Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein sequence design with a learned potential

The primary challenge of fixed-backbone protein design is to find a distribution of sequences that fold to the backbone of interest. This task is central to nearly all protein engineering problems, as achieving a particular backbone conformation is often a prerequisite for hosting specific functions. In this study, we investigate the capability of a deep neural network to learn the requisite patterns needed to design sequences. The trained model serves as a potential function defined over the space of amino acid identities and rotamer states, conditioned on the local chemical environment at each residue. While most deep learning based methods for sequence design only produce amino acid sequences, our method generates full-atom structural models, which can be evaluated using established sequence quality metrics. Under these metrics we are able to produce realistic and variable designs with quality comparable to the state-of-the-art. Additionally, we experimentally test designs for a de novo TIM-barrel structure and find designs that fold, demonstrating the algorithm’s generalizability to novel structures. Overall, our results demonstrate that a deep learning model can match state-of-the-art energy functions for guiding protein design. Significance Protein design tasks typically depend on carefully modeled and parameterized heuristic energy functions. In this study, we propose a novel machine learning method for fixed-backbone protein sequence design, using a learned neural network potential to not only design the sequence of amino acids but also select their side-chain configurations, or rotamers. Factoring through a structural representation of the protein, the network generates designs on par with the state-of-the-art, despite having been entirely learned from data. These results indicate an exciting future for protein design driven by machine learning.
The Role of Administration in Higher Education in Supporting the Commercialization of Research’s Products

Polytechnic as a Vocational Higher Education in Indonesia is under pressure to strengthen the quality of their research products in order to keep going beyond the demand of the society and the industries. Research is an investment for improving people's welfare and increasing economic value. Therefore, commercialization of innovation products from higher education to industry become one of the criteria to measure the institution research performance and reputation. Consequently, the support of administration function become very important. However, nowadays the administration roles regarding the commercialization of research product at Polytechnic tends to be negligent. This paper describes the aspects of commercialization research’s product as a strategy to strengthen Polytechnic research performance. The case study conducted at Bandung State Polytechnic was to understand and evaluate the activities of commercialization and functioning of its administrative support structure. Qualitative research methods and semi-structured interviews have been used toward ten respondents. Basically, the exploration shows thirteen researcher's main tasks that need administrative support which are developed into a research administration framework for higher education. Keywords—administration; higher education; research product; commercialization
EFL Early oral practices in rural primary students : technological tools guiding their Intercultural learning

Early instructions of English as a foreign language are a current tendency in Colombia, although it is noticeable that pupils from rural contexts encounter difficulties to communicate orally in English altering their social interaction skills. This study intended to propitiate spaces to early development of speaking skills of rural primary students from Boyacá, by using technology combined with intercultural contents such as English speaking countries‟ traditions, following a qualitative approach alongside action research. Workshops were applied in three momentums: pre-workshop, workshop and post workshop; the instruments for supporting data collection were focus groups interviews, video recording teacher‟s journals. This study aimed to inquire about; first, what dimensions in rural primary students‟ early oral practices are apparent when they use technological tools to guide their intercultural learning? Followed by how do rural students perceive technological tools employed to guide their intercultural learning when they are developing early oral practices? Along with what intercultural attitudes do rural students manifest when they use technological tools in their early oral practices about English speaking countries traditions? Within the findings of this research, students expressed their acceptance towards technological tools. They prepared oral communication by welcoming other cultures when they imagined themselves being immersed in foreign backgrounds. In order to structure communicative situations, learners reviewed previous linguistic and cultural contents. Regarding technological outcomes, it was encountered that technological tools were a source of empowerment in relation to culture. Technology represented a positive impact in regards to students‟ appropriation and exploration of foreign traditions. Also, it served as a source of motivation that entrusted learners towards actively participate in the EFL classroom. Similarly, technology was seen as a source of linguistic and cultural input. When students had their first encounters with contents belonging to the foreign culture, they expressed willingness; they started a process where they compared, inquired, and embraced foreign culture features. Then, it caused students conceive imaginary scenarios where they were immersed in the foreign culture, thus, they experienced contrasting emotions which ranged from excitement and enjoyment to insecurity and fear to be misunderstood when they made use of the foreign language.
Silicon photonic radio-over-fiber transceivers and microwave photonic up-converters

