Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciding When to Trade Data Freshness for Performance in MongoDB-as-a-Service

MongoDB is a popular document store that is also available as a cloud-hosted service. MongoDB internally deploys primary-copy asynchronous replication, and it allows clients to vary the Read Preference, so reads can deliberately be directed to secondaries rather than the primary site. Doing this can sometimes improve performance, but the returned data might be stale, whereas the primary always returns the freshest data value. While state-of-practice is for programmers to decide where to direct the reads at application development time, they do not have full understanding then of workload or hardware capacity. It should be better to choose the appropriate Read Preference setting at runtime, as we describe in this paper.We show how a system can detect when the primary copy is saturated in MongoDB-as-a-Service, and use this to choose where reads should be done to improve overall performance. Our approach is aimed at a cloud-consumer; it assumes access to only the limited diagnostic data provided to clients of the hosted service.
Promoter library based pathway optimization for efficient (2S)-naringenin production from p-coumaric acid in Saccharomyces cerevisiae.

Pathway optimization plays an important role in fine-tuning metabolic pathways. In most conditions, more than three genes are involved in the biosynthesis pathway of a specific target product. To improve the titer of products, rational regulation of a group of genes by a series of promoters with different strengths is essential. On the basis of a series of RNA-Seq data, a set of 66 native promoters was chosen to fine-tune gene expression in Saccharomyces cerevisiae. Promoter strength was characterized by measuring the fluorescence strength of enhanced green fluorescent protein through fluorescence activated cell sorting. The expression of PTDH1, PPGK1, PINO1, PSED1 and PCCW12 was stronger than that of PTDH3, whereas another 15 promoters were stronger than PTEF1. Then, 30 promoters were chosen to optimize the biosynthesis pathway of (2S)-naringenin from p-coumaric acid. With a high throughput screening method, the highest titer of (2S)-naringenin in a 5-L bioreactor reached 1.21 g/L from p-coumaric acid, which is the highest titer according to the current available reports.
Body Mass Index Trajectory–Specific Changes in Economic Circumstances: A Person-Oriented Approach Among Midlife and Ageing Finns

Economic disadvantage is related to a higher risk of adulthood obesity, but few studies have considered whether changes in economic circumstances depend on a person’s body mass index (BMI) trajectory. We identified latent BMI trajectories among midlife and ageing Finns and captured individual-level changes in economic circumstances within the BMI trajectories utilizing sequence analysis. We used the Helsinki Health Study cohort data of initially 40–60-year-old Finnish municipal employees, with four survey questionnaire phases (2000–2017). Each survey included identical questions on height and weight, and on economic circumstances incorporating household income and current economic difficulties. Based on computed BMI, we identified participants’ (n = 7105; 82% women) BMI trajectories over the follow-up using group-based trajectory modeling. Four BMI trajectories were identified: stable healthy weight (34% of the participants), stable overweight (42%), overweight to class I obesity (20%), and stable class II obesity (5%). Lower household income level and having economic difficulties became more common and persistent when moving from lower- to higher-level BMI trajectories. Differences in household income widened over the follow-up between the trajectory groups, whereas economic difficulties decreased equally in all trajectory groups over time. Our study provides novel information on the dynamic interplay between long-term BMI changes and economic circumstances.
Chromosome Number, Quantitative Genetics and Eusociality

Sherman (1979) has shown that there is a positive correlation between chromosome number and the incidence of eusociality in insects. He hypothesizes that this correlation is caused by the fact that the degree of relatedness between any two sibs is not a constant but rather is a random variable, due to the stochastic nature of meiosis and sexual reproduction. Thus, all sibs are not equally related from a genetic point of view. He then argues that if phenotypic differences are positively correlated with genotypic differences, there may be selection favoring those workers who discriminate and preferentially assist only those sibs that are phenotypically, and thus genotypically, most similar to themselves. Such preferential ssistance would interfere with the evolution of eusociality under Sherman's hypothesis. Finally, Sherman assumes the variance in relatedness among sibs decreases as chromosome number increases; hence, the importance of discrimination in interfering with the evolution of eusociality should be most important when chromosome number is small. The purpose of this note is twofold: (1) to quantify the relationship between chromosome number and variance in relatedness among sibs, and (2) to present some additional mechanisms that could contribute to the observed correlation between chromosome number and eusociality. The relationship between chromosome number and variance in relatedness among sibs in a diploid species has been quantified under the assumptions of no crossingover and equal chromosome sizes (i.e., all chromosomes have the same number of loci) by Barash et al. (1978). They show that the distribution of x, the number of chromosomes hared by two sibs, is binomial,
A predictive dynamic yeast model based on component, energy, and electron carrier balances.

