Miracle-dz/UniFAR-FTUs huggingface dataset:
Pippin: A pipeline for supernova cosmology

Pippin is a python pipeline for supernova cosmology analysis. It is designed to allow a user to specify a cosmological analysis via a configuration file, and then run that analysis, start to finish, in a single execution. Whilst other tools exist to perform various aspects of supernova cosmology analyses independently, connecting the required tasks has so far been a manual process. For the DES-3YR analysis (Abbott et al., 2019), we implemented a basic bash pipeline to reduce manual labour. For the DES-5YR analysis, which greatly increases complexity, we implement this pipeline to increase researcher productivity.
Towards nitrite as a therapy in cardiovascular disease

The nitrite anion has traditionally been considered an inert by-product of nitric oxide (NO) metabolism, but is now thought to be an important source of bioactive NO. Work from our department and others have implicated intrinsic vascular wall heme-proteins in a hypoxia-potentiated release of NO. The experiments presented in this thesis were designed to test the hypothesis that vascular wall myoglobin is one of the responsible proteins, and furthermore that the release of NO in relative hypoxia may be useful therapeutically in conditions such as heart failure and myocardial ischaemia. Experiments using murine aortic rings show that myoglobin is indeed an important vascular wall bioconverter of nitrite. Systemic nitrite infusions in healthy volunteers and patients with advanced heart failure show that this property of nitrite allows it to act as a specific venodilator in the latter condition; potentially overcoming some of the drawbacks of organic nitrates, such as hypotension and tolerance. Finally, studies in healthy volunteers, with and without a common variant of the aldehyde dehydrogenase enzyme, show that nitrite can protect the endothelium from ischaemia-reperfusion injury, depending upon temporal administration of the infusion and the genotype.
Fermentation parameters and total gas production of equine caecal and faecal inocula

This study intended to compare the fermentative activity of equine caecal and faecal inocula using the gas production technique. For that purpose, 2 feeds (oats and barley) were used. Caecal and faecal samples were collected from 2 canulated geldings fed with meadow hay (80%) and concentrate (20%) offered as two equal meals per day. Samples of caecal fluid and fresh faeces were collected 2 hours after the morning feed into pre-warmed flasks filled with CO2. Feed samples were incubated in 60 ml of buffered caecal or faecal fluid, in duplicate in 3 series performed on different days for each type of inoculum. The parameters pH, NH3-N and total VFA were measured after 96 h of fermentation. Gas production was recorded for 96 h using a fully automated system. Data were analyzed by ANOVA using feeds and inoculum as the main factors. Differences between feeds concerning pH (P<0.001), total VFA (P<0.001), NH3-N (P<0.001), acetate/propionate ratio (P<0.001) were observed as a result of different types of fermentation patterns. The type of inoculum showed differences in B (time of incubation at which half of the asymptotic gas production has been formed) parameter of gas production (P<0.05). Results presented in this study indicate similar fermentation patterns between faecal and caecal inocula.
Nutrition of Grazing Ruminants in Warm Climates

From the Preface The objective of this book is to review the basic knowledge and methodology of feeding grazing ruminants in tropical and semitropical countries. It is hoped this information will be of use to farmers, research specialists, teachers, students, extension specialists, feed manufacturers, and others throughout the world concerned with the nutrition of grazing ruminants. A unique feature is the identification of nutritional limitations of grazing ruminants in the tropics, which will be beneficial for increasing animal production efficiency through the application of improved nutrition. A large number of photographs illustrate nutritional deficiencies and conditions in tropical countries. This book contains 18 chapters concerned with the nutrition of grazing ruminants. The first chapter deals with the contributions, locations, and various types of ruminants and their importance to human welfare in the tropics and subtropics. Chapters 2 - 4 progress through nutrient requirements of grazing ruminants in warm climates, the effects of tropical heat on these requirements, and water requirements for ruminant species. Chapters 5 - 7 discuss grass and legume forage species suitable for tropical regions, pasture management procedures, and energy-protein supplementation programs needed during the extensive dry periods. The importance of tropical forages and soils toward meeting mineral requirements is discussed in Chapter 8. Chapters 9 -14 contain concise, up-to-date summaries of minerals emphasizing mineral status, incidence of mineral deficiencies and excesses in tropical regions, and benefits and methods of mineral supplementation for grazing ruminants are discussed in Chapters 15 - 17. Chapter 18 reviews vitamin nutrition considerations for ruminants consuming tropical forages.
Environment in stone chamber of an unexcavated tumulus and preservation of buried relics: Part 1. Environmental monitoring for simulated tumulus

