Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome wide association study of milk composition traits in Swedish Red cows

The aim of this study was to detect QTLs that affect milk composition traits such as fat yield, fat percent, citric acid, free fatty acids as well as milk properties like fat globule size, and determine the phenotypic variation explained by the QTLs. These traits play a crucial role in nutritional and technological properties of milk and its products. However, the underlying genetic basis of most of these traits is not well studied. Hence, a genome wide association study was carried out using variance component method, GRAMMAR-Gamma, in R package GenABEL. There were around 370 Swedish red cows with phenotypic record of the traits and genotypes were available for 617,388 SNPs. The GWAS revealed QTL for fat percentage on BTA14 and 20, and for citric acid on BTA1, 6, 12 and 20. The most significant SNPs on BTA 14 and 20 explained 6.8% and 6.5% of the phenotypic variation respectively; and the most significant SNPs for citric acid on BTA1, 6, 12, and 20 accounted for 6.8%, 6.9%, 7.9% and 8.4% of the phenotype variation respectively. Heritability of the traits ranged from 0.19 to 0.63. Furthermore, suggestive QTLs were found for fat yield on BTA14, 17 and 25; on BTA5, 19 and 24 for fat globule size; and on BTA5 for free fatty acids. Therefore, the findings of this study indicate that the markers identified in this study can be used in genetic improvement of the traits through marker assisted or genomic selection. In addition, since, this is the first analysis of these economically important traits in Swedish red cows; it can be used as a foundation for further research on the traits.
Keep collecting: accurate species distribution modelling requires more collections than previously thought

Aim Species distribution models (SDMs) use the locations of collection records to map the distributions of species, making them a powerful tool in conservation biology, ecology and biogeography. However, the accuracy of range predictions may be reduced by temporally autocorrelated biases in the data. We assess the accuracy of SDMs in predicting the ranges of tropical plant species on the basis of different sample sizes while incorporating real‐world collection patterns and biases.
Structural Determinants of Cold Adaptation and Stability in a Large Protein*

The heat-labile α-amylase from an antarctic bacterium is the largest known protein that unfolds reversibly according to a two-state transition as shown by differential scanning calorimetry. Mutants of this enzyme were produced, carrying additional weak interactions found in thermostable α-amylases. It is shown that single amino acid side chain substitutions can significantly modify the melting point T m , the calorimetric enthalpyΔH cal, the cooperativity and reversibility of unfolding, the thermal inactivation rate constant, and the kinetic parameters k cat andK m . The correlation between thermal inactivation and unfolding reversibility displayed by the mutants also shows that stabilizing interactions increase the frequency of side reactions during refolding, leading to intramolecular mismatches or aggregations typical of large proteins. Although all mutations were located far from the active site, their overall trend is to decrease bothk cat and K m by rigidifying the molecule and to protect mutants against thermal inactivation. The effects of these mutations indicate that the cold-adapted α-amylase has lost a large number of weak interactions during evolution to reach the required conformational plasticity for catalysis at low temperatures, thereby producing an enzyme close to the lowest stability allowing maintenance of the native conformation.
Risk analysis of medical instruments - Case study of Cardiac Output Monitor

Risk analysis, or hazard analysis, is a structured tool for the evaluation of potential problems which could be encountered in connection with the use of any number of things, from driving a car, riding on public transportation, taking a drug, or using a medical instrument. We live in a world full of risks, with varying likelihoods and consequences. Risk analysis and management is a complex subject because each stakeholder places a different value on the probability of harm occurring and its severity. Risk analysis is now routinely used during the design phase for medical instruments. In this paper we will describe the case study of Cardiac Output Monitor with respect to its safety and risk management process that must encompass the life span from its conception to the technology transfer. Optimum safety and performance require cooperation among all those involved in the life span of a medical device: the manufacturer, importer/vendor, government, user and public - each has a specific role to play in risk management. It also provides an introduction to standards and describes the use of voluntary standards and their increasing prominence in medical instrument regulation. In the end, risk analysis using FMEA, FTA and tools is carried out.
1 Alliance Portfolio Internationalization and Firm Performance †

Alliance research has traditionally focused on structural and relational aspects of the networks in which firms are situated, paying less attention to the inherent characteristics of their partners. This study introduces the notion of alliance portfolio internationalization (API), which refers to the degree of foreignness of partners in a firm’s collection of immediate alliance relationships. We develop a framework to explain how API impacts firm performance. We suggest that as a firm’s API increases, financial performance is expected to initially decline, then improve, and finally decline again. This sigmoid relationship between API and financial performance is ascribed to evolving learning effects that shape the net benefits of API. When the firm’s alliance portfolio, on average, consists of proximate foreign partners, the firm may fail to recognize latent national differences, but at moderate levels of API, its absorptive capacity and specialized collaborative routines support the exchange of valuable network resources. Nevertheless, high levels of API undermine firm performance because of the failure of collaborative routines and mounting liabilities of cross-national differences. We test the framework using data on the alliance portfolios of U.S.-based software firms during the period from 1990 to 2001. The results provide support for the sigmoid relationship as well as for our predictions that firms which have gained experience with foreign partners and maintained wholly owned subsidiaries in their partners’ countries of origin can overcome some of the liabilities of API and better leverage its benefits.
Association of high anti‐donor alloreactivity and low frequency of FoxP3‐expressing cells prior to kidney transplantation with acute graft rejection