K. Van Gasse, A. Abassi, M. Mahmoud, J. Verbist, J. Kerrebrouck, G. Torfs, B. Moeneclaey,J. Bauwelinck, X. Yin, G. Roelkens, and G. Morthier Photonics Research Group, Ghent University imec, Technologiepark-Zwijnaarde 126, 9052 Ghent, Belgium Center for Nanoand Biophotonics, Technologiepark-Zwijnaarde 126, 9052 Ghent, Belgium 3 IDLab, INTEC, Ghent University imec, Technologiepark-Zwijnaarde 126, 9052 Ghent, Belgium
Traditional Mexican Dish Is Associated With More Than One Skipper Species (Lepidoptera, Hesperiidae, Megathiminae, Aegialini)

Abstract The white maguey worm, Aegiale hesperiaris (Walker, 1856), is a gastronomic delicacy in Mexico, with high economic value. Aegiale hesperiaris is generally associated with the plant Agave salmiana Otto ex Salm-Dyck (Asparagales: Asparagaceae). However, lack of information about Ae. hesperiaris means that it is often confused with morphologically similar species such as Agathymus remingtoni D. Stallings & Thurner (Lepidoptera: Hesperiidae), a species generally found on Agave lechuguilla Torrey (Asparagales: Asparagaceae). Harvestings are made from all Agave L. (Asparagales: Asparagaceae) species on the assumption that all larvae will be Ae. hesperiaris. This has led to the belief that Ae. hesperiaris may have extended its diet breadth range and is actually infesting other Agave species. We collected larvae from A. lechuguilla and A. salmiana plants, in Hidalgo state, Mexico, and incubated them at 26°C, 50% RH and 12:12 light regime until adult emergence; adults were examined using morphological (male genitalia and wing patterns) and molecular techniques (partial COI sequences) to provide the data necessary for accurate species identification and allocation to host plant. Both species were successfully separated and identified as Ae. herperiaris feeding on A. salmiana and Ag. remingtoni feeding on A. lechuguilla, and a detailed description of the larval developmental stages and feeding behavior described. These results will facilitate the accurate identification of these two species in future studies.
Retrospective study on risk habits among buccal mucosa carcinoma patients in regional cancer Center, Tamil Nadu

Background: Oral squamous cell carcinoma occurrence had geographical variations. In South India, the high incidence of buccal mucosa carcinoma occurs due to widespread use to tobacco chewing. There have been no studies reported on buccal mucosa carcinoma in Tamil Nadu. Objective: The aim of this was to analyze risk habits profile of buccal mucosa carcinoma patients. Materials and Methods: A cross-sectional, retrospective study of buccal cancer patients who reported during 2013–2015 in regional cancer center, Kanchipuram, Tamil Nadu. Data on demographic, socioeconomic, and risk habit profiles of the patients were recorded in a questionnaire. Results: A total of 198 buccal mucosa carcinoma patients included in the study. The buccal mucosa carcinoma was highly prevalent; 195 (98.5%) were reported with risk habits either with tobacco (smoking and smokeless), nontobacco (betel nut, pan masala, and alcohol), and multihabits. Further, an alarming identification that three (1.5%) were not have any habits of tobacco and nontobacco habits. The present study included 125 (63.1%) males and 73 (36.9%) females. The mean age of the patients was 55 years with high frequency of ≥40 years old (range: 12–88 years). Of 198 patients, 124 (62.2%) were reported from lower socioeconomic status who were likely to chew tobacco, smoke bidi, and drink alcohol. The study revealed highly significant relation of risk habits with gender, age, and socioeconomic status by Chi-square analysis at P < 0.001. Conclusions: The prevalence of buccal mucosa carcinoma was higher in the elderly male population with multihabitual. Thus, the study showed etiologic clues for prevention of buccal mucosa carcinoma in Tamil Nadu.
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBio long sequence reads that significantly improve sequence representation and assembly contiguity. The whole genome sequences of 54 domestic cats were aligned to the reference to identify single nucleotide variants (SNVs) and structural variants (SVs). Across all cats, 16 SNVs predicted to have deleterious impacts and in a singleton state were identified as high priority candidates for causative mutations. One candidate was a stop gain in the tumor suppressor FBXW7. The SNV is found in cats segregating for feline mediastinal lymphoma and is a candidate for inherited cancer susceptibility. SV analysis revealed a complex deletion coupled with a nearby potential duplication event that was shared privately across three unrelated dwarfism cats and is found within a known dwarfism associated region on cat chromosome B1. This SV interrupted UDP-glucose 6-dehydrogenase (UGDH), a gene involved in the biosynthesis of glycosaminoglycans. Importantly, UGDH has not yet been associated with human dwarfism and should be screened in undiagnosed patients. The new high-quality cat genome reference and the compilation of sequence variation demonstrate the importance of these resources when searching for disease causative alleles in the domestic cat and for identification of feline biomedical models. Author summary The practice of genomic medicine is predicated on the availability of a high quality reference genome and an understanding of the impact of genome variation. Such resources have lead to countless discoveries in humans, however by working exclusively within the framework of human genetics, our potential for understanding diseases biology is limited, as similar analyses in other species have often lead to novel insights. The generation of Felis_catus_9. 0, a new high quality reference genome for the domestic cat, helps facilitate the expansion of genomic medicine into the felis lineage. Using Felis_catus_9. 0 we analyze the landscape of genomic variation from a collection of 54 cats within the context of human gene constraint. The distribution of variant impacts in cats is correlated with patterns of gene constraint in humans, indicating the utility of this reference for identifying novel mutations that cause phenotypes relevant to human and cat health. Moreover, structural variant analysis revealed a novel variant for feline dwarfism in UGDH, a gene that has not been associated with dwarfism in any other species, suggesting a role for UGDH in cases of undiagnosed dwarfism in humans.
Numerical Study on the Critical Frequency Response of Jet Engine Rotors for Blade-Off Conditions against Bird Strike

