Miracle-dz/UniFAR-FTUs huggingface dataset:
Widespread noncoded amino acids in human proteome

Proteins are usually deciphered by translation of the coding genome; however, their amino acid residues are seldom determined directly across the proteome. Herein, we describe a systematic workflow for identifying all possible protein residues that differ from the coding genome, termed noncoded amino acids (ncAAs). By measuring the mass differences between the coding amino acids and the actual protein residues in human spermatozoa, over a million nonzero delta masses were detected, fallen into 424 high-quality Gaussian clusters and 571 high-confidence ncAAs spanning 29,053 protein sites. Most ncAAs are novel with unresolved side-chains and discriminative between healthy individuals and patients with oligoasthenospermia. For validation, 40 out of 98 ncAAs that matched with amino acid substitutions were confirmed by exon sequencing. This workflow revealed the widespread existence of previously unreported ncAAs in the sperm proteome, which represents a new dimension on the understanding of amino acid polymorphisms at the proteomic level. Highlights 571 ncAAs spanning 108,000 protein sites were identified in human sperm proteome. Most ncAAs are novel with unresolved sidechains and found at unreported protein sites. Exon sequencing confirmed 40 of 98 ncAAs that matched with amino acid substitutions. Many ncAAs are linked with disease and have potential for diagnosis and targeting. eTOC Blurb We describe a systematic identification of all possible protein residues that were not encoded by their genomic sequences. A total of 571 high-confidence most novel noncoded amino acids were identified in human sperm proteome, corresponding to over 108,000 ncAA-containing protein sites. For validation, 40 out of 98 ncAAs that matched to amino acid substitutions were confirmed by exon sequencing. These ncAAs are discriminative between individuals and expand our understanding of amino acid polymorphisms in human proteomes and diseases.
“The child goes back to the trafficking situation”: Consequences of inappropriate assistance procedures during reintegration of child victims of trafficking

Trafficking poses a direct threat to the victim’s rights, development and well-being, with childhood trafficking experiences having far-reaching effects. Thus, assistance provision measures should target each of the areas as impacted by the child’s trafficking experience. This paper sets out to show the consequences of inappropriate assistance procedures during reintegration in relation to transnational trafficked children. It was a qualitative study and data reported on was collected from 22 trafficking experts (stakeholders) in South Africa. The major consequences of inappropriate reintegration assistance provision identified are re-trafficking, stigmatisation, secondary trauma and victimisation and mistrust in victims. The findings show that if inappropriately handled, reintegration procedures related to assistance provision can have negative implications for trafficked children. This paper shows that there is need for preand post-reintegration assistance services and programmes which are trauma-informed, victim-centred, community and culturally sensitive and multidisciplinary in nature.
Effect of Alkali Ions on the Amorphous to Crystalline Phase Transition of Silica

Abstract The effect of the addition of alkali ions to commercial amorphous silica, generally used as support for heterogeneous catalysts, has been investigated from the point of view of morphological and structural changes. Samples of alkali-doped silica were prepared by impregnation and subsequent calcination at various temperatures. The structural effect of Li, Na, K, and Cs was determined by use of techniques such as wide-angle (WAXS) and small-angle X-ray scattering (SAXS). The WAXS diffractograms, analyzed with the Rietveld method using the GSAS program, allowed qualitative and quantitative identification of the fraction of the different silica polymorphs like quartz, tridymite, and cristobalite. SAXS measurements, using the classical method based on Porod's law, yielded the total surface area of the systems. The calculated areas were compared with the surface areas determined by the nitrogen adsorption technique using the analytical method of Brunauer–Emmett–Teller. The results are explained in terms of sizes of the alkali ions and cell volume of the different crystalline phases.
Children’s understanding of representations of basic chemistry after participating in an early childhood drama pedagogical activity

