Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic variation of residual feed consumption in a selected Finnish egg-layer population.

The purpose of the study was to estimate the heritability of residual feed consumption (RFC) and the genetic correlations between RFC and economically important traits. The genetic progress after four generations of selection for RFC and the changes in economically important traits were also investigated. A selection experiment for RFC was carried out from 1983 to 1987. The total data consisted of 3,750 birds and 2,661 records. The (co)variance components were calculated using derivative-free bivariate animal model restricted maximum likelihood (REML). Breeding values were estimated for calculating genetic progress in RFC and correlated responses in the other traits. The heritability of RFC calculated from the whole recorded period (16 to 42 wk) and using all 2,661 records was . 46 (+/- .04). The genetic correlations between RFC and egg mass, number of eggs, egg weight, and body weight were not significant. The genetic correlation between RFC and feed consumption was . 50 (+/- .04). The breeding value estimates indicated a moderate genetic progress in RFC due to selection. Feed consumption was decreased and body weight gain showed reduction in the last two generations. No change could be found in egg mass, number of eggs, egg weight, age at first egg, or body weight.
FixaTons: A collection of Human Fixations Datasets and Metrics for Scanpath Similarity

In the last three decades, human visual attention has been a topic of great interest in various disciplines. In computer vision, many models have been proposed to predict the distribution of human fixations on a visual input. Recently, thanks to the creation of large collections of data, machine learning algorithms have obtained state-of-the-art performance on the task of saliency map estimation. On the other hand, computational models of scanpath are much less studied. Works are often only descriptive or task specific. Computational models of scanpath with general purpose are present in the literature, but are then evaluated in tasks of saliency prediction, losing therefore information about the dynamics and the behaviour. This is due to the fact that the scanpath is harder to model because it must include the description of a dynamic. In addition to the difficulty of the problem itself, two technical reasons have limited the research. The first reason is the lack of robust and uniformly used set of metrics to compare the similarity between scanpath. The second reason is the lack of sufficiently large and varied scanpath datasets. In this report we want to help in both directions. We present FixaTons, a large collection of human scanpaths (and saliency maps). It comes along with a software library for easy data usage, statistics calculation and measures for scanpaths (and saliency maps) similarity.
Phylogenetic analysis as a forensic tool in HIV transmission investigations

&NA; Because HIV is a fast-evolving virus, HIV genomic sequences of several individuals can be used to investigate whether they belong to a transmission network. Since the infamous ‘Florida dentist case’ in the beginning of the 1990s, phylogenetic analyses has been recurrently used in court settings as a forensic tool in HIV transmission investigations, for example cases where one or more complainants allege that a defendant has unlawfully infected them with HIV. Such cases can arise both in the context of HIV-specific criminal laws – in countries where transmission of HIV infection is specifically criminalized – or in the context of general laws, for example, by applying physical or sexual assault laws to HIV-related cases. Although phylogenetic analysis as a forensic technique for HIV transmission investigations has become common in several countries, the methodologies have not yet been standardized, sometimes giving rise to unwarranted conclusions. In this literature review, we revisit HIV court case investigations published in the scientific literature, as well as the methodological aspects important for the application and standardization of phylogenetic analyses methods as a forensic tool. Phylogenetic methodologies are improving quickly, such that more recently, phylogenetic relatedness, directionality of transmission and timing of nodes in the tree are used to assess whether the phylogenetic transmission analysis is consistent with or contradicting the charges. We find that there has been a lack of consistency between methods used in court case investigations and that it is essential to define guidelines to be used by phylogenetic forensic experts in HIV transmission cases in court.
Linked Data Contracts to Support Data Protection and Data Ethics in the Sharing of Scientific Data

In light of the new EU General Data Protection Regulation (GDPR) [1] there are certain challenges in relation to the sharing of scientific data. For a data controller in a research institute, the requirement to monitor, implement and demonstrate conformance to the provisions of data subjects’ rights represents a major upshift in the complexity of research data management. We are trying to address the issues by analysing the details of data subject rights in GDPR fol-lowed by extending existing linked open data vocabularies. We are proposing a concept of machine- readable data protection rights contract through introducing Data Protection Rights Language (DPRL).
Resistance against Salmonella enteritidis cecal colonization in Leghorn chicks by vent lip application of cecal bacteria culture.

