bluuebunny/crossref_metadata_2025 huggingface dataset:
Root cause analysis in the NHS: time for change?
Authors: Kumar Shyam , Kline Roger , Boylin Tracy
Published: April 2020

Root cause analyses were intended to search for system vulnerabilities rather than individual errors, using a human factors engineering approach. In practice, root cause analyses done in the NHS may generally fail to identify components where there are organisational failures, as there may be an inherent desire to protect institutional reputation. A human factors approach to root cause analysis looks at system vulnerabilities, considering the entirety of the environment in which an individual works and taking into account factors such as the physical environment and individual mental characteristics. Other human factors include group dynamics, task complexity and concurrent tasks. It is time that the growing evidence of the potential shortcomings of root cause analysis, especially as frequently applied within the NHS, is heeded. At present, rather than assisting learning it may be an impediment to patient safety. The authors propose that root cause analyses should be performed by a group of people who are not managing the service. External organisations such as the General Medical Council, Nursing and Midwifery Council, Care Quality Commission and Practitioner Performance Assessment are heavily reliant on this tool when concerns are raised. If the flaws in root cause analysis can be eliminated, drawing on the available evidence, cases such as those of Dr Hadiza Bawa-Garba and Mr David Sellu might be avoided.
Regulation of Interferon-γ receptor (IFN-γR) expression in macrophages during Mycobacterium tuberculosis infection
Authors: Kak Gunjan , Tiwari Brijendra K , Singh Yogendra , Natarajan Krishnamurthy
Published: April 2020

Interferon-gamma (IFN-γ) is a key cytokine that mediates immunity to tuberculosis (TB).Mycobacterium tuberculosis(M. tb) is known to downregulate the surface expression of IFN-γ receptor (IFN-γR) on macrophages and peripheral blood mononuclear cells (PBMCs) of patients with active TB disease. ManyM. tbantigens also downmodulate IFN-γR levels in macrophages when compared with healthy controls. In the current study, we aimed at deciphering key factors involved inM. tbmediated downregulation of IFN-γR levels on macrophage surface. Our data showed that bothM.tbH37Rv andM.bovisBCG infections mediate downmodulation of IFN-γR on human macrophages. This downmodulation is regulated at the level of TLR signaling pathway, second messengers such as calcium and cellular kinases i.e. PKC and ERK-MAPK, indicating that fine tuning of calcium response is critical to maintaining IFN-γR levels on macrophage surface. In addition, genes in the calcium and cysteine protease pathways which were previously identified by us to play a negative role duringM. tbinfection, also regulated IFN-γR expression. Thus, modulations in IFN-γR levels by utilizing host machinery may be a key immune suppressive strategy adopted by the TB pathogen to ensure its persistence and thwart host defense.
Assessment of antinuclear antibodies by indirect immunofluorescence assay: report from a survey by the American Association of Medical Laboratory Immunologists
Authors: Peterson Lisa K. , Tebo Anne E. , Wener Mark H. , Copple Susan S. , Fritzler Marvin J.
Published: April 2020

Background

The indirect immunofluorescence assay (IFA) using HEp-2 cell substrates is the preferred method by some for detecting antinuclear antibodies (ANA) as it demonstrates a number of characteristic staining patterns that reflect the cellular components bound as well as semi-quantitative results. Lack of harmonized nomenclature for HEp-2 IFA patterns, subjectivity in interpretation and variability in the number of patterns reported by different laboratories pose significant harmonization challenges. The main objectives of this study were to assess current practice in laboratory assessment of HEp-2 IFA, identify gaps and define strategies to improve reading, interpretation and reporting.

Methods

We developed and administered a 24-item survey based on four domains: educational and professional background of participants, current practice of HEp-2 IFA testing and training, gap assessment and the perceived value of International Consensus on Antinuclear Antibody Patterns (ICAP) and other factors in HEp-2 IFA assessment. The Association of Medical Laboratory Immunologists (AMLI) and American Society for Clinical Pathology administered the survey from April 1 to June 30, 2018, to members involved in ANA testing. This report summarizes the survey results and discussion from a dry workshop held during the 2019 AMLI annual meeting.

Results

One hundred and seventy-nine (n = 179) responses were obtained where a significant number were clinical laboratory scientists (46%), laboratory directors (24%), supervisors (13%) or others (17%). A majority of respondents agreed on the need to standardize nomenclature and reporting of HEp-2 IFA results. About 55% were aware of the ICAP initiative; however, among those aware, a significant majority thought its guidance on HEp-2 IFA nomenclature and reporting is of value to clinical laboratories. To improve ICAP awareness and further enhance HEp-2 IFA assessment, increased collaboration between ICAP and the clinical laboratory community was suggested with emphasis on education and availability of reference materials.

