epstein-Barr virus in situ hybridization). Thirty-four (7.5%) GCs were MSI. Loss of MLH1 and/or PMS2 was found in 30 (88%) MSI-GC, 3 (9%) showed loss of MSH2 and/or MSH6. One (3%) MSI-GC was identified only by molecular biological testing. A single case was heterogeneous and contained microsatellite-stable and instable tumor areas. Twenty-one (62%) MSI-GCs showed unusual histologic features. MSI-GC was not found in diffuse-type or Epstein-Barr virus-positive GC. MSI-GC was significantly more prevalent in elderly patients, distal stomach, and was associated with a significantly lower number of lymph node metastases and a significantly better overall and tumor-specific survival. MSI-GC constitutes a small but relevant subgroup of GC with distinct clinicopathologic characteristics. Our literature review illustrates the shortcomings of missing standardized testing algorithms with prevalences of MSI-GC ranging from 0% to 44.5%. Future studies should test the hypothesis that patients with MSI-GCs may not need adjuvant/perioperative chemotherapy. However, this will require a standardized, quality-controlled diagnostic algorithm of MSI for GC.
Reinforcement Learning or Active Inference?

This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain.
The Effects of Eccentricity and Vergence Angle upon the Relative Tilt of Corresponding Vertical and Horizontal Meridia Revealed Using the Minimum Motion Paradigm

When the corresponding horizontal meridia of the two eyes are aligned, the corresponding vertical meridia are tilted outwards in a temporal direction, a phenomenon first described by Helmholtz. However, it is not known if this effect is confined to the principal meridia or whether the same relationship exists between corresponding horizontal and corresponding vertical meridia at eccentric retinal locations. We sought to address this issue by exploiting the technique of Nakayama (1977 Proceedings of the Society of Photo-Optical Instrument Engineers 120 2–9) in which the positions of alternating dichoptic images that produce minimal apparent motion were used to measure the relative tilt of corresponding meridia at a range of eccentricities up to ±16 deg away from the fovea. Stimuli were composed of dichoptic images, one containing a blank field and the other a pair of dots, which alternated at a rate of 0.63 Hz and the relative tilt (binocular orientation difference) between the pairs of dots presented to the two eyes was varied between ±11°. Nonius lines were used to maintain vergence angle, which was varied between 28 cm and infinity. Subjects judged which pair of alternating images produced the smallest amount of apparent motion (position change). It was found that at all eccentricities examined the corresponding horizontal meridia were generally aligned but the corresponding vertical meridia were consistently offset (extorted) by about ±2°. The tilts of corresponding principal meridia were typically unaffected when vergence angle was varied, indicating that little or no cyclovergence accompanied changes in horizontal vergence. The results suggest that the binocular correspondence system appears to be mapped by a horizontal shear distortion that extends to retinal locations at least as far as 16 deg away from the foveae. The invariant extorsion of corresponding principal vertical meridia with vergence state is consistent with previous suggestions that the empirical vertical horopter becomes progressively inclined with respect to the vertical as viewing distance increases.