Leghorn chicks were treated with cultures of cecal bacteria from adult chickens by crop gavage, upper body spray, or vent lip application on the day of hatch. The chicks were challenged orally with 10(4) Salmonella enteritidis (SE) at 3 d of age and evaluated for SE cecal colonization at 10 d of age. The concentration of volatile fatty acids (VFA) in the cecal contents was determined on the day after culture treatment and at 10 d of age. Compared with controls, SE colonization was significantly decreased in each of the treatment groups. Vent lip application of a single . 05-mL drop of cecal bacteria culture resulted in resistance against SE challenge comparable to crop gavage or spray treatment with . 5 mL of culture. Resistance to SE challenge was directly associated with the concentrations of total VFA and propionic acid in the cecal contents of the treated chicks on the day after culture treatment. The results indicated that cecal bacteria from adult chickens that increase SE colonization resistance may rapidly become established in the ceca of newly hatched chicks following contact with the vent lips.
Synthesis of bismuth vanadate as visible light photocatalyst

Bismuth Vanadate (BiVO4) photocatalyst was synthesized by precipitation methods. Two different sources of bismuth namely bismuth acetate and bismuth nitrate pentahydrate were used. The bismuth solutions were mixed with ammonium metavanadate solution before being titrated against ammonium hydrogen carbonate solution. The precipitate formed using bismuth acetate (B1)was calcined at 450 oC and that of bismuth nitrate was calcined at 450oC (B2) and 300oC (B3) under air flow for 4h.The resulting powder were characterized by XRD, FESEM, IR and its surface area. XRD pattern analysis showed that all BiVO4 sample produced are of monoclinic phase and the FESEM images showed that the particles were agglomerated. The surface area of BiVO4 produced from bismuth nitrate pentahydrate was higher (3.9 m2/g) than that produced from bismuth acetate (2.7 m2/g). Photocatalytic activities of the synthesized BiVO4 were evaluated by photodegrading Methylene Blue dye (MB) under visible light irradiation. The highest photocatalytic activity was observed when using B3 as photocatalyst with percentage removal of 34%.
Implantable Device-Related Infection

ABSTRACT Over half of the nearly two million healthcare-associated infections can be attributed to indwelling medical devices. In this review, we highlight the difficulty in diagnosing implantable device-related infection and how this leads to a likely underestimate of the prevalence. We then provide a length-scale conceptualization of device-related infection pathogenesis. Within this conceptualization we focus specifically on biofilm formation and the role of host immune and coagulation systems. Using this framework, we describe how current and developing preventative strategies target specific processes along the entire length-scale. In light of the significant time horizon for the development and translation of new preventative technologies, we also emphasize the need for parallel development of in situ treatment strategies. Specific examples of both preventative and treatment strategies and how they align with the length-scale conceptualization are described.
Resilience strategies in the face of short- and long-term change: out-migration and fisheries regulation in Alaskan fishing communities