Vibrations are usually induced in aero engines under their normal operating conditions. Therefore, it is necessary to predict the critical frequencies of the rotating components carefully. Blade deformation of a jet engine under its normal operating conditions due to fatigue or bird strike is a realistic possibility. This puts the deformed blade as one of the major safety concerns in commercially operating civil aviation. A bird strike introduces unbalanced forces and non-linearities into the engine rotor system. Such dynamic behavior is a primary cause of catastrophic failures. The introduction of unbalanced forces due to a deformed blade, as a result of a bird strike, can change the critical frequency behavior of engine rotor systems. Therefore, it is necessary to predict their critical frequencies and dynamic behavior carefully. The simplified approach of the one-dimensional and two-dimensional elements can be used to predict critical frequencies and critical mode shapes in many cases, but the use of three-dimensional elements is the best method to achieve the goals of a modal analysis. This research explores the effect of a bird strike on the critical frequencies of an engine rotor. The changes in critical mode shapes and critical frequencies as a result of a bird strike on an engine blade are studied in this research. Commercially available analysis software ANSYS version 18.2 is used in this study. In order to account for the material nonlinearities, a Johnson Cook material model is used for the fan blades and an isotropic–elastic–plastic–hydrodynamic material model is used for modeling the bird. The bird strike event is analyzed using Eularian and smoothed particle hydrodynamics (SPH) techniques. A difference of 0.1% is noted in the results of both techniques. In the modal analysis simulation of the engine rotor before and after the bird strike event, the critical failure modes remain same. However, a change in the critical frequencies of the modes is observed. An increase in the critical frequencies and excitation RPMs (revolution per minute) of each mode are observed. As the mode order is increased, the higher the rise in critical frequency and excitation RPMs. Also, a change in the whirl direction of the different modes is noted.
Adverse Effects of Opioid Dependency on Central and Peripheral Aspects of the Neuromuscular System

Prevalence of chronic pain and health care costs have caused an escalation of opioid dependency. The current national crisis involving opioid dependency and drug overdose are growing problems that need to be addressed. Since 2000, there has been an increased awareness of pain relief; more people are looking at alternative ways to induce pain relief and stricter guidelines in prescription of addictive opioid medications (Manchikanti et al., 2012). Despite growing efforts, opioid use and dependency has risen dramatically in the past few years; since 1999, there has been an increase in the number of opioids sold and opioid-related deaths in the USA (Manchikanti et al., 2012). Opioid misuse is the leading cause of accidental overdose and death (Compton & Volkow, 2006). In 2015, more than 40% of the world’s supply of thebaine, the main ingredient in hydrocodone and oxycodone, two forms of opioids, was consumed by the USA (Hedegaard et al., 2017). In 2008 there were 36,450 drug overdose deaths and 14,800 of those deaths were related to opioid pain relievers (CDC, 2011). By 2017 there were a total of 70,237 drug overdose deaths in the USA (Hedegaard et al., 2017). While short term use of opioids has benign effects, long-term usage has meaningful effects on rates of abuse or addiction (Compton & Volkow, 2006). It is estimated that over 4.3 million US adults are taking opioids regularly in any given week; opioids are one of the most widely prescribed class of drugs in the US based on a nationally-representative telephone survey (Parsells et al., 2008).
Determinants Factor of Technical Efficiency in Machinery Manufacturing Industry in Malaysia