Conclusions

Based on these suggestions, future efforts to optimize HEp-2 IFA reading, interpretation and reporting would benefit from more hands-on training of laboratory personnel as well as continuous collaboration between professional organizations, in vitro diagnostic manufacturers and clinical laboratories.
Nonequilibrium Transport and Phase Transitions in Driven Diffusion of Interacting Particles
Authors: Lips Dominik , Ryabov Artem , Maass Philipp
Published: April 2020

Driven diffusive systems constitute paradigmatic models of nonequilibrium physics. Among them, a driven lattice gas known as the asymmetric simple exclusion process (ASEP) is the most prominent example for which many intriguing exact results have been obtained. After summarising key findings, including the mapping of the ASEP to quantum spin chains, we discuss the recently introduced Brownian ASEP (BASEP) as a related class of driven diffusive system with continuous space dynamics. In the BASEP, driven Brownian motion of hardcore-interacting particles through one-dimensional periodic potentials is considered. We study whether current–density relations of the BASEP can be considered as generic for arbitrary periodic potentials and whether repulsive particle interactions other than hardcore lead to similar results. Our findings suggest that shapes of current–density relations are generic for single-well periodic potentials and can always be attributed to the interplay of a barrier reduction, blocking, and exchange symmetry effect. This implies that in general up to five different phases of nonequilibrium steady states are possible for such potentials. The phases can occur in systems coupled to particle reservoirs, where the bulk density is the order parameter. For multiple-well periodic potentials, more complex current–density relations are possible, and more phases can appear. Taking a repulsive Yukawa potential as an example, we show that the effects of barrier reduction and blocking on the current are also present. The exchange symmetry effect requires hardcore interactions, and we demonstrate that it can still be identified when hardcore interactions are combined with weak Yukawa interactions. The robustness of the collective dynamics in the BASEP with respect to variations of model details can be a key feature for a successful observation of the predicted current–density relations in actual physical systems.
Postgenomic technologies for genomic and proteomic analysis in biological and medical research
Authors: Solodskikh S. A. , Gryaznova M. V. , Dvoretskaya I. D. , Gureev A. P. , Panevina A. V. , Maslov A. Y. , Serzhantova O. V. , Mikhailov A. A. , Chinopolous C. , Popov V. N.
Published: April 2020

Over the 15 years since the decoding of the human genome a large number of individual genomes have been sequenced. Targeted sequencing – sequencing of select genome regions - has been widely used both in research and in medical practice. The use of various types of genetic analysis is starting to be used in daily clinical routine. At the same time, the price of sequencing decreases and as a result, the amount of genetic information available to researchers and physicians increases. These processes together determine the need for creation of databases for the centralized storage of genetic information which is crucial for synchronization and validation of the work of various institutions. One of the first such databases was the NCBI database created and supervised by the US National Center for Biotechnological Information (NCBI) in collaboration with the National Institute for Human Genome Research (NHGRI). At the same time, the available methods for studying associations between DNA polymorphisms and various phenotypic manifestations do not cover the most important layer of regulation of biological processes - the proteome. The methods of high-throughput proteomic analysis that are to be developed will allow identifying driver mutations that make the greatest contribution to the phenotype of the studied object. The application of an integrated analysis of the genome and proteome for the diagnosis and treatment of cancer pathologies is one of the most important research goals now. This approach will allow to identify new genetic biomarkers that could be used for reliable prediction of the treatment response, risks of the most important diseases, and the development of novel medications. This review shows recent advances in proteomic and genomic approaches to the development of more sensitive diagnostic and prognostic biomarkers that can be translated into improved clinical care and treatment of the disease.
Effect of blood serum enzymes on meat qualities of piglet productivity
Authors: Khalak V. , Gutyj B. , Bordun O. , Ilchenko M. , Horchanok A.
Published: April 2020

The article presents the results of studies of fattening and meat qualities of young white pigs of different white breeds of different intensity of formation (Δt) in early ontogeny, biochemical parameters of blood serum (aspartate aminotransferase activity, alanine aminotransferase, alkaline transferase, alkaline phosphatase. It is established that according to the main indicators of fattening and meat qualities (age of reaching live weight of 100 kg, days; thickness of the sleeve at the level of 6-7 thoracic vertebrae, mm; length of chilled carcass, mm) young pigs of the controlled herd belong to the first class and class elite, and serum biochemical parameters are consistent with the physiological norm of clinically healthy animals. Taking into account the class of distribution by intensity of formation (Δt), a significant difference was established between animals of I (Δt = 0.795–0.832) and III (Δt = 0.660–0.703) groups on the average daily gain of live weight and age of reaching live weight of 100 kg. The relationship between the biochemical parameters of serum, fattening and meat characteristics of young pigs ranges from -0.250 to +0.385 and is unlikely. We offer in breeding and breeding work, along with the traditional methods of evaluation and selection of high-yielding animals use the method of evaluation and breeding indices.
Stress–strain behaviour and failure properties of ultra-high-performance concrete
Authors: Carey Ashley S. , McBride Megan N. , Hammi Youssef , Moser Robert , Scott Dylan A. , Seely Denver , Horstemeyer Mark F. , Howard Isaac L.
Published: April 2020

In this paper, ultra-high-performance concrete (UHPC) and its constituents were evaluated by way of instrumented and non-instrumented mechanical-property tests and imaging techniques. Through image analysis, the average size, per cent area, nearest-neighbour distance and relative number density of each inclusion type were determined. Instrumented mechanical-property testing was conducted to obtain estimates for the relative behaviour of UHPC's various constituents. Different combinations of constituents were produced to measure indirect tensile strength, compressive strength, elastic modulus, Poisson's ratio and overall stress–strain behaviour to failure at early and later ages. Stress–strain behaviour and Poisson's ratio of UHPC aligned well with the literature, while constituents of UHPC also showed linear stress–strain relationships and comparable Poisson's ratios. Tensile behaviour at early and late ages was characterised and was found to be driven by inclusion of fibres. Characterisation of UHPC and its constituents is envisioned to be used to further modelling efforts by basing mathematical relationships on physical measurements.
A FICCIONALIZAÇÃO DA AUTORIDADE NA CIROPEDIA DE XENOFONTE
Authors: Cerdas Emerson
Published: April 2020