Vondran FWR, Timrott K, Tross J, Kollrich S, Gwinner W, Lehner F, Klempnauer J, Becker T, Schwinzer R. Association of high anti‐donor alloreactivity and low frequency of FoxP3‐expressing cells prior to kidney transplantation with acute graft rejection. Clin Transplant 2011: 25: 905–914. © 2010 John Wiley & Sons A/S.
Lacrimal drainage-associated lymphoid tissue (LDALT): a part of the human mucosal immune system.

PURPOSE Mucosa-associated lymphoid tissue (MALT) specifically protects mucosal surfaces. In a previous study of the human conjunctiva, evidence was also found for the presence of MALT in the lacrimal sac. The present study, therefore, aims to investigate its morphology and topographical distribution in the human lacrimal drainage system. METHODS Lacrimal drainage systems (n = 51) obtained from human cadavers were investigated by clearing flat wholemounts or by serial sections of tissue embedded in paraffin, OCT compound, or epoxy resin. These were further analyzed by histology, immunohistochemistry, and electron microscopy. RESULTS All specimens showed the presence of lymphocytes and plasma cells as a diffuse lymphoid tissue in the lamina propria, together with intraepithelial lymphocytes and occasional high endothelial venules (HEV). It formed a narrow layer along the canaliculi that became thicker in the cavernous parts. The majority of lymphocytes were T cells, whereas B cells were interspersed individually or formed follicular centers. T cells were positive for CD8 and the human mucosa lymphocyte antigen (HML-1). Most plasma cells were positive for IgA and the overlying epithelium expressed its transporter molecule secretory component (SC). Basal mucous glands were present in the lacrimal canaliculi and in the other parts accompanied by alveolar and acinar glands, all producing IgA-rich secretions. Primary and secondary lymphoid follicles possessing HEV were present in about half of the specimens. CONCLUSIONS The term lacrimal drainage-associated lymphoid tissue (LDALT) is proposed here to describe the lymphoid tissue that is regularly present and belongs to the common mucosal immune system and to the secretory immune system. It is suggested that it may form a functional unit together with the lacrimal gland and conjunctiva, connected by tear flow, lymphocyte recirculation, and probably the neural reflex arc, and play a major role in preserving ocular surface integrity.
Prevalence of blindness and visual impairment in an elderly urban population.

BACKGROUND Accurate data on the prevalence of blindness in urban populations is not readily available. The Australian Longitudinal Study of Ageing is a prospective multidimensional study examining a broad range of age-related health issues, including visual function. METHODS A population-based sample of 1466 persons, 70 years of age and over, from the Adelaide metropolitan area underwent visual acuity measurement. RESULTS Approximately 1% were legally blind by Australian definitions. CONCLUSIONS This percentage is low by world standards, however projections indicate that the absolute number of blind elderly people is rapidly increasing. Data such as this are crucial for the planning of adequate ophthalmic care.
Event-based control of networks modeled by a class of infinite dimensional systems

Cette these propose des contributions sur la commande evenementielle pour des reseaux modelises par une classe des systemes de dimension infinie. Premierement nous nous focalisons sur la modelisation et controle frontiere des reseaux qui sont decrits par des systemes hyperboliques de lois de conservation. En nous inspirant de modeles macroscopiques dans le cadre des reseaux de communications, nous traitons des systemes couples EDP-EDO, dont les noeuds (les serveurs) sont modelises par des EDO non-lineaires alors que des lignes de transmission sont decrites par des systemes hyperboliques lorsque des retards peuvent etre pris en compte. Pour le systeme linearise resultant, autour d'un point d'equilibre optimal, on effectue aussi bien une analyse de stabilite "Input-to-state stable" que de la synthese du controle pour le gain asymptotique grâce a une analyse de fonction de Lyapunov et une formulation LMI.Ensuite, nous considerons des aspects theoriques de la commande evenementielle aux frontieres pour les systemes hyperboliques. D'un cote, avec cette strategie de controle, nous ciblons la reduction de la consommation d' energie en traitant les contraintes de communication et de calcul. D' autre part, nous utilisons cette strategie comme une maniere rigoureuse pour echantillonner temporellement lorsqu' on a besoin de mettre en oeuvre les controleurs continus sur une plateforme numerique. Une etude mathematique sur l'existence et l' unicite des solutions ainsi que sur les aspects de stabilite est realisee.
A new estimation of the recent tropospheric molecular hydrogen budget using atmospheric observations and variational inversion