The present study describes a novel yeast model for the prediction of yeast fermentation. The proposed model considers the possible metabolic pathways of yeast. For each pathway, the time evolution of components, energy (ATP/ADP), and electron carriers (NAD+ /NADH) are expressed with limitation factors for all quantities consumed by each respective pathway. In this manner, the model can predict partition of these pathways based on the growth conditions and their evolution over time. Several biological pathways and their stoichiometric coefficients are well-known from literature. It is important to note that most of kinetics parameters have no effect since actual kinetics are controlled by balance of limiting factors. The few remaining parameters were adjusted and compared with the literature when the dataset was available. The model fits our experimental data from yeast fermentation on glucose in non-aerated batch system. The predictive ability of the model and its capacity to represent the intensity of each pathway over time facilitate an improved understanding of interactions between the pathways. The key role of energy (ATP) and electron carrier (NAD+ ) to trigger the different metabolic pathways during yeast growth is highlighted, while involvement of mitochondrial respiration not being associated with the TCA cycle is also shown. This article is protected by copyright. All rights reserved.
Hakin-1, a New Specific Small-Molecule Inhibitor for the E3 Ubiquitin-Ligase Hakai, Inhibits Carcinoma Growth and Progression

The requirement of the E3 ubiquitin-ligase Hakai for the ubiquitination and subsequent degradation of E-cadherin has been associated with enhanced epithelial-to-mesenchymal transition (EMT), tumour progression and carcinoma metastasis. To date, most of the reported EMT-related inhibitors were not developed for anti-EMT purposes, but indirectly affect EMT. On the other hand, E3 ubiquitin-ligase enzymes have recently emerged as promising therapeutic targets, as their specific inhibition would prevent wider side effects. Given this background, a virtual screening was performed to identify novel specific inhibitors of Hakai, targeted against its phosphotyrosine-binding pocket, where phosphorylated-E-cadherin specifically binds. We selected a candidate inhibitor, Hakin-1, which showed an important effect on Hakai-induced ubiquitination. Hakin-1 also inhibited carcinoma growth and tumour progression both in vitro, in colorectal cancer cell lines, and in vivo, in a tumour xenograft mouse model, without apparent systemic toxicity in mice. Our results show for the first time that a small molecule putatively targeting the E3 ubiquitin-ligase Hakai inhibits Hakai-dependent ubiquitination of E-cadherin, having an impact on the EMT process. This represents an important step forward in a future development of an effective therapeutic drug to prevent or inhibit carcinoma tumour progression.
Applicability of the Ussing Chamber Technique to Permeability Determinations in Functionally Distinct Regions of the Gastrointestinal Tract in the Rat