Historically, communities persisted in remote, isolated areas of Alaska in large part because of the abundance of marine and terrestrial resources, as well as the ability of local people to opportunistically access those resources as they became available. Species switching and the ability to shift effort away from fisheries during poor years allowed local residents to diversify their livelihoods in the face of uncertainties and ecological change. The advent of modern fisheries management, which views Alaskan fisheries as the property of all citizens of the United States, has fundamentally altered the relationship of place-based communities to fishery resources. Local access to fisheries has been particularly affected by the development of transferable fishing privileges, making it possible for fishing rights to leave place-based communities through the choices of individual community members to sell or to move away. When fishing communities in Alaska lose active fishing businesses, over time the loss of various types of community capital will follow, including human, social, cultural, technical, and financial capital. In some cases, communities are able to adapt or transform through diversification of their local economies. In other cases, no alternatives to a fishery-based economy are accessible. We have used resilience theory to explore drivers of change affecting Alaskan fishing communities. Emphasis was placed on two primary change drivers, the regulatory environment and rural out-migration, as well as their interconnections and their impacts on individuals, communities, and the larger social-ecological system. We summarized several government programs that have been implemented to support the continued participation of communities in Alaskan fisheries. In addition, we reviewed informal and private-sector efforts to generate resilience strategies that can facilitate new entry into fisheries or retain fishing businesses and fishing rights within communities, as well as respond to increasing uncertainty related to the global market and climate changes.
Synergism between aflatoxin and ochratoxin A in broiler chickens.

A 2 X 2 factorial experimental design consisting of four treatments (0, 2.5 microgram/g aflatoxin, 2.0 microgram/g ochratoxin A, and 2.5 microgram/g aflatoxin + 2.0 microgram/g ochratoxin A) with six replicates of 10 birds each was used to evaluate the synergism between aflatoxin and ochratoxin A. The chicks (Hubbard X Hubbard) were maintained on these dietary treatments from hatching until they reached 3 weeks of age, when the experiment was terminated. The size of the liver, spleen, pancreas, and proventriculus was significantly (P less than .05) altered by the individual toxins; however, a synergistic effect on the size of these organs was not observed. The kidney and gizzard were sensitive to the coincident exposure to these mycotoxins and were significantly (P less than .05) enlarged. The kidney was the most sensitive organ to the combined toxicity of aflatoxin and ochratoxin A, and nephropathy was the most important characteristic of this interaction. The synergism between aflatoxin and ochratoxin A significantly (P less than .05) decreased growth rate and numerically increased mortality, demonstrating the enhanced toxicity of cocontaminated feed. Liver lipid levels were significantly (P less than .05) increased by aflatoxin and decreased by ochratoxin A. The interaction of both mycotoxins on this parameter was significant (P less than .05) and the combined effect demonstrates that ochratoxin A inhibited lipid accumulation normally induced by aflatoxin. The data show that toxicity-enhancing synergisms exist between mycotoxins and that symptom patterns are altered during multiple mycotoxicoses. The data also demonstrate that nephropathy is the primary effect of this interaction and, thus, is of diagnostic importance.
Complex Gaussian Processes for Regression

In this paper, we propose a novel Bayesian solution for nonlinear regression in complex fields. Previous solutions for kernels methods usually assume a complexification approach, where the real-valued kernel is replaced by a complex-valued one. This approach is limited. Based on the results in complex-valued linear theory and Gaussian random processes, we show that a pseudo-kernel must be included. This is the starting point to develop the new complex-valued formulation for Gaussian process for regression (CGPR). We face the design of the covariance and pseudo-covariance based on a convolution approach and for several scenarios. Just in the particular case where the outputs are proper, the pseudo-kernel cancels. Also, the hyperparameters of the covariance can be learned maximizing the marginal likelihood using Wirtinger’s calculus and patterned complex-valued matrix derivatives. In the experiments included, we show how CGPR successfully solves systems where the real and imaginary parts are correlated. Besides, we successfully solve the nonlinear channel equalization problem by developing a recursive solution with basis removal. We report remarkable improvements compared to previous solutions: a 2–4-dB reduction of the mean squared error with just a quarter of the training samples used by previous approaches.
Effecti ve optical properties of dilute and dense polymer-gold nanoparticle films: theory and experiments