The purpose of this study is to generate insight into how young children in early childhood science education understand representation. Taking many forms: gestural, material and verbal (Gilbert, 2005), representations are critical to science education, already with young children. The empirical data for our analysis consist of interviews conducted with 6-year-old children after having participated in a playfully-formatted activity (van Oers, 2014) in basic chemistry held at a culture centre for children. The interviews are analyzed as social practice, clarifying how the children respond to the conceptual and communicative challenges they face. The results show that there are important differences in how the children show that they understand the forms of representations used in the activity. What these differences are and why they are critical to developing representational insight and basic scientific understanding, and therefore what educational implications our findings have, are discussed.
Antioxidant and antibacterial activity of aqueous , ethanolic and acetonic extracts of Pimenta dioica L . leaves

The aim of the present work was to evaluate the antioxidant and antibacterial activity of crude extracts (aqueous, ethanolic, and acetonic) of Pimenta dioica L. leaves collected in Tabasco, México. The following tests were carried out: total phenols (Folin-Ciocalteu assay), antioxidant activity (DPPH, ABTS, and FRAP methods), and antibacterial activity (disc diffusion and minimum inhibitory concentration techniques) using Gram-positive and Gram-negative bacteria. To identify compounds in the extracts, UHPLC-QToF was utilised. The acetonic extract (AE) yielded the highest phenolic content (626.29 ± 28.11 mg GAE/g dry extract, p < 0.05). The phenolic content of the aqueous (WE) and ethanolic extracts (EE) (488.29 ± 15.56 and 516.35 ± 4.96 mg GAE/g dry extract, respectively) did not show a significant difference. Likewise, AE yielded the highest antioxidant activity of 52.26 ± 11.74 μg/mL (IC50), 116.90 ± 10.82 μg/mL (IC50), and 7.52 ± 0.16 mM TE/g dry extract for DPPH, ABTS, and FRAP assay, respectively. Again, the EE and WE did not show a statistical difference for the DPPH and ABTS assays, while the antioxidant activity with the FRAP assay showed statistically different results for the three extracts in the order of AE > EE > WE. In addition, all three extracts showed antibacterial activity, with B. cereus and S. aureus (Gram-positive bacteria) more sensitive than S. Typhimurium and E. coli (Gram-negative bacteria); however, the minimum inhibitory concentrations were high with respect to the positive control (amikacin). Using the HPLC analysis, it was possible to detect and confirm the presence of some compounds such as phenols, flavonols, triterpenes, sapogenins, and polyalcohol in AE, EE, and WE . The antioxidant activity was closely related to the content of total phenols, although not all phenolic compounds had antibacterial activity. Extracts of P. dioica leaves are a source of phenolic compounds and can be used as antioxidant agents in the food, cosmetic, and pharmaceutical industries.
THE EFFECT OF CORPORATE GOVERNANCE AND AUDIT QUALITY ON TAX AGGRESSIVENESS WITH FAMILY OWNERSHIP AS THE MODERATING VARIABLE

This study aims to prove the allegation of tax aggressiveness activity which is conducted by corporate taxpayers in Indonesia. This study also aims to examine and analyze the effect of corporate governance and audit quality as solutions of tax aggressiveness, and the presence of family ownership as a moderating variable in the effect of corporate governance and audit quality on tax aggressiveness. Tax aggressiveness is measured by using the effective tax rate (ETR) and book tax difference Manzon-Plesko (BTD_MP). The measurement of corporate governance is in accordance with the aspects, principles and recommendations of corporate governance listed in Circular Letter of Otoritas Jasa Keuangan (OJK), or Financial Service Authority, 32/SEOJK.04/2015, concerning Guidelines for Public Corporate Governance. Audit quality measurement uses the type of Public Accounting Firm (PAF), namely Big Four and Non Big Four. Family ownership was obtained in immediate way through company’s stock reports on annual reports and in an ultimate way with the help of OSIRIS database. Samples were procured from public sector of manufacturing companies listed on the Indonesia Stock Exchange (IDX). Based on the purposive sampling method, 66 company samples were collected during the year of 2016-2017. Based on the purposive sampling method, 66 company samples were collected during the year of 2016-2017. The results of this study show that public companies in Indonesia especially manufacturing companies are proven to not doing the tax aggressiveness. It makes the corporate governance and audit quality on the companies sample to have no effect on tax aggressiveness. Furthermore, family ownership cannot moderate the effect of corporate governance on tax aggressiveness, but it can moderate the effect of audit quality on tax aggressiveness. Overall, this study shows that either family companies or non-family companies obey and adhere to the tax provisions even if the implementation level of corporate governance mechanism is still low and they use independent auditors from different public accounting firms.
Impact of Financial and Social Performances on Lending Interest Rate: Evidence from Microfinance Institutions in Vietnam