O objetivo desse artigo é a análise do proêmio da Ciropedia de Xenofonte, visando demonstrar a absorção de elementos do discurso historiográfico por parte do narrador a fim de garantir a veracidade da narrativa da vida de Ciro. Com isso, tais elementos parecem estabelecer um pacto de leitura em que o narrador nega a ficcionalidade do texto. Os proêmios dos historiadores eram textos em que estes afirmavam as suas temáticas, mas também buscavam justificar as suas escolhas e, sobretudo, estabelecer os critérios de pesquisa e análise para fortalecer a impressão de idoneidade e autoridade quanto aos fatos narrados. Uma vez que a vida de Ciro era um tema conhecido dos leitores de Xenofonte no século IV a.C., parece-nos que esta é uma estratégia que não tem a função de enganar o leitor quanto à veracidade dos fatos narrados, já que eles reconheceriam facilmente a ficcionalidade, e sim, granjear a autoridade quanto às reflexões morais e éticas de Xenofonte cuja vida de Ciro exemplifica. Isso ficará mais evidente na análise do proêmio onde o narrador, sob a aparência de historiador, deixa vestígios quanto à quebra de convenções da historiografia, indicando o caráter ficcional da narrativa. Trata-se, portanto, de um complexo proêmio que inaugura uma nova modalidade nos textos em prosa da Antiguidade, uma narrativa ficcional que finge ser verdadeira.
Trimble GPS Protocol v1
Authors: St-Jean Sabine
Published: April 2020

Here we describe the standardised protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to use the Trimble GPS with the NTRIP centimeter-level precision subscription from Cansel to record the precise location of a plot (corner or center) or a plant.
Rare Trees Survey outside Plots (Megantic Only) v1
Authors: St-Jean Sabine
Published: April 2020

Here, we describe the standardized protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to survey additional rare trees as needed to ensure that all tree species observed across the Parc national du Mont-Mégantic site are represented by at least 10 Dominant or Co-dominant individuals, in order to fulfill CABO-wide needs for the calibration of sensor data, as mentioned at step 1 of the Canopy Trees Survey Protocol - Forests of Southern Québec Protocol.
Polymerase Chain Reaction (PCR) v2
Authors: The Nonprofit Plasmid Repository Addgene
Published: April 2020

This protocol is for performing Polymerase Chain Reaction (PCR). To see the full abstract and additional resources, visit https://www.addgene.org/protocols/pcr/. Basic PCR Program Initial Denaturation for at : This initiation step heats the double stranded DNA template strand to the point where the strands start denaturing and the hydrogen bonds are broken between the nucleotide base pairs. Denature at : Continued denaturation of double stranded DNA. Anneal primers for at : The forward and reverse primers are stable within this temperature range to anneal to each of the single stranded DNA template strands. The DNA polymerase is also stable enough to now bind to the primer DNA sequence. Extend DNA for at : The Taq polymerase has an optimal temperature around - so this step enables the DNA polymerase to synthesize and elongate the new target DNA strand accurately and rapidly. Repeat steps 2-5, 25-30 times. Final Extension for at : A final extension to fill-in any protruding ends of the newly synthesized strands.
DAB Solutions v4
Authors: Institute for Brain Science Allen
Published: April 2020

3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol and xylene. Peroxidase catalyzes hydrogen peroxide oxidation of substrate DAB. This SOP provides instructions to prepare four different formulations of DAB. DAB for Immunohistochemical staining (IHC), DAB for Acetylcholinesterase (AChE) Staining, Nickel Enchanced DAB for Biocytin staining, and DAB for Biocytin staining. Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Şanlıurfa’daki Eczanelerde ve Aktarlarda Fitoterapi Amaçlı Satılan Bitkiler
Authors: ÖTNÜ Haşim , AKAN Hasan
Published: April 2020

Bu çalışma, 2018-2019 yıllarında Şanlıurfa merkez ilçelerindeki eczane ve aktarlarda fitoterapi amaçlı satılan bitkisel ürünlerin tespiti için yapılmıştır. Şanlıurfa’da bulunan 48 eczane ve 13 aktar dükkânında araştırma yapılmış olup, 144 bitkinin fitoterapi amaçlı satıldığı tespit edilmiştir. Ayrıca, bu çalışmada fitoterapi amaçlı satılan 84 terkibin muhteviyatı, üretici firmaları, kullanım amaçları ve drogların bilimsel isimleri de belirlenmiştir. Araştırma yapılan eczane ve aktarlardaki bitki ve terkiplerin fotoğrafları da çekilmiştir. Tespit edilen bitki ve bileşimlerin bilimsel isimleri ile yöresel isimlerine de yer verilmiştir.
Estimation of some Nutrient Values of Quinoa, Chia, Teff, Mung Bean and Buckwheat Seeds for Ruminants by In Vitro Methods
Authors: İKİZOĞLU Engin , SOYCAN ÖNENÇ Sibel
Published: April 2020

