Miracle-dz/UniFAR-FTUs huggingface dataset:
L etter to the E ditor Clues to NaCN formation ?

Context. ALMA is providing us essential information on where certain molecules form. Observing where these molecules emission arises from, the physical conditions of the gas, and how this relates with the presence of other species allows us to understand the formation of many species, and to significantly improve our knowledge of the chemistry that occurs in the space. Aims. We studied the molecular distribution of NaCN around IRC +10216, a molecule detected previously, but whose origin is not clear. High angular resolution maps allow us to model the abundance distribution of this molecule and check suggested formation paths. Methods. We modeled the emission of NaCN assuming local thermal equilibrium (LTE) conditions. These profiles were fitted to azimuthal averaged intensity profiles to obtain an abundance distribution of NaCN. Results. We found that the presence of NaCN seems compatible with the presence of CN, probably as a result of the photodissociation of HCN, in the inner layers of the ejecta of IRC +10216. However, similar as for CH3CN, current photochemical models fail to reproduce this CN reservoir. We also found that the abundance peak of NaCN appears at a radius of 3 × 1015cm, approximately where the abundance of NaCl, suggested to be the parent species, starts to decay. However, the abundance ratio shows that the NaCl abundance is lower than that obtained for NaCN. We expect that the LTE assumption might result in NaCN abundances higher than the real ones. Updated photochemical models, collisional rates, and reaction rates are essential to determine the possible paths of the NaCN formation.
Factors Affecting the Organization of Group 1 Capsular Polysaccharides on the Surface of Escherichia coli

FACTORS AFFECTING THE ORGANIZATION OF GROUP 1 CAPSULAR POLYSACCHARIDES ON THE SURFACE OF Escherichia coli Megan Caroline Massey Advisor: University of Guelph, 2015 Chris Whitfield Many pathogenic isolates of Escherichia coli produce capsular polysaccharide (CPS). CPS make up a network of interacting polysaccharide chains to create a capsule layer covering the cell surface. Capsules protect E. coli from elements of host immune defenses. While some aspects of the E. coli group 1 CPS assembly and export are understood, details of their association with the cell surface and interplay with other surface structures are unresolved. It has been proposed that lipopolysaccharide (another class of surface glycoconjugate) molecules help stabilize the attachment of CPS. To test this, deletions in certain lipopolysaccharidebiosynthesis genes were made in a prototype isolate of E. coli E69 and their effect on capsule formation was examined by Western immunoblotting using CPS-specific antibodies, and sensitivity to a capsule-specific bacteriophage. An ELISA was developed to quantitate CPS production in the wild-type and mutants, leading to better understanding of influence of lipopolysaccharide structure on capsule
Generation and Characterization of Induced Pluripotent Stem Cells and Retinal Organoids From a Leber’s Congenital Amaurosis Patient With Novel RPE65 Mutations

RPE65-associated Leber congenital amaurosis (LCA) is one of highly heterogeneous, early onset, severe retinal dystrophies with at least 130 gene mutation sites identified. Their pathogenicity has not been directly clarified due to lack of diseased cells. Here, we generated human-induced pluripotent stem cells (hiPSCs) from one putative LCA patient carrying two novel RPE65 mutations with c.200T>G (p.L67R) and c.430T>C (p.Y144H), named RPE65-hiPSCs, which were confirmed to contain the same mutations. The RPE65-hiPSCs presented typical morphological features with normal karyotype, expressed pluripotency markers, and developed teratoma in NOD-SCID mice. Moreover, the patient hiPSCs were able to differentiate toward retinal lineage fate and self-form retinal organoids with layered neural retina. All major retinal cell types including photoreceptor and retinal pigment epithelium (RPE) cells were also acquired overtime. Compared to healthy control, RPE cells from patient iPSCs had lower expression of RPE65, but similar phagocytic activity and VEGF secretion level. This study provided the valuable patient specific, disease targeted retinal organoids containing photoreceptor and RPE cells, which would facilitate the study of personalized pathogenic mechanisms of disease, drug screening, and cell replacement therapy.
Orbital alignment of circumbinary planets that form in misaligned circumbinary discs: the case of Kepler-413b