This paper focuses on assessing the impact of financial and social performance on the lending interest rate of microfinance institutions (MFIs) in Vietnam during 2012-2016. Data collected is mainly from 26 MFIs in Vietnam through the Microfinance Information Exchange (Mix Market) and the Vietnam Microfinance Working Group (VMFWG). Financial performance is evaluated through variables of data such as return on assets (ROA), return on equity (ROE) and operational self-sufficiency (OSS), whereas social performance is measured by indicators such as average loan size (AVGLS) and number of credit clients (CC). For MFIs, the lending rate is a weighted average of the interest rates actually received by the MFIs from their clients. The authors also used some control variables to capture variations in size, age, funding cost (FC) and legal status. This paper applies panel data estimation techniques to calculate the correlation between selected variables. Research results indicate three financial performance varibles: ROA, ROE and OSS, which have a significantly positive impact on MFIs’ lending interest rate in Vietnam, whereas a variable size in social performance variables creates a significant negative impact on the lending interest rate. Moreover, legal status and AVGLS have a significant inverse relation with the lending interest rate. However, variables, in terms of depth outreach and breadth outreach, make different impacts on the lending interest rate, mainly due to the way MFIs operate, that is, they are more specialised than other financial institutions.
Is There a Link Between Quote Competition

This paper investigates the link between the quotes made by market makers and the order flows they receive. Using data from the London Stock Exchange, it is shown that quotes and trades are closely related despite the heavy presence of preferenced orders. Specifically, market makers receive relatively more buy (sell) orders when they change the quotes by posting only the best ask (bid) price or when they stop posting the best bid (ask), and they receive balanced orders when they post the best quotes or neither. Moreover, the fewer market makers there are that post the best quotes, the more unbalanced the orders will be that each one receives. The link between quote and trades is most pronounced in trades of medium or large sizes. JEL classification: G10, G13, G18
Cash-Flow News, Discount-Rate News and the Co-skewness Risk

The current paper considers an extension of the two-beta model of Campbell and Vuolteenaho (2004) to the higher-moment asset pricing model which includes co-skewness risk. We break down co-skewness risk into the co-skewness with the cash-flow news, coskewness with the discount-rate news and the covariance with the product of the two — the co-variation risk. We find that stocks with high past returns have higher exposure to the covariation risk in comparison to the stocks with low past returns. We also document positive and statistically significant market price of the co-variation risk, while no such evidence is found for the cash-flow and discount-rate co-skewness risk factors. The two-beta model of Campbell and Vuolteenaho, when it is augmented with the co-variation risk factor, explains about 73% of the variation of the size/book-to-market, size/momentum and industry-sorted portfolio excess returns. Finally, we compare and find the performance of the augmented two-beta model to be superior to empirical multifactor asset pricing models used in the prior literature. JEL classification: G12, G14
The Effect of Innovation and Entrepreneurial Orientation on Business Performance with Knowledge Management as Mediation Variables in MSMES West Java