Background: Ussing chambers are commonly utilized for in vitro investigations into gastrointestinal permeability. However, their sensitivity and applicability to the small intestine have not been well characterized. Methods: In order to investigate the effects of experimentally induced damage and the relative contribution of the mucosa and muscularis externa layers to transmural permeability in the small intestine, stomach and colon, normal rat intestinal tissues were mounted in Ussing chambers with or without removal of the muscularis externa or mucosal layers. Gastric tissues were damaged in vivo by exposure to indomethacin (100 r mg r kg m 1 ), while ileal tissues were damaged in vitro by 0.4 r M NaCl. Tissue damage was assessed histologically, while permeability parameters included conductance (G), potential difference (PD) and mucosal to serosal flux of horseradish peroxidase (HRP). Results: Damage localized to the tissue edges (edge damage) accounted for 25%-50% of the exposed epithelial length in the ileum, while less than 20% of stomach and colon epithelium was affected by edge damage. In the damaged stomach, a 20% reduction in epithelialization was accompanied by increases in G ( P r < r 0.001) and HRP ( P r < r 0.01) flux. Removal of the muscularis externa did not affect mucosal viability in the undamaged ileum or colon although HRP flux in the colon, but not ileum, was increased ( P r < r 0.01). Removal of the ileal mucosa produced increases in G and HRP flux, while PD was maintained. Conclusion: We conclude that the Ussing chamber technique is suitable for application to studies of gastric and colonic permeability in rats. However, owing to the prevalence and extent of edge damage in the small intestine, we would caution against the use of this technique for permeability studies in this region of the gastrointestinal tract in the rat.
Privacy Preserving Calculation in Cloud using Fully Homomorphic Encryption with Table Lookup

To protect data in cloud servers, fully homomorphic encryption (FHE) is an effective solution. In addition to encrypting data, FHE allows a third party to evaluate arithmetic circuits (i.e., computations) over encrypted data without decrypting it, guaranteeing protection even during the calculation. However, FHE supports only addition and multiplication. Functions that cannot be directly represented by additions or multiplications cannot be evaluated with FHE. A naïve implementation of such arithmetic operations with FHE is a bit-wise operation that encrypts numerical data as a binary string. This incurs huge computation time and storage costs, however. To overcome this limitation, we propose an efficient protocol to evaluate multi-input functions with FHE using a lookup table. We extend our previous work, which evaluates a single-integer input function, such as $f(x)$. Our extended protocol can handle multi-input functions, such as $f(x,y)$. Thus, we propose a new method of constructing lookup tables that can evaluate multi-input functions to handle general functions. We adopt integer encoding rather than bit-wise encoding to speed up the evaluations. By adopting both permutation operations and a private information retrieval scheme, we guarantee that no information from the underlying plaintext is leaked between two parties: a cloud computation server and a decryptor. Our experimental results show that the runtime of our protocol for a two-input function is approximately 13 minutes, when there are 8,192 input elements in the lookup table. By adopting a multi-threading technique, the runtime can be further reduced to approximately three minutes with eight threads. Our work is more practical than a previously proposed bit-wise implementation, which requires 60 minutes to evaluate a single-input function.
Kinematics of terrestrial snake locomotion

The lateral undulatory, sidewinding and concertina modes of limbless terrestrial locomotion were analyzed from cinematographic films of five species of snakes and one amphisbaenian crawling on a variety of substrates. For single points on each animal, graphs of V, (overall velocity), V, (longitudinal component) and V, (lateral component) vs time were used to characterize locomotor modes and to detect their simultaneous use. Only concertina locomotion was used by the amphisbaenian Rhineura floridana. While performing lateral undulation, the constricting colubrid snake Elaphe obsoleta did not attain a maximum mean V, as great as that of Nerodia fasciata, a nonconstricting colubrid. Concertina locomotion is described for the snakes Acrochordus javanicus and N. fasciata. Sidewinding is described for N.fasciata, Cerberus rynchops and Crotalus cerastes. Cerberus rynchops moving on sand combined sidewinding with lateral undulation. The relation between V, and frequency of movement is described and compared among each of the terrestrial modes and with aquatic lateral undulation.
An improved selective and diagnostic medium for the isolation and enumeration of Bacillus cereus in foods

The use and performance of an improved diagnostic and selective medium, PEMBA (polymyxin pyruvate egg yolk mannitol bromothymol blue agar), for the detection of Bacillus cereus in foods is described. The distinct colonial appearance of B. cereus on PEMBA permitted the recognition of both strains: those that do precipitate egg yolk and those that do not react with egg yolk. A staining procedure, used to demonstrate microscopically both the presence of lipid globules in vegetative cells and spore morphology of isolates, proved a rapid and reliable confirmatory test which gave complete agreement with a battery of biochemical tests used for this purpose. The quantitative recovery of B. cereus on PEMBA from 143 food samples was not significantly different from counts on KG (Kim and Goepfert), MYP (mannitol egg yolk phenol red), and McClung's media, and the selectivity of PEMBA was generally superior.
Histopathological and Cell Biological Factors of Ductal Carcinoma in Situ Before and After the Introduction of Mammographic Screening