This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N2 fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H2 soil uptake is −59±9 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H2 sources and sinks.
Review of Medical Encounters in the 5 Years Before a Diagnosis of HIV-1 Infection: Implications for Early Detection

Early detection of HIV infection improves prognosis and reduces transmission, but 30%–40% of cases are diagnosed late. A comprehensive and systematic review of medical encounters before diagnosis has not been done. This study reviews 5 years of medical encounters before the diagnosis of HIV infection in members of a large managed care organization where access to care is reasonably good. Patient characteristics, HIV risk factors, and clinical events preceding diagnosis were examined and tested for association with late diagnosis (CD4 cell count of <200/&mgr;L at diagnosis). Of 440 HIV-infected patients, 62% had CD4 cell counts of <350/&mgr;L, 43% had CD4 cell counts of <200/&mgr;L, and 18% had CD4 cell counts of <50/&mgr;L at diagnosis. Twenty-six percent of all patients had risks documented >1 year before diagnosis. Only 22% of patients had one of eight clinical indicators suggested in the literature as reasons to test for HIV >1 year before diagnosis. In multiple logistic regression, older age, male sex, race, risk group, no prior HIV testing, physician-initiated testing, and having any of eight clinical indicators before diagnosis were each associated with late diagnosis (p ≤ .05). Late diagnosis remains a challenge despite good access to care. In our setting, effective risk assessment before symptoms arise offers greater potential for raising the mean CD4 cell count at diagnosis than does increased awareness of selected HIV-associated clinical prompts.
Colloidal Gold Nanoparticles as a Blood-Pool Contrast Agent for X-ray Computed Tomography in Mice

Objectives:To present the pharmacokinetics and computed tomographic imaging efficacy of colloidal gold nanoparticles (AuNPs) as a blood-pool agent for x-ray computed tomography (CT). Methods and Materials:To prepare the colloidal AuNPs, gold nanocrystals were modified using sulfhydrated polyethylene glycol (PEG). Cytotoxicity and histopathologic tests were carried out for toxicity evaluation. Six adult Balb/c mice underwent microcomputed tomography scans after injection of colloidal AuNPs (2.5 &mgr;mol Au/g body weight). Four mice with HT-1080 tumors were imaged for visualization of the tumor vasculature. Results:The PEG coated colloidal AuNPs appeared as spherical nanoparticles with 38-nm diameters. The AuNPs-PEG showed a biocompatibility without toxicity in the mice. We identified a stable imaging window for visualizing the vasculature system, immediately to 24 hours after injection. Microcomputed tomography imaging using AuNPs-PEG clearly visualized the tumor vascular structures. Conclusion:Colloidal AuNPs show potential as a blood-pool agent for x-ray CT imaging.
Morphologic parameters of early cleavage-stage embryos that correlate with fetal development and delivery: prospective and applied data for increased pregnancy rates.

BACKGROUND Many different embryo selection criteria have been used in assisted reproductive technologies (ART), but there are no published prospective studies to ascertain their usefulness in predicting implantation. METHODS In a prospective trial, 20 early scoring parameters previously reported to influence clinical outcome were collected, but embryos were selected for transfer by current laboratory protocols; day 1 pronuclear (PN) (Z) score combined with day 3 or 5 morphology. Data points for each oocyte/embryo were scored independently and tracked individually. Data were analysed retrospectively for parameters most likely to result in a positive pregnancy test, fetal heartbeat (FHB) and delivery. RESULTS Results indicated that day 1 PN morphology and nucleolar precursor body (NPB) ratio, day 2 cell number, blastomere symmetry and nucleation and the ability to cleave from day 2 to day 3 were the six most significant factors in fetal development. This outcome was then applied prospectively over 8 months. The implantation rate (IR) and clinical pregnancy rate (CPR) increased in each age group, and the number of embryos used decreased. CONCLUSION In conclusion, early parameters that include PN morphology, number and ratio of NPBs per nucleus and the day 2 morphology of cleaving embryos are stronger positive predictors of implantation than day 3 morphology or the ability to achieve the blastocyst stage of development. Parameters that were most consistently correlated with no delivery were lack of PN symmetry, day 2 multinucleation and uneven cell size. Day 3 and day 5 parameters were not significant compared with the combination of early parameters.
A highly conserved repeated chromosomal sequence in the radioresistant bacterium Deinococcus radiodurans SARK