Objective: The aim of this study was to investigate the availability of quinoa, chia, teff, mung bean, and buckwheat as an alternative feed in ruminant nutrition.Material and Methods: The materials were composed of quinoa (white, black, red), chia (white, black), teff, mung beans and buckwheat, which have passed their shelf life due to tear or damage in their package. Fatty acid components as well as enzyme soluble organic matter (ESOM) under in vitro conditions were also determined in addition to crude nutrient contents. Metabolic energy (ME), using the obtained data, was also calculated.Results: It was found out that the crude protein (CP) contents were 14.04-15.38% in quinoa, 19.90-21.73% in chia, 11.98% in teff, 25.20% in mung bean, and 13.72% in buckwheat. Ether extract (EE) contents; however, were found out to be 7.13-7.97%, 30.84-35.75%, 2.46, % 3.48%, and 5.25%. The highest amount of linoleic acid was found in chia (60.71-66.17%). ESOM contents was determined at high level in white quinoa, mung bean, and buckwheat. However, in vitro ME contents were found at the highest level in chia.Conclusion: Quinoa has the potential to be an alternative to traditional cereals during early lactation period in ruminant animals, in which energy need is at its highest level, or as a source of energy in fattening period. Chia has a high potential to be effective in preventing heat stress, especially in dairy cattle. The high linolenic acid content of chia oil may allow the milk fat to be enriched by conjugated linoleic acid (CLA), one of the polyunsaturated fatty acids. It has been determined that teff and buckwheat can be alternatives to other cereals, whereas mung bean, due to its crude protein being high and being rich in minerals is a significant alternative for feed producers who have been in search of new sources of protein recently.
Una teoría para la educación transdisciplinaria (Basada en el Manifiesto de Basarab Nicolescu)
Authors: Chávez Cáceres María Luz
Published: April 2020

Se hace un análisis de la propuesta de Nicolescu para la elaboración de una teoría de la educación desde la perspectiva de la transdisciplinariedad. Se pone énfasis en varias categorías que complementan muy bien la  propuesta, a saber: El pensamiento complejo, la metodología transdisciplinar. Luego se desarrolla la perspectiva transdisciplinaria en relación a la educación matizando lo teórico con la realidad educativa misma.
Salud mental y el rendimiento escolar en adolescentes que trabajan en los distritos de Yarinacocha y Callería – Ucayali, 2012
Authors: Sánchez Yarmas Elsa Maximina
Published: April 2020

El objetivo de la investigación fue de analizar la relación entre la salud mental y el rendimiento escolar en adolescentes que trabajan en los distritos de Yarinacocha y Callería – Ucayali. El diseño aplicado fue  descriptivo correlacional. Se trabajó con adolescentes de 13 a 18 años pertenecientes a varias instituciones educativas de los distritos mencionados. Empleando un criterio aleatorio simple se seleccionó 204 escolares de ambos sexos (129 hombres y 75 mujeres). La variable salud mental se evaluó a través del Cuestionario de Salud Mental de Perales y cols. (1993), y la variable rendimiento escolar  fue el  promedio general de las calificaciones obtenidas al finalizar el año lectivo 2012. Se encontró diferencias significativas (p<.05) entre la salud mental y rendimiento escolar en adolescentes de ambos sexos. Se concluyó que una baja salud mental en los adolescentes que estudian y trabajan de los distritos de Yarinacocha y Callería, se asocia a un menor rendimiento escolar.
Contraintes et opportunités pour l’amélioration génétique des ruminants
Authors: VERRIER E. , SAINT-DIZIER M.
Published: April 2020

Après un aperçu des cheptels de ruminants élevés en France et dans l’Union Européenne, les caractéristiques des espèces qui influent sur les possibilités de mettre en oeuvre des programmes d’amélioration génétique et sur leur efficacité sont mentionnées. L’accent est mis sur les conséquences des paramètres de la reproduction, sur la nécessité d’une organisation rigoureuse et sur la diversité des situations rencontrées, entre espèces, races, territoires et filières. Les perspectives offertes par le développement en cours de la sélection génomique sont brièvement évoquées.
Principes de base de la sélection génomique
Authors: ROBERT-GRANIÉ C. , LEGARRA A. , DUCROCQ V.
Published: April 2020

Avec l’arrivée de données de génotypage à haut débit, il est maintenant possible d’estimer la valeur génétique d’animaux candidatsà la sélection dès leur naissance, sans attendre la collecte de phénotypes. La sélection génomique bouleverse complètement les perspectivesen amélioration génétique. Elle nécessite la constitution d’une population de référence formée d’animaux génotypés (jusqu’àrécemment, il s’agissait principalement de mâles) et ayant des performances précises, par exemple la performance moyenne de leursfilles. Les évaluations génomiques consistent à prédire les phénotypes dans cette population de référence comme la somme des effetsdes marqueurs moléculaires. Le problème méthodologique principal est que le nombre d’effets à estimer est typiquement beaucoupplus élevé que le nombre de phénotypes disponibles. Nous décrivons les idées générales de diverses familles de méthodes proposées :BLUP génomique basé sur une parenté entre individus calculée à partir des marqueurs, méthodes Bayésiennes plus flexibles maisaussi plus coûteuses, méthodes de sélection de variables, méthode en une seule étape qui combine évaluation génétique nationale etévaluation génomique. La précision des évaluations génomiques est faite par validation croisée chez les animaux les plus jeunes de lapopulation de référence. La taille de la population de référence, la manière de prendre en compte les QTL à effet fort et le degré d’apparentemententre candidats à la sélection et animaux de la population de référence ont un impact non négligeable sur l’efficacité desméthodes de sélection génomique.
Sélection sur gènes et sélection assistée par marqueurs
Authors: ELSEN J.M.
Published: April 2020