Although most of the circumbinary planets detected by the Kepler spacecraft are on orbits that are closely aligned with the binary orbital plane, the systems Kepler-413 and Kepler-453 exhibit small misalignments of $\sim 2.5^\circ$. One possibility is that these planets formed in a circumbinary disc whose midplane was inclined relative to the binary orbital plane. Such a configuration is expected to lead to a warped and twisted disc, and our aim is to examine the inclination evolution of planets embedded in these discs. We employed 3D hydrodynamical simulations that examine the disc response to the presence of a modestly inclined binary with parameters that match the Kepler-413 system, as a function of disc parameters and binary inclinations. The discs all develop slowly varying warps, and generally display very small amounts of twist. Very slow solid body precession occurs because a large outer disc radius is adopted. Simulations of planets embedded in these discs resulted in the planet aligning with the binary orbit plane for disc masses close to the minimum mass solar nebular, such that nodal precession of the planet was controlled by the binary. For higher disc masses, the planet maintains near coplanarity with the local disc midplane. Our results suggest that circumbinary planets born in tilted circumbinary discs should align with the binary orbit plane as the disc ages and loses mass, even if the circumbinary disc remains misaligned from the binary orbit. This result has important implications for understanding the origins of the known circumbinary planets.
Studies on the Feasibility of Producing Biogas from Rice Waste

Biogas is considered as one of the alternative sources of energy which is used in many applications such as power generation, heating and refrigeration. The quantity and quality of biowastes vary due to the intensity and nature of human activity. Since the methane (CH4) composition in biogas is influenced by the ingredients of the biowaste, specific research is needed to check the biogas yield from locally available biowastes and to predict the usage of biogas as alternative energy in all levels. In countries like India, rice is a staple crop and the common food source for people. The food waste collected from common places like student’s hostels, restaurants and houses consists of wasted rice along with other wastes of meat, fish, vegetables and fruits. In this study, analytical & experimental work was done on the biogas production from various biowastes collected from an engineering college campus. The Anaerobic Digestion Model 1 (ADM1) was used for analytical studies, and four anaerobic digesters were used in the experimental investigation. Mesophilic condition was considered for this study. From the experimental studies it is observed that the methane content in the biogas produced from rice waste, mixed rice waste, cow dung and vegetable waste are 52.01%, 52.98%, 61.13% and 51.11% respectively. The results obtained from the simulation study are also close to the experimental values.
Conditional Correlations between Stock Index, Investment Grade Yield, High Yield and Commodities (Gold and Oil) during Stable and Crisis Periods

We analyzed the conditional correlation between the returns of five assets (S&P 500, investment grade bond, high-yield bond, crude oil and gold). The results obtained with the AGDCC model lead to several conclusions. The correlations between the assets retained are feeble during stable periods. In periods of financial crisis with sustained economic growth, adding gold, crude oil, high-yield bonds and investment-grade bonds in a portfolio can improve the benefit of this portfolio. However, investors should adjust their portfolio when concerns about the economic growth appear as crude oil is negatively correlated with the returns of the S&P 500 and the high-yield bond during crisis periods, but it is positively correlated with those assets’ returns when the crisis is coupled with economic recession. Regarding the high yield bond, it losses less value than stock index during bear market and it appreciates as much as stock index during bull market. As for the gold, it is a strong safe haven during periods characterized by fears of recession, concerns regarding the credit markets, target rate cuts, as well as uncertainties regarding inflation rate. Thus, gold was not a safe haven during the Asian and the Russian crises, whereas it was a weak safe haven during the dot-com crisis and a strong safe haven during the subprime crisis. During these crises, due to the "flight-to-quality" gold value appreciated strongly compared to the other assets retained. Furthermore, with the aggravation of the economic and financial situation the negative impacts of the subprime crisis have spread from stock market and high-yield bonds to other financial markets (contagion), except to the gold market.
Emergent electronic matter : Fermi surfaces, quasiparticles and magnetism in manganites and pnictides