Japan has many unexcavated tumuli, most of which were buried along with artifacts of precious cultural heritage. For such a tumulus, it is essential to understand how changes in its exterior environment affect its interior environment, and how those interior changes affect the deterioration of the relics buried in the stone chamber. In this study, an underground space was constructed in the forest of the Katsura Campus of Kyoto University to simulate the environment of an unexcavated tumulus, and long-term monitoring was implemented in the simulated stone chamber, including the temperature, humidity, water potential, wetness, and oxygen and carbon dioxide concentrations, along with metal corrosion tests. This article is focused on environmental monitoring, and the results demonstrate that the simulated tumulus has the general characteristics of the hygrothermal environments of an unexcavated tumulus that has small temperature fluctuation and near-saturation humidity. The ceiling of the simulated chamber condensed significantly from October to April, which is related to the variations of the ceiling and floor temperatures. Also, the wetness of the walls in the simulated chamber was affected by rainfall. The oxygen concentration in the simulated stone chamber varied in the range of 13%–19% in 2015, and the variation of carbon dioxide concentration in the simulated stone chamber was contrary to the oxygen concentration and varied in the range of 3%–9% in 2016. The oxygen concentration in the stone chamber was similar to that in the surrounding soil that decreased at times of rainfall, contrary to the fluctuations in the soil water content.
Taxonomy of Three-Qubit Mermin Pentagrams

Given the fact that the three-qubit symplectic polar space features three different kinds of observables and each of its labeled Fano planes acquires a definite sign, we found that there are 45 distinct types of Mermin pentagrams in this space. A key element of our classification is the fact that any context of such pentagram is associated with a unique (positive or negative) Fano plane. Several intriguing relations between the character of pentagrams’ three-qubit observables and ‘valuedness’ of associated Fano planes are pointed out. In particular, we find two distinct kinds of negative contexts and as many as four positive ones.
Effects of Tinnitus on Cochlear Implant Programming

Clinical observations suggest that tinnitus may interfere with programming cochlear implants (CIs), the process of optimizing the transmission of acoustic information to support speech perception with a CI. Despite tinnitus being highly prevalent among CI users, its effects and impact on CI programming are obscure. This study characterized the nature, time-course, and impact of tinnitus effects encountered by audiologists and patients during programming appointments. Semistructured interviews with six CI audiologists were analyzed thematically to identify tinnitus effects on programming and related coping strategies. Cross-sectional surveys with 67 adult CI patients with tinnitus and 20 CI audiologists in the United Kingdom examined the prevalence and time-course of those effects. Programming parameters established at CI activation appointments of 10 patients with tinnitus were compared with those of 10 patients without tinnitus. On average, 80% of audiologists and 45% of patients reported that tinnitus makes measurements of threshold (T) levels more difficult because patients confuse their tinnitus with CI stimulation. Difficulties appeared most common at CI activation appointments, at which T levels were significantly higher in patients with tinnitus. On average, 26% of patients reported being afraid of “loud” CI stimulation worsening tinnitus, affecting measurements of loudest comfortable (C) stimulation levels, and 34% of audiologists reported observing similar effects. Patients and audiologists reported that tinnitus makes programming appointments more difficult and tiresome for patients. The findings suggest that specific programming strategies may be needed during CI programming with tinnitus, but further research is required to assess the potential impact on outcomes including speech perception.
The challenge to make a difference