Jusqu’à une date très récente (l’émergence de la sélection génomique), l’essentiel des plans de sélection était basé sur l’évaluation desvaleurs génétiques à partir des informations phénotypiques et de pedigree. Cependant, ont aussi été mis en place plusieurs exemplesréussis de sélection valorisant la connaissance de gènes à effets importants sur les caractères ou utilisant l’aide de marqueurs moléculaires(la «Sélection Assistée par Marqueurs»). Ces exemples sont riches en enseignements pour l’avenir de la sélection. Les applicationsfurent variées, tant en termes de type de caractères (reproduction, qualité de carcasse, résistance aux maladies...) que d’organisation(éliminations d’allèles défavorables, introgression, accouplements ciblés…). Les limites, qui sont détaillées, de ces plans desélection sur gènes ou marqueurs, sont autant de contraintes qu’il faudra intégrer dans l’organisation de la sélection génomique.
Nouvelles approches de phénotypage pour la sélection animale
Authors: LAGARRIGUE S. , TIXIER-BOICHARD M.
Published: April 2020

Le phénotype correspond aux valeurs mesurables prises par des caractères choisis pour leur intérêt socio-économique ou cognitif. Lesbesoins de phénotypage dépendent de l'évolution des méthodes de sélection et des systèmes d'élevage ainsi que des développements technologiquespermettant une approche standardisée, à haut débit et automatisable. En matière de sélection animale, la mise en place de lasélection génomique introduit le concept de population de référence sur laquelle des phénotypes difficilement mesurables en routine peuventêtre obtenus pour établir les relations entre marqueurs génétiques et performance. L'association marqueurs-phénotype ouvre égalementla voie au diagnostic individuel en appui à la gestion du troupeau. La robotisation et l'identification électronique individuellesupposent des investissements importants mais offrent des perspectives très nouvelles pour le phénotypage de caractères comme l'efficacitéalimentaire ou le comportement. De façon complémentaire, les technologies de génomique fonctionnelle et l'analyse de l'empreinte spectraledes protéines permettent d'accéder aux mécanismes sous-jacents et d'affiner la définition du phénotype à l'échelle moléculaire. Leconcept de biomarqueur capable de prédire le phénotype est en plein essor en médecine humaine et pourra aussi s'appliquer aux animauxd'élevage. Plus le phénotypage sera proche du mécanisme d'action, plus la détection des gènes contrôlant la variation du phénotype seraprécise. En particulier, la recherche de régions du génome (eQTL) contrôlant l'expression d'un gène permet d'explorer les mécanismesresponsables de la variabilité de caractères complexes. On attend donc de grands progrès dans l'identification des gènes qui sous-tendentles QTL grâce aux progrès conjoints du phénotypage et du séquençage du génome.
Les gaz à effet de serre en élevage bovin : évaluation et leviers d'action
Authors: DOLLÉ J.B. , AGABRIEL J. , PEYRAUD J.L. , FAVERDIN P. , MANNEVILLE V. , RAISON C. , GAC A. , LE GALL A.
Published: April 2020

Le contexte environnemental actuel, tant politique (objectifs de réduction des émissions de gaz à effet de serre) que sociétal (informationdu consommateur), nécessite de préciser les impacts de l'activité d'élevage bovin en matière de changement climatique. L'enjeuest de connaître précisément les niveaux d'émissions de gaz à effet de serre (GES) et de stockage de carbone, des différents modes deproduction. Pour cela, une évaluation basée sur la méthodologie de l'Analyse du Cycle de Vie (ACV) est mise au point à l'échelle dusystème d'élevage. Cette approche permet d'avoir une vision globale de l'activité d'élevage intégrant l'ensemble des processus interneset externes au fonctionnement de l'exploitation. Ainsi pour les systèmes laitiers français, l'empreinte carbone brute du lait est enmoyenne de 1,26 kg CO2/kg de lait. La prise en compte du stockage de carbone sous les prairies et les haies se traduit par une compensationcomprise entre 6 et 43% selon les systèmes, en fonction de la part de prairies. L'empreinte carbone nette du lait françaisest alors en moyenne de 1,0 kg CO2/kg de lait. Dans les systèmes bovins viande français, l'empreinte carbone brute est comprise entre14,8 et 16,5 kg CO2/kg viande vive en fonction du système de production (naisseur vs naisseur/engraisseur). Après prise en comptedu stockage de carbone qui permet une compensation comprise entre 24 et 53%, l'empreinte carbone nette est comprise entre 7,9 et11,3 kg CO2/kg viande vive. De nombreux leviers d'action sont identifiés dans les systèmes d'élevage de ruminants pour réduire l'empreintecarbone des produits au portail de la ferme. Certains concernent une optimisation des systèmes de production (ajustementdes apports alimentaires, gestion de la fertilisation…) et se traduisent par des économies en matière d'intrants. D'autres nécessitentla mise en place de nouvelles technologies et se traduiront donc par un investissement ou un coût de fonctionnement supérieur auxschémas actuels de production.
Leviers d’action pour réduire la production de méthane entérique par les ruminants
Authors: DOREAU M. , MARTIN C. , EUGÈNE M. , POPOVA M. , MORGAVI D.P.
Published: April 2020