Machinery manufacturing industry has been introduced since the beginning of the industrial era from European countries and developed until today. However, major challenges in machinery industry still driven by traditional production factors such as capital and labour that caused the industry still left out. Thus, the objective of the study are to analyse the level of TE and identifying determinant factors influenced to technical efficiency in the machinery manufacturing industry in Malaysia. The study was conducted by using the method of Data Envelopment Analysis (DEA) two stages. The first stage involves the calculation a score of efficiency through the DEA by using firmâ€™s data while the second stage Regression Tobit Analysis used to identify significant factors influencing to technical efficiency in machinery industrial. This firmâ€™s data are categorized into 3 sub-industry 3-digit according to the Malaysian Standard Industrial Classifications which are consists of Manufacture Of General Purpose Machinery, Manufacture Of Special Purpose Machinery and Manufacture Of Installation Machinery Industrial And Equipment. A total of 636 machinery industry firms were involved in this study. Results showed the average efficiency score is at the medium level while the determinant factors were significant are wage rates, the standard of education and research and development (R&D). The implications of this study shows that the machinery industry should focus their attention to the significant factors to improve the level of technical efficiency of the machinery industry.
Ultrasonographic Monitoring of Uterine Involution in Postpartum Buffalo Cows

A description of normal ultrasonographic alternations of the uterus in the postpartum (PP) in buffaloes is essential for the diagnosis of pathological conditions and improves the ability to differentiate puerperal pathology from normal physiological changes. The current study aimed to characterize the changes in uterine features assessed ultrasonographically in normal parturient Egyptian buffaloes (n=20) during the post-calving period (Until Day 60 PP). In the current data, ultrasonographic findings indicated that the uterine involution was completed at 4-6 weeks PP in normal calved Egyptian buffaloes. Moreover, calving during the spring season and female new born calves were associated with an enhanced uterine involution. Early cyclicity positively influences endometrial thickness (during early PP), dorsal and ventral uterine curvature, and uterine lumen diameter (during late PP) as compared with the late cyclic group. In conclusion, the uterine involution is ended by the 6th weeks PP in normal parturient Egyptian buffaloes. Moreover, season and calves gender implicate in the changes associated with uterine involution in buffaloes. It is extremely recommended to employ ultrasound examinations in the dairy herd to improve the reproductive efficiency of females by reducing the days open and increasing the number of milking animals.
Risk aversion over price variability: experimental evidence

ABSTRACT Eliciting risk attitudes is of crucial importance in economics. We test whether the degree of risk aversion that an individual exhibits in the context of the direct utility function is equivalent to that elicited in the context of the indirect utility function, as implied by duality theory. Our lab experiment uses payoff-based lottery choices (which are based on the direct utility function) and equivalent price-based lottery choices (which are based on the indirect utility function). We reject the equivalence of risk preferences from these two contexts. Subjects are more sensitive to price uncertainty than to equivalent payoff uncertainty.
Perceptions of Preconception Health and Prenatal Care by Young Adult Women and Men at Risk for Unintended Pregnancies

Perceptions of Preconception Health and Prenatal Care by Young Adult Women and Men at Risk for Unintended Pregnancies by Broderick Crawford MA, Walden University, 2013 BS, Park University, 2010 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Health Psychology Walden University January 2018
Agent, Steward, and Dividend Policy

: Purpose: The main objective of this study is to examine whether the dividend policy of Indonesian firms is based on agency theory or stewardship theory. The study investigates the relationship between profitability, non-discretionary accruals, discretionary accruals and dividend policy. Design/Methodology/Approach: The final sample of this study is a total of 28 firms of consumers‘ goods industries listed in Indonesia Stock Exchange during the period of 2010 to 2017 and conducts logistic regression for hypotheses testing. Findings: The result of the first model shows that ROA and non-discretionary accruals (non-disc) have positive sign and they are significant on dividend policy. The second model shows that ROA has a positive and significant effect on dividend policy, while non-disc is insignificant on dividend policy. The third model shows that ROA and non-disc are consistently positive and significant, while discretionary accruals are consistently insignificant on dividend policy. The fourth model shows that ROA and non-disc have positive sign and significant on dividend policy, while disc is insignificant on dividend policy. The fifth model shows that ROA and non-disc have a positive and significant sign on dividend policy, while DAR, AG and disc are insignificant on dividend policy. The results of profitability on all models also indicate that the objective of managers for most Indonesian dividend payers are align with the objective of stockholders in context of stewardship. The findings imply that most of firms as payers tend to increase dividends when their profitability increases. Practical Implications: It appears that dividend payers with strong profitability as based on their policy, generally do not engage in managing its earnings while reporting the accounting information. Originality/Value: The study provides empirical evidence for dividend policy in context of agency and stewardship perspectives. This study also identifies the behavior of firm insiders whether play as an agent or steward in relationship with their principals. earnings management, good corporate non-discretionary, discretionary.