Miracle-dz/UniFAR-FTUs huggingface dataset:
An Abstraction Technique for Verifying Shared-Memory Concurrency

Modern concurrent and distributed software is highly complex. Techniques to reason about the correct behaviour of such software are essential to ensure its reliability. To be able to reason about realistic programs, these techniques must be modular and compositional as well as practical by being supported by automated tools. However, many existing approaches for concurrency verification are theoretical and focus primarily on expressivity and generality. This paper contributes a technique for verifying behavioural properties of concurrent and distributed programs that balances expressivity and usability. The key idea of the approach is that program behaviour is abstractly modelled using process algebra, and analysed separately. The main difficulty is presented by the typical abstraction gap between program implementations and their models. Our approach bridges this gap by providing a deductive technique for formally linking programs with their process-algebraic models. Our verification technique is modular and compositional, is proven sound with Coq, and has been implemented in the automated concurrency verifier VerCors. Moreover, our technique is demonstrated on multiple case studies, including the verification of a leader election protocol.
Growth and nutrient efficiency of meagre (Argyrosomus regius , Asso1801) fed extruded diets with different protein and lipid levels

Four commercial diets containing different levels of crude protein and crude lipid (44/25, 43/21, 46/20 and 47/20%) were assayed in duplicated groups in juvenile meagre (Argyrosomus regius) (initial individual weights were 94 g) in an experiment lasting 173 days. The essential amino acid contents (expressed in g/kg of diet basis) in diets 46/20 and 47/20 were higher than in diets 44/25 and 43/21. The HUFAs represented 184 and 207 g/kg in diets 46/20 and 47/20, respectively and 98 and 116 g/kg in diets 44/25 and 43/21, respectively. The fish fed diet 47/20 obtained the best growth and efficiency results, reaching a final individual weight of 393 g, followed by the meagre fed with diet 46/20. Meagre from the 47/20 group retained more of the ingested protein and energy than those fed diets 46/20. Fish fed 44/25 and 43/21 obtained the significantly lowest protein and energy efficiency. The retention of individual amino acids (AAs) in fish fed diets generally decreased in order of diets 46/20, 43/21 and 44/25. The IAA retention of meagre fed diet 47/20 was around 24.8% in phenylalanine and 39.7% in lysine. The results of the current experiment show that the fish fed commercial diet 47/20 obtained the best results in meagre growth, followed by fish fed diet 46/20. Diets 43/21 and 44/25 presented the worst growth and feed efficiency results. Key words: Meagre, protein level, lipid level, extruded diets.
Seasonal growth, erosion rates, and nitrogen and photosynthetic ecophysiology of Undaria pinnatifida (Heterokontophyta) in southern New Zealand 1

The goal of this study was to examine growth, erosion rates, and the photosynthetic and nitrogen ecophysiology of the invasive seaweed Undaria pinnatifida (Harv.) Suringar. Sporophytes of U. pinnatifida that appeared in Otago Harbour, southeastern New Zealand, in late autumn (May) 1996 were tagged, and their growth rates followed until the onset of senescence in early summer (November 1996). Blade growth rates were maximal between May and August when they ranged from 0.77 ± 0.05 to 0.93 ± 0.05 cm · d−1 and declined from September onward. In laboratory experiments, U. pinnatifida took up nitrate and ammonium simultaneously at rates ranging from 21.3 ± 2.1 to 179.3 ± 65.1 μmol · g−1 dry weight (dwt) · h−1. When monthly patterns of growth rate, seawater inorganic nitrogen, nitrogen uptake kinetics, soluble tissue nitrate, % tissue carbon (C) and nitrogen (N), and C:N ratio were considered together, there was no evidence that N limited the growth of U. pinnatifida. Furthermore, the photosynthetic parameters Pmax, α, Ek, Ec, and Rd derived from P versus E curves indicated that the growth of U. pinnatifida was not light limited, and that the population could potentially grow deeper than its observed location at 4 m depth. Nitrogen and light ecophysiological parameters of U. pinnatifida more closely resemble those of small, ephemeral seaweeds, such as Ulva, than other members of the Laminariales. We suggest that a “plastic” physiology may allow U. pinnatifida sporophytes to match their physiology to a range of environments, which is one reason for its success as an invasive seaweed.
Role of the Tcell genotype in the development of allogeneic responses after stem cell transplantation and cellular immunotherapy.