Cet article fait le point des connaissances sur différentes pistes pour réduire la production de méthane entérique par les ruminants,en privilégiant les approches in vivo, et évalue les possibilités d'application pratique. Il est connu que l'accroissement du pourcentagede concentré dans la ration réduit la production de méthane par kg de matière sèche ingérée. Cet effet est toutefois plus sensible pourdes proportions élevées de concentré. Les céréales diminuent plus la production de méthane que les concentrés riches en fibres.L'addition de lipides à la ration a un effet significatif pour réduire les émissions de méthane. Parmi les fourrages, l'ensilage de maïsentraîne des émissions plus faibles que l'ensilage d'herbe ou le foin ; mais les différences induites entre stades de végétation de l'herbeou entre graminées et légumineuses sont faibles, et parfois controversées. De très nombreux extraits de plantes et autres additifsaux modes d'action divers ont été testés. Les plantes riches en tannins et les tannins extraits des plantes sont efficaces pour réduire leméthane mais le risque de diminution de la digestibilité de la ration doit être considéré. Les autres additifs nécessitent des étudessupplémentaires pour attester leur efficacité sur le long terme. Parmi les biotechnologies, celles visant à réorienter la productiond'hydrogène vers d'autres produits que le méthane sont séduisantes, mais pas encore mises au point. L'accroissement du niveau deproduction des animaux entraîne une réduction de la production de méthane qui est particulièrement marquée quand elle estrapportée au kg de lait ou de viande. Enfin, il y a des différences entre animaux dans l'efficacité globale de production, appréciée parl'ingestion rapportée à un même niveau de production. Les animaux les plus efficaces produisent moins de méthane par kg de lait oude viande. L'article met l'accent sur la nécessité de ne pas considérer la diminution du méthane seule, mais d'évaluer l'efficacité desstratégies proposées sur l'ensemble des GES.
Identification of the Existence and Type of Microplastic in Code River Fish, Special Region of Yogyakarta
Authors: Nurfitriyani Sulistyo Elita , Rahmawati Suphia , Amalia Putri Rizqia , Arya Nolanda , Amertha Eryan Yolanda
Published: April 2020

Microplastics are plastic fragments with size less than 5mm in length, according to the U.S. National Oceanic and Atmospheric Administration (NOAA). Microplastics occur and spread in the environment as a result of plastic pollution. Although further assessment is needed to find the health impact of microplastic exposure to humans, several studies show that microplastic might harm the ocean and aquatic life. Code river is one of the big rivers in Yogyakarta. According to the Regional Environmental Agency of Yogyakarta, Code river was highly polluted by domestic waste and wastewater from the settlement along the river and its tributaries. Therefore, the objectives of this research are to investigate the abundance and characteristic of microplastics in fish from Code River Yogyakarta. Fish samples were collected from the fisherman in the upstream, middle, and downstream areas of Code River from February to May 2019. In the laboratory, the samples were analyzed using Wet Peroxide Oxidation (WPO) method. Fish gills and intestine were oxidized using WPO method followed by density separation for 24 hours. Nikon SMZ445 Stereoscopic Microscope with 35x magnification was used to analyze the shape, color, and total of microplastics. The highest abundance was found in fish samples collected from the upstream area (4.33 particles/gram) compare with the downstream area (3.25 particles/gram). The dominant color is blue, while the dominant type of microplastics is fiber.
Can Zinc Correction in SARS-CoV-2 Patients Improve Treatment Outcomes?
Authors: Noeparast Amir , Verschelden Gil
Published: April 2020

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic for which there is no established treatment available yet, has caused more than 68,000 deaths so far. Following the SARS-CoV outbreak in 2003, an Italian group described a hypothesis about the efficacy of two old drugs: Chloroquine (CQ) and Hydroxychloroquine (HCQ), against SARS-CoV and its future emergents. Later, this hypothesis was shown to be relevant in-vitro. Due to the high genetic similarity of SARS-CoV-2 and SARS-CoV, the hypothesis introduced by Savarino et al. and the further supportive in-vitro evidence served a rational ground for three different Chinese groups to test the efficacy of CQ or HCQ against SARS-CoV-2 in-vitro. These studies showed promising in-vitro efficacy of CQ and HCQ against SARS-CoV-2. Unfortunately, in the absence of sufficient clinical data on the (in)efficacy of CQ and HCQ in SARS-CoV-2 patients, the compassionate and off-label use of these medications is becoming politicized. Herein, we underline some critical features of the CQ/HCQ mechanism of action concerning SARS-CoV-2. Moreover, we put forward a hypothesis based on three lines of evidence on a probable link between zinc-deficiency/zinc correction and response to CQ/HCQ- and possibly other SARS-CoV-2 treatments.
Simulation of the Dynamic Behaviour of the ZTA Composites Obtained by Additive Technologies
Authors: Promakhov Vladimir , Korobenkov Maksim , Schults Nikita , Zhukov Ilia , Klimenko Viktor , Vorozhtsov Alexander , Zhukov Alexander
Published: April 2020