In the first part of this chapter angle integrated photoemission data taken with hard x-ray radiation on cleaved single crystals of the bilayered, colossal magnetoresistant manganite La2−2xSr1+2xMn2O7 (LSMO) with 0.30 ≤ x < 0.50 are presented. Making use of the increased bulk-sensitivity upon hard x-ray excitation it is shown that the core level footprint of the electronic structure of the LSMO cleavage surface is identical to that of the bulk. Furthermore, by comparing the core level shift of the different elements as a function of doping level x, it is shown that microscopic phase separation is unlikely to occur for this particular manganite well above or below the Curie temperature. The second part of this chapter deals with angle resolved photoemission on the same doping series of bilayered LSMO. As phase separation does not occur at high and low temperatures, the discrepancy between the bulk transport behavior and the temperature dependence of the quasiparticle peaked ARPES spectra described in the previous chapter can definitely not be explained with such a scenario. It is shown that the quasi particle peaked signature in APRES experiments does not, in fact, belong to bilayered LSMO, but to local stacking faults in the crystal, which posses a more robust metallic character than the bilayered matrix they reside in. The real spectroscopic signature of bilayered LSMO is that of a psuedo-gapped semi-metal, without a real Fermi surface. This would reconcile the electronic structure as probed with ARPES with bulk probes such as transport and optical conductivity. 78 Chapter 4. Phase separation and spectral signature of LSMO
Haematology, serum and organ weight of broiler chickens fed boiled mucuna sloanei seed meal treated with enzyme

The haematology, serum and organ weight of broiler chickens fed boiled Mucunasloanei seed meal mixed with enzyme was investigated. The experiment was conducted with140 Anak broiler chickens divided into 3 treatments of 3 replicates and 10 birds per replicate. Birds fed diet 2 {7.5% boiled Mucuna mixed with enzyme (BME)} had higher final body weight of 2216.70g. The test diets gave lower total feed in-take value that was significantly ( P < 0.05) lower than that of the control. Diet 2 (D2) gave the bestfeed-to-gain ratio (1.72) that was significantly ( P <0.05) different from those of the control (2.09), diet 3 (D3)(2.08) and diet 4(2.27). For the carcass characteristics, D2 compared favourably with the control for percent dressed weight and back cut. The control had the lowest value for kidney and gizzard weights while D3 had the lowest weight of spleen. Serum albumin, urea, and creatinine were significantly ( P <0.05) affected. Diet 2 and 3 had a higher ( P <0.05) than that of the control diet (2.67g/dl. Diet 2 had urea content (19.66mg/dl that was lower ( P <0.05) than those of diet3 (23.67mg/dl) and 4(25.67mg/dl) but compared with that of the control diet919.00mg/dl). For creatinine value D3and D4 compared with D1 but significantly ( p <0.05) lower than D2.Urea concentration was increased as the percentage inclusion of MSS boiled and mixed with Maxi-grain enzyme increased from 0 to 12.5%. In conclusion, 7.5% of boiled Mucuna sloanei seed meal treated with enzyme (Maxi-grain) is recommended for inclusion in broiler ration since the birds placed on this ration were able to perform better than those fed with the conventional soya meal based ration. Keyword: mucuna haematology, serum, organ, broiler chicken, Maxi-grain
Interpretable factor models of single-cell RNA-seq via variational autoencoders

Single cell RNA-seq makes possible the investigation of variability in gene expression among cells, and dependence of variation on cell type. Statistical inference methods for such analyses must be scalable, and ideally interpretable. We present an approach based on a modification of a recently published highly scalable variational autoencoder framework that provides interpretability without sacrificing much accuracy. We demonstrate that our approach enables identification of gene programs in massive datasets. Our strategy, namely the learning of factor models with the auto-encoding variational Bayes framework, is not domain specific and may be of interest for other applications.
State of residual stresses after the process of milling selected aluminium alloys