Allogeneic hematopoietic stem cell transplantation (SCT) following high-dose systemic chemo- or chemoradiotherapy is the most effective curative treatment for patients with leukemia. Donor graft-derived T cells can mediate an immunological elimination of residual leukemic cells. Relapse of leukemia after allogeneic SCT can be successfully treated with donor lymphocyte infusions (DLI). The genotype of the bone marrow, or, the extent of hematopoietic chimerism, at the time of relapse, may influence the inititation and magnitude of T cell mediated graft-versus-malignancy reactivity. The mechanisms by which either donor-derived or recipient-derived T cells contribute to tolerance or non-responsiveness of infused donor lymphocytes have not been clearly demonstrated yet. The research described in this thesis focusses on the role of the T cell genotype in the development of alloreactive immune responses. The first part of the thesis describes the development of a methodology to study the fate of infused T cells, and its implementation in in vivo mouse and rat transplantation models. In Chapter 2 we showed that the period of in vitro stimulation and expansion of syngeneic murine splenic T cells before infusion strongly influences their survival and trafficking patterns. Using an optimized culture and gene transduction protocol we studied the capacity of T cells to evoke allogeneic responses in a rat model after BMT, supplemented with retrovirally transduced T cells (Chapter 3). In Chapter 4 we identified a mechanism that may contribute to unresponsiveness to DLI in relapsed patients. Recurrent T cells of recipient origin, present at the time of DLI, may inhibit alloreactivity of infused donor lymphocytes by eliminating these cells. In the final part of this thesis we described the development of a method to quantitatively monitor the genetic origin of hematopoietic cells (Chapter 5), and used this technique in a clinical study to monitor changes in chimerism in relation to altered alloimmune reactivity (Chapter 6)
Clinical Implications of the Associations Between Intestinal Microbiome and Colorectal Cancer Progression

Abstract Intestinal microbiome influences host immunity and several diseases, including cancer, in their areas of colonization. Microbial dysbiosis and over-colonization of specific microbes within the colorectal mucosa can impact the progress of carcinogenesis. Investigations initially focused on the mechanisms by which the intestinal microbiome initiates or promotes the development of colorectal cancer, including DNA damage, induction of chromosomal instability, and regulation of host immune responses. Some studies on the clinicopathological features have reported that specific strains present at high abundance are associated with advanced stage and positive lymph nodes in colorectal cancer. In this context, we reviewed the relationship between the intestinal microbiome and the clinical features (patient age, disease staging, prognosis, etc.) of patients with colorectal cancer, and evaluated the potential pathogenesis caused by the intestinal microbiome in disease progress. This article assessed whether changes in distinct species or strains occur during the period of cancer advancement. Overall, age grouping does not bring about significant differences in the constitution of microbiome. The disease stages show their distinct distribution in some species and strains. Oncogenic species are generally enriched in patients with poor prognosis, including low infiltration of CD3+ T cells, poor differentiation, widespread invasion, high microsatellite instability, CpG island methylator phenotype, BRAF mutation, short overall survival, and disease-free survival. The implications of those changes we discussed may assist in comprehensive understanding of the tumorigenesis of colorectal cancer from a microbiological perspective, finding potential biomarkers for colorectal cancer.
Overcoming the Taste Stigma of Soy