We study the effective optical properties of composite films made of 14-nm spherical gold nanoparticle in a polymer matrix, both in dilute (5% gold fraction) and dense (20%) regimes. Optical indices and permittivities are extracted from spectroscopic ellipsometry measurements and show effective resonant properties around the plasmon resonance, exhibiting effective negative permittivity for dense samples in a finite frequency range (finite-band metallic behaviour). Measurements are compared to Maxwell-Garnett (MG) predictions: we show that the classical MG formula does not reproduce the experimental results, even in the dilute regime, due to nanoagregation effects in the samples which entails couplings between particles. Since couplings create deformations of the polarizability tensor of the individual particles, we propose to take them into account in an empirical way using a modified MG formula based on a distribution of ellipsoids. We show that this modified Maxwell Garnett model works sucessfully, allowing for good fits of the experimental data in the dilute regime (using a distribution of ellispoidal polarizabilities centered on a mean isotropic polarizability) as well as in the dense regime up to 20% (using polarizability distribution centered on a mean ellipsoidal polarizability).
Neuroprotective Effects of C-terminal Domain of Tetanus Toxin on Rat Brain Against Motorneuron Damages After Experimental Spinal Cord Injury

Study Design. Experimental animal study investigating the efficacy of C-terminal domain of tetanus toxin application as neuroprotective effects on rat brain in a model of spinal cord injury (SCI). Objective. The aim of the present study was to investigate the possible role of C-terminal domain of tetanus toxin (Hc-TeTx) on cell death mechanisms including apoptosis and autophagy following SCI. Summary of Background Data. Traumatic SCI can lead to posttraumatic inflammation, oxidative stress, motor neuron apoptosis, necrosis, and autophagy of tissue. To promote and enhance recovery after SCI, recent development of devices and therapeutic interventions are needed. Methods. Twenty-eight adult rats were divided into four groups (n = 7 each) as follows: sham, trauma (SCI), SCI + Hc-TeTx, and SCI + methylprednisolone groups. The functional neurological deficits due to the SCI were assessed by behavioral analysis using the Basso, Beattie and Bresnahan (BBB) open-field locomotor test. The alterations in pro-/anti-apoptotic and autophagy related-protein levels were measured by Western blotting technique. Results. In this study, Hc-TeTx promotes locomotor recovery and motor neuron survival of SCI rats. Hc-TeTx also decreased expression of bax, bad, bak, cleaved caspase-3, Ask1, and autophagy-related proteins including Atg5 and LC3II in brain. Our study provides an evidence that cell death mechanisms play critical roles in SCI and that the nontoxic peptides including Hc-TeTx may exert protective effect and decrease cell death following SCI. Conclusion. Our preliminary findings suggest a possible therapeutic agent to improve survival after spinal cord trauma, but further analysis are still needed to evaluate the difference between acute and chronic injuries. Level of Evidence: N/A
Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques

ABSTRACT Introduction: While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered: This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g., SWATH). Corresponding bioinformatics strategies, as well as application in biological and clinical studies are presented. Expert commentary: Nascent application of highly-multiplexed untargeted DIA, such as SWATH, for accurate protein quantification from clinically relevant and disease-related samples shows great potential to comprehensively investigate biomarker candidates and understand disease.
pANCA and ASCA in Children with IBD-Unclassified, Crohn's Colitis, and Ulcerative Colitis—A Longitudinal Report from the IBD Porto Group of ESPGHAN