This paper presents a physical and mathematical model that has been developed in the framework of the approach used in the computational mechanics of materials. The model is designed to enable the study of the patterns of deformation and fracture of ceramic composites with a transformation-hardened matrix that are obtained by additive technologies at the mesoscopic and macroscopic levels under intense dynamic loading. The influence of the loading rate on the formation of the fracture and energy dissipation fronts for composite materials, based on the Al2O3 20%ZrO2 system, is shown. Nonlinear effects under intense dynamic loading in the considered composites are associated with the processes of self-organization of structural fragments at the mesoscopic level, as well as the occurrence of martensitic phase transformations in matrix volumes adjacent to the strengthening particles.
Low-Salinity Water, CO2, Alkaline, and Surfactant EOR Methods Applied to Heavy Oil in Sandstone Cores
Authors: Al-Saedi Hasan N. , Flori Ralph E. , Al-Jaberi Soura K. , Al-Bazzaz Waleed
Published: April 2020

Generally, injecting carbon dioxide (CO2) into oil reservoirs is an effective enhanced oil recovery (EOR) technique that improves oil recovery, but injecting CO2 alone can be compromised by problems, such as early breakthrough, viscous fingering, and gravity override. The base CO2 injection method was improved by water-alternating-gas (WAG) injection with formation water (FW) and with low-salinity (LS) water (LSW), with LSW WAG achieving greater recovery than WAG with FW.

This study investigates various combinations of standard waterflooding (with FW); flooding with nonmiscible gaseous CO2; WAG with CO2 and FW and/or LSW; foam flooding by adding a surfactant with CO2; adding an alkaline treatment step; and finally adding an LSW spacer between the alkaline step and the foam. These various EOR combinations were tested on Bartlesville sandstone cores (ϕ of approximately12%, K of approximately 20 md) saturated with a heavy oil diluted slightly with 10% heptane for workability. The ultimate outcome from this work is a “recipe” of EOR methods in combination that uses alkaline, LSW, surfactant, and CO2 steps to achieve recovery of more than 63% of the oil originally in place (OOIP) in coreflooding tests.

Combining CO2 injection with surfactant [sodium dodecyl sulfonate (SDS)] to produce a foam resulted in better recovery than the WAG methods. Adding alkaline as a leading step appeared to precipitate the surfactant and lower recovery somewhat. Adding an LSW spacer between the alkaline treatment and the foam resulted in a dramatic increase in recovery. The various cases of alkaline + LSW spacer + surfactant + CO2 (each with various concentrations of alkaline and surfactant) achieved an average improvement of 7.71% of OOIP over the identical case(s) without the LSW spacer. The synergistic effect of the LSW spacer was remarkable.

ERRATUM NOTICE:An erratum has been added to this paper detailing addition of an omitted reference.
Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae
Authors: Zhang Chao , Kong Nana , Cao Minxuan , Wang Dongdong , Chen Yue , Chen Qin
Published: April 2020

Background: Nitrogen is an indispensable nutrient for plant growth. It is used and transported in the form of amino acids in living organisms. Transporting amino acids to various parts of plants requires relevant transport proteins, such as amino acid permeases (AAPs), which were our focus in this study.Results: We found that 5 AAP genes were present in Chlorophyte species and more AAP genes were predicted in Bryophyta and Lycophytes. Two main groups were defined and group I comprised 5 clades. Our phylogenetic analysis indicated that the origin of clades 2, 3, and 4 is Gymnospermae and that these clades are closely related. The members of clade 1 included Chlorophyta to Gymnospermae. Group II, as a new branch consisting of non-seed plants, is first proposed in our research. Our results also indicated that the AAP family was already present in Chlorophyta and then expanded accompanying the development of vasculature. Concurrently, the AAP family experienced multiple duplication events that promoted the generation of new functions and differentiation of sub-functions.Conclusions: Our findings suggest that the AAP gene originated in Chlorophyta, and some non-seed AAP genes clustered in one group. A second group, which contained plants of all evolutionary stages, indicated the evolution of AAPs. These new findings can be used to guide future research.
EphB4/ TNFR2/ERK/MAPK signaling pathway comprises a signaling axis to mediate the positive effect of TNF-α on osteogenic differentiation
Authors: Zhang Yu , Yang Chengzhe , Ge Shaohua , Wang Limei , Zhang Jin , Yang Pishan
Published: April 2020