Can labels unknowingly influence a person’s taste perceptions? Using a "phantom ingredient" taste test, the presence or absence of a labeled ingredient (soy) was shown to influence sensory evaluations of a food. In particular, a nutrition bar wrongly purporting to contain soy generated negative ratings of taste, aftertaste, and attitude, yet generated favorable ratings of its nutritiousness. Because there was actually no soy in the product, these differences represent biases caused by ingredient labeling. Given the appropriate segment of consumers (health-oriented), ingredient labeling may have more favorable consequences. This power of suggestion might also be expanded to other ingredients or processes, such as those involving biotechnology or organic production.
Consequences of long- and short-term fragmentation on the genetic diversity and differentiation of a late successional rainforest conifer

The east Australian rainforests provide a unique system with which to study historic climate-driven habitat fragmentation. The long life span of rainforest conifers and consequent lag effects on genetic variation, offer insights into demographic stochasticity in small populations and persistence in increasingly fragmented systems. Microsatellite markers were used to investigate the genetic diversity and structure of Podocarpus elatus (Podocarpaceae), a long-lived rainforest conifer endemic to Australia. Twenty-seven populations throughout the east Australian rainforests were screened and two divergent regions separated by the dry Clarence River valley (New South Wales) were discovered. This biogeographic barrier may be referred to as the Clarence River Corridor. Niche modelling techniques were employed to verify the incidence of habitat divergence between the two regions. Significantly high inbreeding was detected throughout the species range with no evidence of recent bottlenecks. Most of the diversity in the species resides between individuals within populations, which suggest the species would be sensitive to the adverse effects of inbreeding, yet evidence suggests that these populations have been small for several generations. Slightly higher diversity estimates were found in the southern region, but it is likely that the species survived historic population contraction in dispersed refugia within each of these genetically differentiated regions.
Moon phase and nocturnal activity of native Australian mammals

Moon phase and variation in ambient light conditions can influence predator and prey behaviour. Nocturnal predators locate prey visually, and prey may adjust their activity to minimise their predation risk. Understanding how native mammals in Australia respond to varying phases of the moon and cloud cover (light) enhances knowledge of factors affecting species’ survival and inference regarding ecological and population survey data. Over a two-year period within a fenced conservation reserve, in south-eastern Australia, with reintroduced native marsupial predator and prey species (eastern barred bandicoot, southern brown bandicoot, long-nosed potoroo, rufous bettong, Tasmanian pademelon, brush-tailed rock-wallaby, red-necked wallaby, eastern quoll, spotted-tailed quoll, and naturally occurring swamp wallaby, common brushtail possum, common ringtail possum), we conducted monthly spotlight surveys during different moon phases (full, half and new moon). We found an interaction between cloud cover and moon phase, and an interaction of the two depending on the mammal size and class. Increased activity of prey species corresponded with periods of increasing cloud cover. Predators and medium-sized herbivores were more active during times of low illumination. Our findings suggest that moon phase affects the nocturnal activity of mammal species and that, for prey species, there might be trade-offs between predation risk and foraging. Our findings have implications for: ecological survey design and interpretation of results for mammal populations across moon phases, understanding predator and prey behaviour and interactions in natural and modified (artificial lighting) ecosystems, and potential nocturnal niche partitioning of species.
Tidying-up the plant nuclear space: domains, functions, and dynamics

Abstract Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
Chemical Constituents and Bacterial Activity of Essential Oils of Five Wax Apples (Syzygium samarangense) from Dong Thap Province, Vietnam

120 Normal 0 21 false false false HR X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Obicna tablica"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri",sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} In the present study, essential oils from the leaves of five varieties of wax apple trees, ('An Phuoc', 'Hoa An', 'Hong Dao', 'Sua', and 'Xanh Duong') collected in Dong Thap Province, Vietnam were isolated using hydrodistillation, and their constituents were for the first time identified via gas chromatography - mass spectrometry. A total of 74 compounds from essential oils were identified. These compounds were classified into four clusters by hierarchical clustering analysis. The main constituents of the essential oils isolated from the leaves of five varieties of wax apple trees were o-cymene, α-cubebene, epizonarene, β-gurjunene, and α-selinene. The antibacterial activity of the essential oils isolated from the leaves of five varieties of wax apples were evaluated for the first time. The results showed that the essential oils could inhibit the growth of four tested microorganisms: Bacillus cereus, Escherichia coli, Salmonella enteritidis and Staphylococcus aureus .
Enhancement of the Arabidopsis floral dip method with XIAMETER OFX-0309 as alternative to Silwet L-77 surfactant