Introduction:No study to date has evaluated perinuclear antineutrophil cytoplasmic antibody (pANCA) and anti–Saccharomyces cerevisiae antibody (ASCA) in pediatric inflammatory bowel disease–unclassified (IBDU) as compared with Crohn's colitis (CC) and ulcerative colitis (UC), which represent the diagnostic challenge. We aimed to explore the diagnostic utility of serology and to assess whether serology can predict disease severity in these subgroups. Methods:This was a multicenter retrospective longitudinal study including 406 children with inflammatory bowel diseases (IBD) from 23 centers affiliated with the Porto group of European Society of Pediatric Gastroenterology, Hepatology and Nutrition (mean age 10.5 ± 3.9, 54% males); 117 (29%) with CC, 143 (35%) with UC, and 146 (36%) with IBDU. Median follow-up period was 2.8 years (interquartile range, 1.6–4.2). Results:The most prevalent serologic profile in IBDU was pANCA−/ASCA− (41%), followed by pANCA+/ASCA− (34%) and pANCA−/ASCA+ (17%). pANCA−/ASCA+ differentiated well between CC versus IBDU (83% specificity, 96% positive predictive value [PPV]) and UC (97% specificity, 90% PPV) patients, albeit with a low negative predictive value (13% and 40%, respectively). pANCA+/ASCA− did not differentiate as well between IBD subgroups, but UC children with pANCA+/ASCA− had more often severe disease at diagnosis (36 [62%] versus 22 [38%], P = 0.033) and needed more often calcineurin inhibitors, biologics, or colectomy (25 [80%] versus 6 [20%], P = 0.026). In CC, double positivity for ASCA and not pANCA−/ASCA+ profile was associated with disease severity. Conclusions:Serology may have some role in predicting disease course and outcomes in colonic IBD, but its routine use needs to be supported by more studies. Serology cannot routinely be recommended for differentiating between IBDU versus CC or UC as a sole diagnostic criterion given its low diagnostic utility.
Surgical Treatment of Cervical Radiculopathy: Meta-analysis of Randomized Controlled Trials

Study Design. Meta-analysis of published randomized controlled trials (RCTs). Objective. To determine whether anterior cervical discectomy and fusion (ACDF), cervical disc replacement (CDR), or minimally invasive posterior cervical foraminotomy (MI-PCF) provides the best outcomes for patients with symptomatic single-level, single-side, and cervical radiculopathy. Summary of Background Data. The surgical treatment of cervical radiculopathy is still controversial. ACDF has been widely used as a “gold standard. ” CDR has evolved and become a motion-preserving alternative with a potentially lower incidence of adjacent segment disease. However, both techniques require anterior neck dissection that carries a potential for serious morbidity. MI-PCF is a motion-preserving technique that can be performed with minimal invasiveness but has not gained universal acceptance. Methods. Electronic database search for RCTs comparing the efficacy and effectiveness of ACDF, CDR, and MI-PCF was performed. Meta-analysis was done for secondary surgical procedures and adverse events. Results. A total of 358 studies were retrieved, of which four RCT reports met the inclusion criteria for this study. Three studies present clinical data comparing ACDF and CDR, and one study presents data comparing ACDF and MI-PCF. Available data from the RCTs analyzed concluded that ACDF, CDR, and MI-PCF result in significant improvements in relevant symptoms, clinical, and functional outcomes in patients with single-level, single side cervical radiculopathy refractory to nonoperative treatment. CDR had the lowest percentage of secondary surgical procedures (P = 0.0178) whereas MICPF had the lowest percentage of adverse events (P < 0.0001). Conclusion. All three techniques are effective in treating cervical radicular symptoms. MI-PCF has the lowest rate of adverse events whereas CDR has the lowest rate of secondary procedures. There is insufficient evidence to show which technique is the most effective and provides the longest-lasting symptom relief. Level of Evidence: 1
Passage rate of feed in very young chicks.

White Leghorn chicks were reared on diets in which soybean oil at 4% or corn oil at 5 or 10% was substituted isocalorically for carbohydrate calories. The transit time ( TRT ) of diets was determined in these chicks with ferric oxide as a marker. The average TRT for three experiments was 167 min. Overall, there was no significant effect (P greater than .05) for the addition of the vegetable oils to alter TRT . A significant interaction was detected for TRT to be shorter as chicks aged from 7 to 21 days of age when provided with 4 to 5% vegetable oil but not when provided with 10% corn oil. An extra metabolic effect was detected from the isocaloric substitution of lipid calories for carbohydrate calories but not necessarily only when TRT was longer. Thus, the chick was affected differently than the hen in which lipid produced longer TRT .