With the introduction of mammographic screening the incidence of ductal carcinoma in situ (DCIS) has increased to 10-15% of all breast cancers. The aim of this study was to investigate whether there were any morphological and cell biological differences between DCIS detected during the pre-screening (n = 39) as opposed to the screening period (n = 120). We could not demonstrate any statistically significant differences between the pre-screening and the screening period with regard to nuclear grade, presence of necrosis, the Van Nuys classification system, growth pattern, or cell biological factors (estrogen and progesterone receptors, c-erbB-2, p53, DNA ploidy status, Ki67, and Auer classes). These findings suggest that DCIS tumors detected during the two time periods have a similar malignant potential. DCIS detected during the screening period was further divided into the prevalence period versus the period thereafter, and symptomatic versus screening-detected asymptomatic cases. More cases with diffuse growth patterns were seen during the prevalence period than after the prevalence period, and screening-detected asymptomatic DCISs were more often 15 mm or smaller in diameter than DCISs detected symptomatically.
The nutritive value and phosphorus availability of yellow- and dark-seeded rapeseed cakes and the effects of phytase supplementation in broilers.

Three experiments on 242 Ross 308 broiler females were conducted to evaluate the nutritive value of expeller cakes cold-pressed from 3 yellow-seeded lines (YRC 041, 036, and 022) and black-seeded winter rape (BRC), and the effects of phytase supplementation. The total P content and phytase activity were similar in YRC and BRC and averaged 9.5 g/kg and 411 U/kg, respectively. Total glucosinolate contents in YRC were from 8.7 to 10.2 μmol/g dry matter (DM), in BRC, 12.6 μmol/g DM, in which progoitrin constituted 6% to 15% in YRC, and 35% in BRC. In the first experiment, the apparent metabolizable energy (AME N ) and nutrient digestibility of cakes were determined on 5 groups of 10, three-week-old chickens. Apparent protein digestibility did not differ between YRC and BRC and averaged 79.8%. Apparent crude fat digestibility and AME N were higher in YRC in comparison with BRC due to the lower fat content in the latter, but AME N averaged 8.95 MJ/kg of fat-free DM and did not differ between YRC and BRC. In the second experiment, a digestibility trial was conducted on 12 groups of 8 three-week-old chickens fed semisynthetic diets containing 45% cakes unsupplemented or supplemented with phytase (500 or 1000 U/kg). Phosphorus retention from YRC and BRC did not differ and averaged 39%. It increased due to phytase supplementation to 45.5% and 51.7%, on average. The third experiment was conducted on 8 groups of 12 chickens between 8-35 days of age fed low-phosphorus diets containing 30% cakes, unsupplemented or supplemented with 1000 U phytase/kg. Birds fed diets with BRC had a lower feed conversion ratio and higher thyroid weight in comparison with YRC-fed birds. Phytase supplementation increased feed intake (P<0.01), body weight gain (P<0.01) and tibia
Impact of Disadvantaged Neighborhoods and Lifestyle Factors on Adult Obesity: Evidence From a 5-Year Cohort Study in Australia

