Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey on Renamings of Software Entities

More than 70% of characters in the source code are used to label identifiers. Consequently, identifiers are one of the most important source for program comprehension. Meaningful identifiers are crucial to understand and maintain programs. However, for reasons like constrained schedule, inexperience, and unplanned evolution, identifiers may fail to convey the semantics of the entities associated with them. As a result, such entities should be renamed to improve software quality. However, manual renaming and recommendation are fastidious, time consuming, and error prone, whereas automating the process of renamings is challenging: (1) It involves complex natural language processing to understand the meaning of identifers; (2) It also involves difficult semantic analysis to determine the role of software entities. Researchers proposed a number of approaches and tools to facilitate renamings. We present a survey on existing approaches and classify them into identification of renaming opportunities, execution of renamings, and detection of renamings. We find that there is an imbalance between the three type of approaches, and most of implementation of approaches and evaluation dataset are not publicly available. We also discuss the challenges and present potential research directions. To the best of our knowledge, this survey is the first comprehensive study on renamings of software entities.
The Breeding Biology, Food, Social-Organization, Demography and Conservation of the Major Mitchell or Pink Cockatoo, Cacatua-Leadbeateri, on the Margin of the Western Australian Wheat-Belt

The breeding biology of the Major Mitchell or pink cockatoo, Cacatua leadbeateri, was studied over six years at Yandegin on the margin of the Western Australian wheatbelt. Neither winter nor annual rainfall influenced the timing of egg-laying, which was spread over August and September. Most clutches (n = 63) were of three or four eggs, 84% of which hatched; 64% of nestlings fledged successfully and, on average, 1.27 independent young per pair were added to the population each autumn. Breeding pairs remained together throughout the year, spending the non-breeding season in a Local Nomadic Flock of 30-50 individuals. Pairs usually renested in the same area each season, never closer than 1 km to another pair (mean nearest neighbour 2732 m). Hollows used by C. leadbeateri were characteristically shallow (< 1 m) and high up, whereas other cockatoos tend to be less selective. Such specific nest hollow requirements led to regular reuse of scarce traditional sites and consequent easy 'farming' of nestlings for the aviary trade; specificity also rendered the species more susceptible to loss of rare nest sites by clearing than were other cockatoos. Although C. leadbeateri are long-lived (adult c. 88% survival) and productivity at Yandegin appeared adequate to maintain a stable population, the shrinking distribution in the face of expanding wheat farming is irreversible. Conservation of the species depends on the protection of large areas of the remaining suitable semiarid woodland and the continuing strict enforcement of the complete ban on harvesting wild birds for the aviary trade.
THE INVASION OF NATIVE FOREST BY PH YTOPHTHORA CINNAMOMI

Disease within an open sclerophyll forest dominated by Eucalyptus species of relatively low stature (15-20 m) was shown to be caused by Phytophthora cinnamomi Rands, an introduced root pathogen. Diseased sites were mapped and measured. The rate of advance of the pathogen over a period of 5 months was calculated at 4 m per month through moderately drained soils compared with 7 m per month through soils subject to waterlogging. Areas showing disease symptoms increased from 10.8 to 90%, the major extensions occurring along gullies. Spread of the fungus was associated with road-making activities, waterlogging, and the presence of drainage channels. Symptom expression in the different species was studied and shown to be similar to that associated with water stress. Most of the 42 species comprising the woody flora were susceptible to the disease, those particularly susceptible including the dominants. During a period of 8 months mortalities occurred in 50 % of the species. Grasses, sedges, and Eucalyptus goniocalyx appeared to be field-resistant, but were uncommon in the Aora of the sites studied. The fungus Phytophthova cinnamomi Rands is causing great concern in Australia. Podger (1968) demonstrated that the extensive die-back of jarrah (Eucalyptus mavginata Donn ex Sm.) was due to this pathogen which had spread during the past 40 years over large areas of dry sclerophyll forests in the south-west of Western Australia. For about 30 years P. cinnamomi has been periodically isolated from diseased plants growing in gardens, nurseries, and peach orchards in Victoria (McLennan, personai communicarionj. Recently it has invaded areas of forest and bush within the State causing death to many native plants and die-back or death to many forest trees. In the Brisbane Ranges, an existing water catchment and likely National Park about 50 miles south-west of Melbourne, Podger and Ashton (1970) observed chlorotic, dying, and dead plants in four small areas along the roadside and P. cinnamomi was isolated from seven different species of shrub from the forest understorey. The area has an average rainfall of about 25 inches, hot dry periods during summer and autumn, and a wet winter and spring. The vegetation of the invaded areas is open sclerophyll forest of two strata, trees and woody understorey,
The Rondeletia Complex (Rubiaceae): An Attempt to Use ITS, rps16, and trnL-F Sequence Data to Delimit Guettardeae, Rondeletieae, and Sections within Rondeletia1