Background: Low concentrations of tumor necrosis factor-alpha (TNF-α) and its receptor TNFR2 are both reported to promote osteogenic differentiation of osteoblast precursor cells. Moreover, low concentrations of TNF-α up-regulate the expression of EphB4. However, the molecular mechanisms underlying TNF-α-induced osteogenic differentiation and the roles of TNFR2 and EphB4 have not been fully elucidated.Results: The ALP activity, as well as the mRNA and protein levels of RUNX2, BSP, EphB4 and TNFR2, was significantly elevated in MC3T3-E1 murine osteoblast precursor cells when stimulated with 0.5 ng/ml TNF-α. After TNFR2 was inhibited by gene knockdown with lentivirus-mediated shRNA interference or by a neutralizing antibody against TNFR2, the pro-osteogenic effect of TNF-α was partly reversed, while the up-regulation of EphB4 by TNF-α remained unchanged. With EphB4 forward signaling suppressed by a potent inhibitor of EphB4 auto-phosphorylation, NVP-BHG712, TNF-α-enhanced expressions of TNFR2, BSP and Runx2 were significantly decreased. Further investigation into the signaling pathways revealed that TNF-α significantly increased levels of p-JNK, p-ERK and p-p38. However, only the p-ERK level was significantly inhibited in TNFR2-knockdown cells. In addition, the ERK pathway inhibitor, U0126 (10μM), significantly reversed the positive effect of TNF-α on the protein levels of RUNX2 and BSP. Conclusions: The EphB4, TNFR2 and ERK/MAPK signaling pathway comprises a signaling axis to mediate the positive effect of TNF-α on osteogenic differentiation.
The Role of Complement Immune Response on Artemisinin Combination Therapy in a Population from Malaria Endemic Region of Western Kenya
Authors: Wanjala Christine , Bergmann-Leitner Elke , Akala Hoseah M , Odhiambo Geoffrey , Ogutu Bernhards R , Andagalu Ben , Kamau Edwin , Ochiel Daniel
Published: April 2020

BACKGROUND Naturally acquired immunity which is characterized by protection against overt clinical disease and high parasitemia is acquired with age and transmission intensity. The role of naturally acquired immunity on the efficacy of antimalarial drugs including artemisinin combination therapies (ACTs), the first-line treatments for uncomplicated Plasmodium falciparum has been demonstrated. This study investigated the role of naturally acquired immunity in the response to malaria ACT drug treatment in symptomatic patients living in a malaria high-transmission area of Western Kenya. METHODS This study used samples obtained from a therapeutic efficacy study conducted in western Kenya, an areas of high transmission which assessed ACTs. Sera samples from malaria immune (n = 105) and naïve participants (n = 6) were assessed for in vitro growth inhibitory activity against 3 D7 P. falciparum using a fluorescent-based Growth Inhibition Assay (GIA). Participants’ age and parasite clearance parameters were used in the analysis. RESULTS The key observations of the study are: (1) Sera with intact complement displayed higher GIA activity at lower serum dilutions; (2) there was significant relationship between GIA activity, parasite clearance rate, and slope half-life; (3) Age was a confounding factor when comparing the GIA activity with parasite clearance kinetics. CONCLUSION Taken together, this study demonstrates for the first time there is synergy of complement, pre-existing immunity, and drug treatment in younger patients with symptomatic malaria in a high-transmission area.
Gender differences in the relationship between dietary energy and macronutrients intake and body weight outcomes in Chinese adults
Authors: Author) Jian Zhao(Former Corresponding , Sun Jian , New Chang Su
Published: April 2020

Background To explore the the gender differences in the relationship between dietary energy and macronutrients intake and body weight outcomes in Chinese adults. Methods Data from the China Health and Nutrition Survey (CHNS, 2015) for10,898 participants aged 18-64 years. Three consecutive 24-h dietary recalls was used to assess the dietary intake. Quantile regression models for body mass index (BMI) and waist circumference (WC) were performed separately for each sex. Results Adult males showed greater absolute intakes of energy and macronutrients as compared to females as per the body weight outcomes. A 10% increase in BMI resulted in an additional intake of 0.002-0.004 kcal/d of dietary energy, 0.032-0.057 g/d of fats, 0.039-0.084 g/d of proteins, and 0.018-0.028 g/d of carbohydrates across all quantiles in males (p < 0.05). A 10% increase in WC resulted in an additional intake of 0.004-0.008 kcal/d of dietary energy, 0.051-0.052 g/d of carbohydrates across the entire quantile in males (p < 0.05), and an increased intake of 0.060-0.150 kcal/d of fat in females (p < 0.05). Conclusions Dietary Fat intake could be the risk factor of abdominal obesity in women. The importance of gender- specific evidence should be considered before promoting macronutrient allocation for the prevention and treatment of obesity.
Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistan families
Authors: Zhou Yingjie , Tariq Muhammad , Author) Sijie He(Former Corresponding , Abdullah Uzma , Author) Jianguo Zhang(New Corresponding , Baig Shahid Mahmood
Published: April 2020

Background Hearing loss is the most common sensory defect that affects over 6% of the population worldwide. About 50%-60% of hearing loss patients are attributed to genetic causes. Currently more than 100 genes have been reported to cause non-syndromic hearing loss. It’s possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES). Methods We collected 5 consanguineous pedigrees with hearing loss from Pakistan and applied WES on selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causing genes for them. Results Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate for 3 pedigrees, which were GIPC3 (c.937T>C), LOXHD1 (c.2935G>A) and TMPRSS3 (c.941T>C). And the remaining 2 pedigrees each contained two candidates, which were TECTA (c.4045G>A) and MYO15A (c.3310G>T and c.1705G>C) for one pedigree and DFNB59 (c.494G>A) and TRIOBP (c.1952C>T) for the other pedigree. The candidates were validated in all available samples by Sanger sequencing. Conclusion The candidate variants in hearing loss genes were validated to be co-segregated in the pedigrees, which may indicate the reasons for such patients. We also suggested that WES may be suitable strategy for hearing loss screening in clinical detection.