The purpose of this paper was to analyse the structure and the state of residual stresses in the samples made of rolled AW-2024 and AW-7075 aluminium alloy plates, prior to machine cutting and after the process of milling under various machining conditions. The state of stresses was evaluated on the basis of measurements by means of sin2vF X-ray diffractometry and layer removal method. Furthermore, top layer microstructures were compared in half-finished product, machined product, and core material samples.
Agriculture as an Engine of Growth and Poverty Reduction

still the single most important productive sector in most low-income countries, often in terms of its share of Gross Domestic Product and almost always in terms of the number of people it employs. In countries where the share of agriculture in overall employment is large, broad-based growth in agricultural incomes is essential to stimulate growth in the overall economy, including the non-farm sectors selling to rural people. Research has shown that every dollar of growth from agricultural products sold outside the local area in poor African countries leads to a second dollar of local rural growth from additional spending on services, local manufactures, construction materials, and prepared foods.
Response of eggplant genotypes to avirulent and virulent populations of Meloidogyne incognita (Kofoid & White, 1919) Chitwood, 1949 (Tylenchida: Meloidogynidae)

Patlican dunyada yaygin bir sekilde yetistirilmektedir. Bununla birlikte bazi patlican genotipleri kok-ur nematodlarina ( Meloidogyne spp.) karsi duyarlidir. Bu nedenle Solanum torvum (Sw.) dunyada kok-ur nematodlarina karsi dayanikli anac olarak yaygin bir sekilde kullanilmaktadir. Kok-ur nematodlarina dayanikli yeni patlican genetik kaynaklarinin arastirilmasi islah icin gereklidir. Bu calismada yabani kaynaklar, yabani anaclar, yabani x yabani anaclar, yabani x kultur formu patlican anaclari, kultur formu anaclar, saf hatlar, standart ticari cesitler ve ticari hibritler olmak uzere toplam 60 genotip Meloidogyne incognita Kofoid & White, 1919) Chitwood, 1949 (Tylenchida: Meloidogynidae) ’ nin avirulent S6 ve Mi-1 virulent V14 populasyonu ile kontrollu kosullar altinda testlenmistir. Calisma 2016-2017 yillarinda yurutulmustur. Patlican fideleri M. incognita’ nin 1000 ikinci donem larvasi ile inokulasyon yapilmis ve bitkiler inokulasyondan 8 hafta sonra sokulmustur. Koklerdeki yumurta ve ur sayilari ile topraktaki larva sayilari sayilmistir. Solanum torvum (Y28)’un M. incognita ’nin S6 ve V14 populasyonlarina dayanikli, diger genotiplerin tumumun ise her iki populasyona duyarli oldugu belirlenmistir. Bu sonuclar kok-ur nematodlarinin kontrolu icin yapilacak olan islah ve mucadele calismalarinda kullanilabilir.
Lateral Geniculate Nucleus in Hypertensive and Normotensive Glaucoma

Objective: To find whether changes in lateral geniculate nucleus (LGN) can be determined in vivo in hypertensive and normotensive glaucoma, and whether these changes correlate with the advancement of glaucoma disease.Methods and subjects: The authors examined two groups of patients, 9 patients with hypertensive glaucoma (HTG) and 9 patients with different stages of normotensive glaucoma (NTG). The diagnosis was based on a comprehensive ophthalmological examination. The results of both groups were compared with a group of 9 healthy subjects. A comprehensive ophthalmological examination was supplemented by examination of the visual field by means of a fast threshold program. The sum of sensitivity in the field of vision of homolateral halves (range 0 to 22 degrees) was compared with the size of contralateral corpus geniculatum laterale.Data collected from patients were compared with a group of nine healthy controls.We carried out MRI tests at 3-Tesla MRI scanner (Philips Achieva TX series release 3.2.1.1) using eight-channel sense head coil.Results: The measured values were subjected to statistical analysis using the Wilcoxon test and Spearman´s rank correlation coefficient.The authors proved reduction of LGN in both HTG and NTG (p=0.0000). The LGN reduction dependence on the stage of changes in visual fields was not statistically significant, in HTG for the right half of visual fields (RH VF) and the left LGN r=0.3255, p=0.3926, and for the left half of visual fields (LHVF) and the right LGN r=0.0033, p=0.9934. Similarly, in NTG, statistically significant correlation between RH VF and L LGN (r=0.0496, p=0.1745) and between LHVF and R LGN (r=0.5399, p=0.1335) was not found either. The authors demonstrated median duration dependence in hypertensive glaucoma treatment to the reduction of the LGN. R=-0.4908, p=0.179 for the right LGN and r=-0.7743, p=0.0143 for the left LGN.Conclusion: The reduction of LGN volume was proved both in patients with HTG and those with NTG.
Vessels with Gold or Guilt: Emotional Reactions to Family Involvement Associated with Glorious or Gloomy Aspects of the Colonial Past