Arabidopsis thaliana (L.) Heynh. has emerged as the dominant plant species used in molecular genetics and functional genomics. Although it possesses several attributes of model organisms, the ease with which it can be transformed genetically is a paramount factor that has led to its widespread application as a tool for functional genomics. Progress made in the late 1990s has relieved users of the need to use a vacuum chamber for transformation, substituting its function with a surfactant known as Silwet L-77, to facilitate access to ovules by bacterial solution. Here, we evaluate the substitution of Silwet L-77 by XIAMETER OFX-0309. We demonstrate that transformation efficiency can be increased by an average of 3-fold (and up to 10-fold) solely by replacing Silwet L-77 with XIAMETER OFX-0309. Because downstream selection of transgenic plants, in either soil or Petri dishes, can be long and tedious, this substitution represents a significant reduction of time and materials required to retrieve transgenic lines. Resume : Arabidopsis thaliana (L.) Heynh. est apparue comme principale espece vegetale utilisee en genetique moleculaire et en genomique fonctionnelle. Meme si elle possede plusieurs attributs des organismes modeles, la facilite avec laquelle elle peut etre transformee genetiquement constitue un facteur cle qui a conduit asa vaste utilisation comme outil en genomique fonction- nelle. Les progres realises depuis les annees 90 ont permis aux utilisateurs d'eviter d'avoir autiliser une chambre avide pour la transformation, substituant sa fonction par un surfactant connu sous le nom de Silwet L-77, afin de faciliter l'acces aux ovules par la solution bacterienne. Les auteurs ont evalue la substitution du Silwet L-77 par le XIAMETER OFX-0309. Ils demontrent que l'efficacite de transformation peut etre accrue de trois fois en moyenne (et jusqu'adix fois), simplement en remplacant le Silwet L-77 par le XIAMETER OFX-0309. Puisque la selection en aval de plantes transgeniques, que ce soit en sol ou en petri, peut etre longue et fastidieuse, cette substitution represente une reduction significative du temps et du materiel requis pour recuperer les lignees transgeniques. (Traduit par la Redaction) Mots-cles : trempage floral, Arabidopsis thaliana, transgenique, surfactant, Silwet L-77, transformation d'Arabidopsis.
Characterization of optimal growth conditions and carotenoid production of strain Rhodotorula mucilaginosa HP isolated from larvae of Pieris rapae

Yeasts have been studied because of their production of a pigment known as carotenoid with potential application in food and feed supplements. A carotenoid‐producing yeast was isolated from the larvae of Pieris rapae, named HP. The strain HP was identified as Rhodotorula mucilaginosa classified by its carbohydrate fermentation pattern and physiological tests. Rhodotorula mucilaginosa HP produces several exogenous enzymes: alkaline phosphatase, esterase, leucine arylamidase, valine arylamidase, acid phosphatase and β‐glucosidase. Using response surface methodology, selected medium components (yeast extract, malt extract, peptone, glucose) were tested to find the optimum conditions for carotenoid production and the growth of R. mucilaginosa HP. Central composite design was used to control the concentrations of medium components. Peptone and glucose had the largest effects on carotenoid production and cell growth of R. mucilaginosa HP, respectively. The estimated optimal growth conditions of R. mucilaginosa HP were: yeast extract 3.23%, malt extract 2.84%, peptone 6.99% and glucose 12.86%. The estimated optimal conditions for carotenoid production were: yeast extract 2.17%, malt extract 2.11%, peptone 5.79% and glucose 12.46%. These results will assist in the formulation of an appropriate culture medium for optimal carotenoid production of R. mucilaginosa HP for commercial use.
An Ecological Study of the Effect of Certain Management Practices on Native Prairie in Iowa