My first degree was in political and social sciences. This study became an eye-opener and introduced me to the intriguing world of ‘the political’. Ever since I have retained a fascination for (political) decision-making. When I switched to planning and got involved in major planning projects (Albrechts, 1999), I developed a good understanding of how decisionmaking in these projects worked out. My own experience in practice was confirmed by ample examples of well-documented cases of ‘plan-making’ and formal decision-making in the planning literature (Altshuler, 1965; Benveniste, 1989; Flyvbjerg, 1998; Meyerson and Banfield, 1955) and by substantive literature on implementation (Gualini, 2001; Majone and Wildavsky, 1979; Mastop and Faludi, 1997; Pressman and Wildavsky, 1974; Wildavsky, 1979). However, I also noticed that hardly any examples of cases analyzed from the perspective of the political class were available. Understandably political decision-making often seems like a black box to planners. Research by Flyvbjerg (1998) makes it clear that critical analysis of cases is needed to discover the ‘whys and wherefores’ of how elected representatives or preferential actors change the plan and why and how executive officers depart from the formally approved plan. A few years after a major planning process I was heavily involved in came to an end I started a small research project that focused on understanding the power dynamics of the wider political context in this particular process (Albrechts, 2003a, 2003b, 2006; see also Huxley, 2000; Flyvbjerg, 1998; Forester, 1989; Tewdwr-Jones and Allmendinger, 1998; Yiftachel, 1998). What I really wanted to understand was how regional government
Adipose Tissue in Persons With HIV Is Enriched for CD4+ T Effector Memory and T Effector Memory RA+ Cells, Which Show Higher CD69 Expression and CD57, CX3CR1, GPR56 Co-expression With Increasing Glucose Intolerance

Chronic T cell activation and accelerated immune senescence are hallmarks of HIV infection, which may contribute to the increased risk of cardiometabolic diseases in people living with HIV (PLWH). T lymphocytes play a central role in modulating adipose tissue inflammation and, by extension, adipocyte energy storage and release. Here, we assessed the CD4+ and CD8+ T cell profiles in the subcutaneous adipose tissue (SAT) and blood of non-diabetic (n = 9; fasting blood glucose [FBG] < 100 mg/dL), pre-diabetic (n = 8; FBG = 100–125 mg/dL) and diabetic (n = 9; FBG ≥ 126 mg/dL) PLWH, in addition to non- and pre-diabetic, HIV-negative controls (n = 8). SAT was collected by liposuction and T cells were extracted by collagenase digestion. The proportion of naïve (TNai) CD45RO−CCR7+, effector memory (TEM) CD45RO+CCR7−, central memory (TCM) CD45RO+CCR7+, and effector memory revertant RA+(TEMRA) CD45RO−CCR7− CD4+ and CD8+ T cells were measured by flow cytometry. CD4+ and CD8+ TEM and TEMRA were significantly enriched in SAT of PLWH compared to blood. The proportions of SAT CD4+ and CD8+ memory subsets were similar across metabolic status categories in the PLWH, but CD4+ T cell expression of the CD69 early-activation and tissue residence marker, particularly on TEM cells, increased with progressive glucose intolerance. Use of t-distributed Stochastic Neighbor Embedding (t-SNE) identified a separate group of predominantly CD69lo TEM and TEMRA cells co-expressing CD57, CX3CR1, and GPR56, which were significantly greater in diabetics compared to non-diabetics. Expression of the CX3CR1 and GPR56 markers indicate these TEM and TEMRA cells may have anti-viral specificity. Compared to HIV-negative controls, SAT from PLWH had an increased CD8:CD4 ratio, but the distribution of CD4+ and CD8+ memory subsets was similar irrespective of HIV status. Finally, whole adipose tissue from PLWH had significantly higher expression of TLR2, TLR8, and multiple chemokines potentially relevant to immune cell homing compared to HIV-negative controls with similar glucose tolerance.
Effects of Hand Configuration on the Grasping, Holding, and Placement of an Instrumented Object in Patients With Hemiparesis