In two studies we examined whether forging a psychological bond with a nation’s colonization past facilitates the experience of positive and negative group-based self-conscious emotions as a function of a positive or negative manipulation of this past. Because people need to belong, we hypothesized that stronger family involvement in a nation’s colonization past (i.e. involved ancestors) evokes stronger a positive self-conscious emotions after positive descriptions of the nation’s colonizing past, and stronger negative self-conscious emotions after negative descriptions. In Study 1, we found support for these hypotheses in a real-life setting in which Dutch people actually found out whether their ancestors were involved in the colonization of Indonesia or not. In Study 2, we manipulated family involvement and valence of the past. Results offered support for the tested hypotheses. Implications of the results are discussed in relation to theories on identity and emotion.
Genetic factors underlying the bidirectional relationship between autoimmune and mental disorders – Findings from a Danish population-based study

Background Previous studies have indicated the bidirectionality between autoimmune and mental disorders. However, genetic studies underpinning the co-occurrence of the two disorders have been lacking. In this study, we examined the potential genetic contribution to the association between autoimmune and mental disorders. Methods We used diagnostic information for patients with seven autoimmune diseases and six mental disorders from the Danish population-based case-cohort sample (iPSYCH2012). We explored the epidemiological association using survival analysis and modelled the effect of polygenic risk scores (PRSs) on two diseases. The genetic factors were investigated using GWAS and HLA imputation data based on iPSYCH cohort. Results Among 64,039 individuals, a total of 43,902 (68.6%) were diagnosed with mental disorders and 1,383 (2.2%) with autoimmune diseases. There was a significant comorbidity between the two diseases (P=2.67×10-7, OR=1.38, 95%CI=1.22-1.56), with an overall bidirectional association wherein individuals with autoimmune diseases had an increased risk of subsequent mental disorders (HR=1.13, 95%CI: 1.07-1.21, P=7.95×10-5) and vice versa (HR=1.27, 95%CI=1.16-1.39, P=8.77×10-15). Though PRSs were significantly correlated with both types of diagnosis, PRSs had little effect on the bidirectional relationship. Importantly, we for the first time observed 12 human leukocyte antigen (HLA) loci and 20 HLA alleles strongly associated with overall autoimmune diseases, but we did not find significant evidence of their associations with overall mental disorders. Conclusions Our findings confirm the overall comorbidity and bidirectionality between autoimmune and mental disorders and discover HLA genes which are significantly associated with overall autoimmune diseases, but not with overall mental disorders.
Urbanization effects on hotel performance: A case study in China

Abstract This paper studied the impacts of urbanization regarding the performance of hotel in Guangdong through the study of panel data from 1994 to 2014. Urbanization was measured by economic, geographical landscape, population, and social cultural dimensions. This research suggested that urbanization generally improves hotel performance, but with different effects. Therefore, stakeholders, such as hospitality managers, could provide corresponding governance strategies according to the characteristics of the city and province in China.
Using R‐Based Image Analysis to Quantify Rusts on Perennial Ryegrass

An automated open‐source analysis system was developed to rate crown and stem rust. The system was validated against manual measurements and visual rater ability. Consistency in rater (n = 9) ability was excellent for crown rust and fair to good for stem rust. Agreement in rater scores for individual images was low and showed high levels of variation. The automated system can replace visual rating of crown rust in the field but not stem rust.
The Developing Approaches to Evolutionary Epistemology: An Historical Perspective

Evolutionary epistemology has been developed in various historical stages that responds to different approaches, namely, adaptationism, non-adaptationism and interactionism. This paper gives an account of three approaches in terms of the hot debate on confirming the mechanism of biological evolution and elucidates why these approaches have been developed in different contexts. It is suggested that the development of evolutionary epistemology should be of implications on the studies of epistemology. Keywords—evolutionary epistemology, adaptationism, non-adaptationism, organism, environment