MATERIALS AND METHODS . 115 Experimental Area 115 Treatment Application on the Experimental Area 117 Climatological Measurements . 117 Air Temperature 117 Weather Bureau Data . 117 Soil Measurements 118 Soil Temperature 118 Soil Moisture Determinations . 118 Soil Structure Characteristics . 118 Soil Nutrient Determinations . 118 Vegetation Measurements 118 Plant Growth 118 Seedstalk Production . 118 Forage Production 119 Litter Measurements 119
Molecular Study of Broomrape (Orobanche Spp.) by Rapd Analyses

ABSTRACT Broomrapes (Orobanche spp.) are the most devasting parasitic weeds, causing extensive damage to many important agricultural crops worldwide. Despite the tremendous economic impact of broomrapes on the agriculture little is known of the pattern of the genetic variation within this group until now and particularly in Bulgaria and other South-Eastern European countries. The present paper describes the application of six RAPD markers for the study of Orobanche species—O. cumana Wallr. /O. cernua Loefl. and O. ramosa L. using seed samples originating from different agro-ecological regions in South-Eastern Europe and middle East. Genetic variation among some of O. cumana Wallr. /O. cernua Loefl. samples representing populations originating from different geographical regions was detected.
Should Cardaria draba (L.) Desv. be classified within the genus Lepidium L. (Brassicaceae)? Evidence from subunit polypeptide composition of RUBISCO

The polypeptide composition of the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxy-genase (RUBISCO) from Cardaria draba (L.) DESV. (Brassicaceae) and from representatives of the related genus Lepidium L. have been studied by isoelectric focusing (IEF) analysis. In the literature Cardaria DESV. is either treated as a separate genus or as a section within the genus Lepidium Cardaria draba (L.) DESV. and three Lepidium taxa of section Lepia (DESV.) DC. are characterized by identical polypeptide patterns otherwise not found in Lepidium. RUBISCO data would preliminarily suggest that C. draba has its closest relatives within Lepidium section Lepia and therefore could possibly be placed best within this section. Mithilfe der isoelektrischen Fokussierungsmethode wurde die Polypeptidzusammensetzung der grosen und kleinen Untereinheiten des Enzyms Ribulose-1,5-Bisphosphat Carboxylase/Oxygenase (RUBISCO) von Cardaria draba (L.) DESV. (Brassicaceae) und Vertretern der verwandten Gattung Lepidium L. analysiert. In der Literatur wird Cardaria DESV. entweder als eigenstandige Gattung oder als eine Sektion innerhalb von Lepidium aufgefast. Cardaria draba und Vertreter der Sektion Lepia (DESV.) DC. aus der Gattung Lepidium sind durch identische Polypeptid muster der RUBISCO-Untereinheiten charakterisiert, die ansonsten nicht in der Gattung Lepidium auftreten. Diese Ergebnisse lassen vermuten, das sich die nachsten Verwandten von C. draba in der Sektion Lepia der Gattung Lepidium befinden und das somit C. draba in die Sektion Lepia zu stellen ist.
CRYOPRESERVATION OF THE CONCHOCELIS OF PORPHYRA (RHODOPHYTA) BY APPLYING A SIMPLE PREFREEZING SYSTEM 1

The conchocelis cells of four strains of Porphyra yezoensis Udea and four other Porphyra species were cryopreserved in liquid nitrogen (LN) using a programmable freezer or a simple prefreezing system, which consisted of a styrofoam box and a deep‐freezer at −40° C. The cells differed in their freezing tolerance but survived maximally when prefrozen to −40° C in a cryoprotective solution composed of 10% dimethylsulfoxide and 0.5 M sorbitol in 50% seawater. The cryopreservation was successfully performed by applying the simple prefreezing system as well as by a programmable freezer. Conchocelis cells thawed from the LN temperature formed colonies and retained the ability to form conchospores that grew into gametophytic thalli. This technique using a simple prefreezing system will accelerate the spread of Porphyra cryopreservation.