Objective: Limitations with manual dexterity are an important problem for patients suffering from hemiparesis post stroke. Sensorimotor deficits, compensatory strategies and the use of alternative grasping configurations may influence the efficiency of prehensile motor behavior. The aim of the present study is to examine how different grasp configurations affect patient ability to regulate both grip forces and object orientation when lifting, holding and placing an object. Methods: Twelve stroke patients with mild to moderate hemiparesis were recruited. Each was required to lift, hold and replace an instrumented object. Four different grasp configurations were tested on both the hemiparetic and less affected arms. Load cells from each of the 6 faces of the instrumented object and an integrated inertial measurement unit were used to extract data regarding the timing of unloading/loading phases, regulation of grip forces, and object orientation throughout the task. Results: Grip forces were greatest when using a palmar-digital grasp and lowest when using a top grasp. The time delay between peak acceleration and maximum grip force was also greatest for palmar-digital grasp and lowest for the top grasp. Use of the hemiparetic arm was associated with increased duration of the unloading phase and greater difficulty with maintaining the vertical orientation of the object at the transitions to object lifting and object placement. The occurrence of touch and push errors at the onset of grasp varied according to both grasp configuration and use of the hemiparetic arm. Conclusion: Stroke patients exhibit impairments in the scale and temporal precision of grip force adjustments and reduced ability to maintain object orientation with various grasp configurations using the hemiparetic arm. Nonetheless, the timing and magnitude of grip force adjustments may be facilitated using a top grasp configuration. Conversely, whole hand prehension strategies compound difficulties with grip force scaling and inhibit the synchrony of grasp onset and object release.
Range Query Processing for Monitoring Applications over Untrustworthy Clouds

Privacy is a major concern in cloud computing since clouds are considered as untrusted environments. In this study, we address the problem of privacy-preserving range query processing on clouds. Several solutions have been proposed in this line of work, however, they become inefficient or impractical for many monitoring applications, including real-time monitoring and predicting the spatial spread of seasonal epidemics (e.g., H1N1 influenza). In this case, a system often confronts a high rate of incoming data. Prior schemes may thus suffer from potential performance issues, e.g., overload or bottleneck. In this paper, we introduce an extension of PINED-RQ to address these limitations. We also demonstrate experimentally that our solution outperforms PINED-RQ.
Charcuteries et cancérogenèse colorectale : additifs alimentaires et procédés de fabrication inhibant la promotion chez le rat

La consommation de charcuterie est associee au risque de cancer colorectal. L'objectif de cette these etait (i) valider l'effet promoteur des charcuteries dans un modele animal de cancerogenese et (ii) de trouver des composes antagonistes de cet effet promoteur. De l'epaule de porc riche en heme, salee et nitritee, puis cuite et oxydee (a l'air 5 j a 4°C) est promotrice des lesions precancereuses chez le rat chimio-induit par la dimethylhydrazine. Cette promotion s'accompagne d'une augmentation de composes N-nitroses fecaux. L'ajout de calcium dans le regime ou d'a-tocopherol dans la viande inhibe la promotion induite par cette viande saumuree. Par ailleurs, la saucisse de type hot-dog est promotrice des lesions precancereuses, cette promotion etant aussi inhibee par le calcium du regime. Nous pensons donc que l'on pourrait diminuer l'incidence du cancer par la consommation de produits riches en calcium ou par des modifications du procede de fabrication des charcuteries.
Sustainable Processes and Chemical Characterization of Natural Food Additives: Palmyra Palm (Borassus Flabellifer Linn.) Granulated Sugar

Palmyra palm (Borassus flabellifer Linn.) is an important sugar-producing plant that is widely distributed in tropical Asian countries. Its jaggery and sweet sap are prevalent in Cambodia as a substitute for table sugar. They contain essential minerals, vitamins, and biological compounds. We investigated the changes in the nutritional composition, antioxidant properties, and biological activity of palm granulated sugar prepared by using three different drying–solidification processes under vacuum conditions: the drying temperature was controlled at 80 °C, 90 °C, and 100 °C, and the drying time was 60, 75, and 90 min, respectively. Palm granulated sugar contains 10 kinds of vitamins (mainly vitamin E 52.15–55.12 mg/100 g), 5-hydroxymethylfurfural (2.18 to 41.92 mg/100 g), and 38 volatile compounds that belong to the alcohol, ketones, pyrazines, acids, and phenols groups, and an aldehyde group. Moreover, palm granulated sugar exhibits a high total phenolic content (2.77–8.94 mg gallic acid equivalent/100 g), 2,2-diphenyl-1-1picrylhydrazyl (DPPH) radical scavenging activity (20.15%–37.88%), and ferric reducing antioxidant power (FRAP) value (322.68–378.23 μmol Fe2+/mL). Furthermore, palm granulated sugar-treated NIH3T3 cells showed a higher cell viability of 18.10% to 23.68%. This study confirmed that palm granulated sugar prepared at 90 °C for 75 min can have a better product quality with increased vitamin and mineral contents, antioxidant properties, and biological activity, while also being low in 5-hydroxymethylfurfural (HMF) content.
Non-lysosomal Activation in Macrophages of Atlantic Salmon (Salmo salar) After Infection With Piscirickettsia salmonis