The development of the contribution of GDP to micro, small, and medium enterprises is seen to have increased from year to year. Besides being able to have a positive impact on the country, MSMEs also have a good impact on several provinces in Indonesia, one of which is West Java. MSMEs take part in increasing income in West Java. However, in reality, West Java only provides the fourth largest contribution (14.33%) to the National Gross Domestic Product (GDP) after DKI Jakarta, East Java and East Kalimantan (Ministry of Industry, 2017). Even though 50% of the total national industry is in West Java. This indicates that the performance of MSMEs in West Java has not improved over time. So it can be stated that the performance of the MSME business in West Java is still low. The cause of the weak performance of MSMEs is allegedly due to weak innovation and entrepreneurial orientation as well as inadequate knowledge management in managing businesses. Based on this phenomenon, this study aims to find, describe, and analyze the effect of innovation and entrepreneurial orientation on performance through the development of knowledge managementin MSMEs West Java. This research uses descriptive and verification quantitative methods with the number of analytical observations of 100 respondents, who were analyzed by the Path Analysis method. The results showed that innovation and entrepreneurial orientation through knowledge management could not affect the performance of MSMEs, meaning that knowledge management could not affect the performance of MSMEs.
Real Surface Observations in the Analysis of Slums Situated on Hilly Terrain

The main goal of this study is to evaluate how area calculations on the real surface differ from the results on a planimetric reference surface, while alternating the analysis of variables in slums located on a mountainous area known as the Tijuca massif in Rio de Janeiro (Brazil). The study area was chosen from disordered urban expansion areas, which resulted in the construction of irregular settlement, known as slums on the massif, usually in steeply sloped areas. Researchers used some information acquired from the Pereira Passos Institute (IPP): data on slums included in the study area; hypsometry and the drainage to the construction of the associated Digital Elevation Model. The results indicated major differences between the real surface observations and the planimetric surface, generating an increase of around 0.79 km2, and a reduction of around 2417.25 people/km2 and 691.94 homes/km2.
Replacement of fish meal with fermented Moringa leaves meal and its effect on the growth performance of red tilapia (Oreochromis sp.)

The purpose of the present research was to evaluate the nutritional content of fermented Moringa oleifera leaves meal and to find out the effect of fish meal replacement with fermented Moringa leaves meal (FMLM) in diets on the growth performance of red tilapia (Oreochromis sp.). The treatments include replacement of the fish meal with FMLM at 0, 10, 20, and 30%. Red tilapia with total length of 9-10 cm was fed twice daily for two months at a feeding rate of 3% of total biomass. The results revealed that fermentation increased the moisture, protein, ash, total lipid, calcium, and phosphorous content in Moringa leaves meal (MLM). The fermentation process actually reduced the anti-nutrient substances (phenol, tannin, phytic acid, and hydrogen cyanide (HCN)) in MLM. Fish meal replacement with FMLM in diets significantly affected feed digestibility. FMLM can be used as a replacement for fish meal in diet at 30% with only limited effect on the growth performance of red tilapia.
Robotic mobile fulfillment systems: a mathematical modelling framework for e-commerce applications

Robotic Mobile Fulfillment Systems (RMFSs) are a recent type of automated warehouse deployed in e-commerce. In this parts-to-picker system, a fleet of small robots is tasked with retrieving and storing shelves of items in the warehouse. Due to the nature of the e-commerce market, and the high flexibility of RMFSs, there are many opportunities to improve the productivity of the warehouse by optimising operational decisions. Online retailers promise extremely fast deliveries, which requires that new orders be included in the set of requests to fulfil as soon as they are revealed. For this reason, and because of the very dynamic nature of the robots' cycles, decision-making needs to be done in real time, in an uncertain environment. Because such a problem often lacks a formal description, we propose a mathematical framework that models the operational decisions taking place in an RMFS as a stochastic dynamic program. Our objective is to formalise optimisation opportunities, to allow researchers to develop more advanced methods in a well-defined environment. Embedded in a discrete event simulator, this model is illustrated by simulations to compare against standard storage decision rules.
Sticky dividends: A new explanation