Purpose: This study aims to investigate the impact of disadvantaged neighborhoods and lifestyle factors on obesity among Australian adults. Design: Quantitative, longitudinal research design. Setting: Cohort. Sample: Data for this study came from a cohort of 10 734 adults (21 468 observations) who participated in the Household, Income and Labour Dynamics in Australia survey. The participants were interviewed at baseline in 2013 and were followed up in 2017. Measures: Generalized Estimating Equation model with logistic link function was employed to examine within-person changes in obesity due to disadvantaged neighborhoods and lifestyle factors at 2-time points over a 4-year follow-up period. Results: Adults living in the most disadvantaged area were 1.22 (odds ratio [OR]: 1.22, 95% CI: 1.08-1.38) and 1.30 (OR: 1.30, 95% CI: 1.20-1.42) times, respectively, more prone to be overweight and obese compared with peers living at least disadvantaged area. Study results also revealed that adults who consume fruits regularly and perform high levels of physical activity were 6% (OR: 0.94, 95% CI: 0.91-0.98) and 12% (OR: 0.88, 95% CI: 0.85-0.92) less likely to be obese, respectively, compared to their counterparts. Current alcohol drinkers were 1.07 (OR: 1.07, 95% CI: 1.01-1.13) times more likely to be obese compared to peers not consuming alcohol. Highly psychologically distressed adults were 1.08 times (OR: 1.08, 95% CI: 1.02-1.13) more likely to be obese than their peers. Conclusion: This study contributes to the literature regarding disadvantaged neighborhoods and lifestyle factors, which have an influence on adult obesity rates and thus help health decision-makers to formulate effective obesity prevention strategies.
Liming of wetlands in the acidified Lake Røynelandsvatn catchment in southern Norway: effects on stream water chemistry

En 1990, des milieux humides et des bogs en couverture formant 4,0% du bassin versant du lac Roynelandsvatn, dans le sud de la Norvege, ont fait l'objet d'un chaulage par helicoptere. La chaux a ete appliquee sous forme d'une poudre fine a raison de 20 t.ha -1 . Le traitement a cause une augmentation rapide du pH et de la concentration de calcium (Ca) dans le cours d'eau et une diminution des concentrations d'aluminium (AI) monomerique reactif et inorganique. Trois ans apres le traitement, les concentrations d'Al reactif etait encore 50% plus faible et celles de Ca deux fois plus elevees que les valeurs enregistrees avant le chaulage. Les potentiels de neutralisation de l'acide moyen et minimal de l'emissaire s'etablissaient a 23 et 8 μequiv. L -1 , respectivement, et bien que le pH ait chute pour se stabiliser autour de 5,2-5,3, l'eau etait encore d'une qualite suffisante pour permettre la survie de la truite brune (Salmo trutta). Aucune augmentation significative des concentrations de nitrate, d'azote organique ou de carbone organique total n'a ete observee dans le cours d'eau apres le chaulage. Le chaulage terrestre semble etre une approche utile pour neutraliser le ruissellement acide, etant donne la retention de l'Al monomerique inorganique dans le bassin recepteur et la hausse prolongee des concentrations de Ca et du potentiel de neutralisation de l'acide durant les debits d'orage et la fonte des neiges. Le chaulage des surfaces d'ecoulement dans le bassin peut aider a limiter l'ampleur des effets indesirables dans les ecosystemes terrestres, tels la mort des mousses du genre Sphagnum.
Serum Iodine and Breast Cancer Risk: A Prospective Nested Case–Control Study Stratified for Selenium Levels

Background: Iodine has been suggested to protect against breast cancer, but there are no epidemiologic studies on individual risk. An interesting finding is that in areas where the exposure to both selenium and iodine are high (e.g., Japan), the risk of breast cancer is lower than in areas where selenium is high and iodine low (e.g., United States), or in areas where both are low (e.g., Northern Europe). The aim of this study was to investigate the association between prediagnostic serum iodine levels and subsequent breast cancer risk, and to investigate if this potential association was modified by selenium levels. Methods: The Malmö Diet and Cancer Study provided prediagnostic serum samples and the current analysis included 1,159 breast cancer cases and 1,136 controls. Levels of baseline serum iodine and selenium were analyzed. A logistic regression analysis yielded ORs with 95% confidence intervals adjusted for potential confounders. Results: There was no evidence of an overall association between iodine levels and risk of breast cancer. Among women with high selenium levels (above the median), high iodine levels were associated with a lower risk of breast cancer; the OR for above versus below the median was 0.75 (0.57–0.99). The corresponding OR for women with low selenium was 1.15 (0.87–1.50), and the Pinteraction was 0.06. Conclusions: The combination of high serum iodine levels and high selenium levels was associated with a lower risk of breast cancer. Impact: A high iodine and selenium exposure may decrease the risk of breast cancer.