Piscirickettsia salmonis is a facultative intracellular pathogen and etiological agent of the systemic disease salmonid rickettsial septicemia. It has been suggested that P. salmonis is able to survive in host macrophages, localized within a vacuole like-compartment which prevents lysosomal degradation. However, the relevant aspects of the pathogenesis of P. salmonis as the host modulation that allow its intracellular survival have been poorly characterized. In this study, we evaluated the role of lysosomes in the response to P. salmonis infection in macrophage-enriched cell cultures established from Atlantic salmon head kidneys. Bacterial infection was confirmed using confocal microscopy. A gentamicin protection assay was performed to recover intracellular bacteria and the 16S rDNA copy number was quantified through quantitative polymerase chain reaction in order to determine the replication of P. salmonis within macrophages. Lysosomal activity in Atlantic salmon macrophage-enriched cell cultures infected with P. salmonis was evaluated by analyzing the lysosomal pH and proteolytic ability through confocal microscopy. The results showed that P. salmonis can survive ≥120 h in Atlantic salmon macrophage-enriched cell cultures, accompanied by an increase in the detection of the 16S rDNA copy number/cell. The latter finding suggests that P. salmonis also replicates in Atlantic salmon macrophage-enriched cell cultures. Moreover, this bacterial survival and replication appears to be favored by a perturbation of the lysosomal degradation system. We observed a modulation in the total number of lysosomes and lysosomal acidification following infection with P. salmonis. Collectively, the results of this study showed that infection of Atlantic salmon macrophages with P. salmonis induced limited lysosomal response which may be associated with host immune evasion mechanisms of P. salmonis that have not been previously reported.
Relationship of online Gaming addiction and study skills and habits of College Students

Online gaming is one of the major trends today and is one of the most common source of entertainment for people specially students. However, it can be addictive and may have negative effect to students. This study described the college students’ experiences in online gaming addiction. Also, it described the domains of study skills and habits of college students in terms of attitude, time management, goal setting, class preparation, and exam preparation. Further, it determined the relationships of college students’ sex and year level with their online gaming experiences and the domains of study skills and habits. This study used the descriptive method. The researcher circulated a survey questionnaire with Likert-scale responses to a total of 115 college students consisting of 40 male students and 75 female students which year levels are 30 first year, 34 second year, 22 third year and 29 fourth year students. Based on the results of the study, the researcher concluded that college students’ experiences in online gaming are as follows: they are not comfortable limiting their game time, they are bored when they do not play online games, they forgot to eat and they have stolen for gaming. However, college students did not necessarily neglect their responsibilities in school. In term of study skill and habits, the researcher concluded that college students have positive attitude to learn new things from school. They can start studying and they can keep it going. They do review practice problems to prepare for their class. Likewise, college students can adjust their study methods in terms of exam preparation. However, it is also concluded that they have on average goal setting plan though they are setting high standards for themselves in school. Furthermore, their sex and year level have nothing to do with their online gaming experiences and their study skills and habits. Same with their online gaming experiences are not associated with their study skills and habits. Since online gaming can be addicting, the researcher recommends that a school intervention should be done for the college students from where their experiences on it are quite alarming. Further study can be conducted focusing on the compulsive and obsessive behaviors of college students in relation to online gaming. Though positive results are present in terms of the study skills and habits of students, it is still recommended to have continuous monitoring not only of their skills and habits but on their academic performance in terms of academic grades, problems and deficiencies.