This study proposes a generalized partial adjustment model of dividends in which managers set target dividends based on adaptively-formed earnings prospects. We show that firms adjust dividends to their target payouts much faster than previously documented. When managers form future earnings expectations based on a longer time-series of earnings, target dividends tend to become more stable. Thus, actual dividends tend to be more in line with the targets, driving up the speed of adjustment. Our model offers an insight that sticky dividends could be a consequence of managers’ attempts to match dividend payouts with the smooth targets.
Image Retrieval Using Image Captioning

The rapid growth in the availability of the Internet and smartphones have resulted in the increase in usage of social media in recent years. This increased usage has thereby resulted in the exponential growth of digital images which are available. Therefore, image retrieval systems play a major role in fetching images relevant to the query provided by the users. These systems should also be able to handle the massive growth of data and take advantage of the emerging technologies, like deep learning and image captioning. This report aims at understanding the purpose of image retrieval and various research held in image retrieval in the past. This report will also analyze various gaps in the past research and it will state the role of image captioning in these systems. Additionally, this report proposes a new methodology using image captioning to retrieve images and presents the results of this method, along with comparing the results with past research.
Performance and emission characteristics of the diesel engine running on neem (Azadirachta indica) biodiesel with effect of exhaust gas recirculation at optimum injection strategies

Environmental pollution and strict emission norms are promoting researchers to explore the methods for reducing pollution and provide optimum solution. By considering these situation as the baseline, study was conducted to analyse the effect of exhaust gas recirculation (EGR) on performance and emission of the DI diesel engine. The effects of Injection Timings (IT), split injection and Exhaust Gas Recirculation on performance, emission characteristics of diesel engine fuelled neem biodiesel blends are investigated. Initially experiments are conducted with diesel, NB5, NB10 with original injection timing of 23° bTDC with direct injection and are considered as base reading. The fuel injection is optimized (at 19° bTDC and 16% split injection) and the effect of EGR rate at this optimized condition is analysed. Significant reduction of about 65.3%, 67% and 57% in the amount of NOx was obtained at full load as compared to base readings. Smoke emissions reduced by 2.8-3.4% and CO emissions reduced by around 52% for diesel and biodiesel blends at full load.
Corruption – Why and How ; A Moral-Economic Analysis

Corruption emerged as one of main socio-political and economic problems of the countries which lead fortitude of its governments. No doubt, corruption has major implications for the distribution of income and wealth in the country, for its leading to specific patterns of expenditure and investment which leads to the illegal generation of wealth and the black money economy. As a consequence, in this paper we analysed those significant causes of corruption on which insufficient attention has been given and ignored to the social dimension of emerging economic issues, despite the fact that social and economic issues are interlinked. Pertaining to this, we provided strong evidence of the existence of a causal link of corruption by presenting exploratory scholarship estimates using in-depth interviews of our sample households as instruments in the ground level, and by showing that our explanatory factors are actual predictors of corruption. In contrast to the previous literature, we found strong evidence in favour of the theory that institutional amelioration on moral-economic basis reduces corruption. Hence there is a growing recognition about making different and essential approach theoretically on the subject of elucidation of corruption with the intention of social institutions in moral-economic dimension. Recommended Citation: Ali, F. & Khan, N.A. (2017). Corruption– Why and How; A Moral-Economic Analysis. The Journal for Social Advancement. 1
The effect of deregulation of the “Act concerning the Industry Restriction”

Rapid population growth in large cities in Japan was seen from the mid 50’s to 60’s. This situation led to the enactment of the Act concerning the Industry Restriction (AIR) which mainly restricted manufacturing activity to avoid congestion and environmental problems in the central area of Metropolitan region and the central area of the Kinki region in Japan. Given the legislation’s concentrated impact in areas highly dependent on the manufacturing sector, deregulating the AIR thus assumes a similar effect in the Kinki. We conduct causal inference on this place-based policy to assess whether such an deregulation take effect. Our results support this view.