A DNA fragment containing a portion of a DNA damage-inducible gene from Deinococcus radiodurans SARK hybridized to numerous fragments of SARK genomic DNA because of a highly conserved repetitive chromosomal element. The element is of variable length, ranging from 150 to 192 bp, depending on the absence or presence of one or two 21-bp sequences located internally. A putative translational start site of the damage-inducible gene is within the reiterated element. The element contains dyad symmetries that suggest modes of transcriptional and/or translational control.
Isonymic structure of the Argentine Northwest

Surname distribution may be used as a substitute for quantitative information on the genetic structure of human populations due to panmictic deviations. This study analysed the isonymic structure of the Argentine Northwest (ANW) populations. Surname distribution of 2 576 548 voters (year 2001) in the 117 departments of the region was analysed. Fisher's α and coefficient of random relationship by isonymy were estimated. A dendrogram of the 117 departments was constructed from the matrix of Euclidean distances. In general, α values found were lower than country averages, while kinship values were higher. Ten clusters were identified showing a spatial distribution closely related to geographic characteristics, means of communication, and location of economic activities of the region. The resulting pattern could be basically characterized by grouping the departments into two large clusters: (a) Those located in the centre of the region, which include the provincial capitals, presented greater diversity of surnames and a lower degree of kinship. (b) Those located in the regional periphery showed greater isolation and kinship. Isonymic parameters estimated agree with the demographic characteristics of populations, historical antecedents of population settlement and ANW geographic features.
Doxastic Morality: A Moderately Skeptical Perspective

ABSTRACT:Beliefs can cause moral wrongs, no doubt, but can they also constitute moral wrongs in their own right? This paper offers some grounds to be skeptical of the idea that there are moral norms which operate directly on belief, independently of any epistemic norms also operating on belief. The resultant skepticism is moderate in the following sense: it holds that the motivations underlying the doxastic morality approach should not be dismissed lightly; they are genuine insights and serve to bring to light important new issues concerning the interaction between our notions of moral and epistemic responsibility. Nonetheless, it is also skeptical, in holding that these concerns are ultimately best voiced in more traditional categories which distinguish the epistemology of belief from the morality of action.
Apprentissage de la Cohérence Photométrique pour la Reconstruction de Formes Multi-Vues

L'essor des technologies de realite virtuelle et augmentee s'accompagne d'un besoin accru de contenus appropries a ces technologies et a leurs methodes de visualisation. En particulier, la capacite a produire des contenus reels visualisables en 3D devient preponderante. Nous considerons dans cet article le probleme de la reconstruction de scenes 3D dynamiques a partir d'images couleurs. Nous interessons tout particulierement a la possibilite de beneficier des reseaux de neurones convolutifs dans ce processus de reconstruction pour l'ameliorer de maniere effective. Les methodes les plus recentes de reconstruction multi-vues estiment des cartes de profondeur par vue et fusionnent ensuite ces cartes dans une forme implicite 3D. Une etape cle de ces methodes reside dans l'estimation des cartes de profondeurs. Cette etape est traditionnellement effectuee par la recherche de correspondances multi-vues a l'aide de criteres de photo-coherence. Nous proposons ici d'apprendre cette fonction de photo-coherence sur des exemples au lieu de la definir a travers la correlation de descripteurs photometriques, comme c'est le cas dans la plupart des methodes actuelles. L'intuition est que la correlation de descripteurs d'images est intrinsequement contrainte et limitee, et que les reseaux profonds ont la capacite d'apprendre des configurations plus larges. Nos resultats sur des donnees reelles demontrent que cela est le cas. Entraine sur un jeu de donnees statiques standard, les reseaux de convolution nous permettent de recuperer des details sur une forme en mouvement que les descripteurs d'images classiques ne peuvent extraire. Les evaluations comparatives sur ces donnees standards sont par ailleurs favorables a la methode que nous proposons.
All three SOS‐inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis

Most organisms contain several members of a recently discovered class of DNA polymerases (umuC/dinB superfamily) potentially involved in replication of damaged DNA. In Escherichia coli, only Pol V (umuDC) was known to be essential for base substitution mutagenesis induced by UV light or abasic sites. Here we show that, depending upon the nature of the DNA damage and its sequence context, the two additional SOS‐inducible DNA polymerases, Pol II (polB) and Pol IV (dinB), are also involved in error‐free and mutagenic translesion synthesis (TLS). For example, bypass of N‐2‐acetylaminofluorene (AAF) guanine adducts located within the NarI mutation hot spot requires Pol II for −2 frameshifts but Pol V for error‐free TLS. On the other hand, error‐free and −1 frameshift TLS at a benzo(a)pyrene adduct requires both Pol IV and Pol V. Therefore, in response to the vast diversity of existing DNA damage, the cell uses a pool of ‘translesional’ DNA polymerases in order to bypass the various DNA lesions.