Abstract In the present study, a molecular phylogeny of the Rondeletia L. complex (Rubiaceae, Rondeletieae) was constructed with the following main objectives: (1) to evaluate the sections of Rondeletia proposed by Fernández Zequeira; (2) to test if Stevensia Poit. belongs to the Rondeletieae s. str. ; (3) to check if ITS data from Rondeletieae support previous phylogenetic results from trnL-F data regarding circumscription of Rondeletieae; and (4) to verify if Hodgkinsonia F. Muell. belongs to Guettardeae or elsewhere. Two analyses were performed, one with ITS sequences from 46 taxa in the Rondeletieae–Guettardeae complex, and the other with combined ITS, rps16, and trnL-F sequences of 21 taxa. Representatives of nine of the 10 sections of Rondeletia recognized by Fernández Zequeira were included in the ITS analysis. Five of her sections could be tested for monophyly. Support was only found for Rondeletia sect. Leoninae M. Fernández Zeq. , while representatives from section Chamaebuxifoliae M. Fernández Zeq. , section Hypoleucae Standl. , and section Nipenses M. Fernández Zeq. together form a well-supported clade that could be distinguished also based on morphology. The latter clade is sister to Stevensia, which is thus placed within Rondeletia s. str. In addition, ITS sequence data confirm the separation of Rovaeanthus Borhidi from Rogiera Planch. Support is low for inclusion of Blepharidium Standl. , Mazaea Krug & Urb. , Phyllomelia Griseb. , Rachicallis DC. , part of Rogiera, and Suberanthus Borhidi & M. Fernández Zeq. in Rondeletieae. Rachicallis, Mazaea, and Phyllomelia form a clade with strong support. The tribe Rondeletieae s. str. was found to be monophyletic in all trees, although with low support; however, a re-delimitation of the tribe is proposed here based on this study and previous phylogenetic analyses. The monophyly for the tribe Guettardeae is weakly supported, with the inclusion of Arachnothryx Planch. (including Cuatrecasasiodendron Steyerm.), Gonzalagunia Ruiz & Pav. , Hodgkinsonia, and Timonius DC. Although it was recently the subject of a molecular phylogenetic study, the tribe Guettardeae is still in need of a wide-ranging survey in order to confirm its monophyly and delimit its taxonomic boundaries. Because Cuatrecasasiodendron was found within the Arachnothryx clade, the two genera are here synonymized as Arachnothryx, and in turn positioned within the tribe Guettardeae. In addition, based on herbarium and field studies, the two species described under Cuatrecasasiodendron (C. spectabile Steyerm. and C. colombianum Standl. & Steyerm.) are treated as synonyms to the new combination Arachnothryx spectabilis (Steyerm.) Rova, Delprete & B. Bremer, which is proposed here.
Pursuing Quantum Difference Equations II: 3D mirror symmetry

Let $\textsf {X}$ and $\textsf {X}^{! }$ be a pair of symplectic varieties dual with respect to 3D mirror symmetry. The $K$-theoretic limit of the elliptic duality interface is an equivariant $K$-theory class $\mathfrak {m} \in K(\textsf {X}\times \textsf {X}^{! })$. We show that this class provides correspondences $$ \begin{align*} & \Phi_{\mathfrak{m}}: K(\textsf{X}) \leftrightarrows K(\textsf{X}^{! }) \end{align*}$$mapping the $K$-theoretic stable envelopes to the $K$-theoretic stable envelopes. This construction allows us to relate various representation theoretic objects of $K(\textsf {X})$, such as action of quantum groups, quantum dynamical Weyl groups, $R$-matrices, etc., to those for $K(\textsf {X}^{! })$. In particular, we relate the wall $R$-matrices of $\textsf {X}$ to the $R$-matrices of the dual variety $\textsf {X}^{! }$. As an example, we apply our results to $\textsf {X}=\textrm {Hilb}^{n}({{\mathbb {C}}}^2)$—the Hilbert scheme of $n$ points in the complex plane. In this case, we arrive at the conjectures of Gorsky and Negut from [10].
Japanese white-eyes (Aves: Zosteropidae) as potential pollinators of summer-flowering Taxillus kaempferi (Loranthaceae)

ABSTRACT The pollination of summer-flowering plants by birds has rarely been reported in temperate Asia and Europe. However, we recorded the Japanese white-eye Zosterops japonicus (Passeriformes: Zosteropidae) visiting the flowers of the hemiparasitic plant Taxillus kaempferi (Loranthaceae) during mid-summer (July to August) in a temperate forest in central Japan. Field observations showed that Z. japonicus was an almost exclusive flower visitor of T. kaempferi. Specifically, Z. japonicus inserted their bills frequently into the flower tubes of T. kaempferi. The corollas of T. kaempferi were shorter than Z. japonicus bills, suggesting that Z. japonicus is able to obtain floral nectar from T. kaempferi. Close-up pictures of Z. japonicus visiting flowers showed that the upper bill and facial feathers of Z. japonicus came into contact with the reproductive organs of T. kaempferi, leading to the attachment of pollen to these body parts. Thus, Z. japonicus might act as an important pollinator of the summer-flowering plant T. kaempferi.
Suetonius’ Tiberius: A Proxemic Approach

Bodel, J. 1999. Death on Display: Looking at Roman Funerals. In The Art of Ancient Spectacle, ed. B. Bergmann and C. Kondoleon. New Haven, Conn. Clausen, W. 1987. Virgil’s “Aeneid” and the Tradition of Hellenistic Poetry. Berkeley and Los Angeles. Feeney, D. 1983. The Taciturnity of Aeneas. CQ 33: 204–19. Frier, B. , and T. McGinn. 2004. A Casebook on Roman Family Law. Oxford. Georges, H. , ed. 1905–6. Tiberi Claudi Donati ad Tiberium Claudium Maximum Donatianum filium suum “Interpretationes Vergilianae. ” Leipzig. Green, R. P. H. 1986. Conubium in the “Aeneid. ” In Studies in Latin Literature and Roman History IV, ed. C. Deroux, 393–421. Brussels. McGinn, T. 1998. Prostitution, Sexuality and the Law in Ancient Rome. Oxford. Monti, R. 1981. The Dido Episode and the “Aeneid”: Roman Social and Political Values in the Epic. Leiden. Moskalew, W. 1982. Formular Language and Poetic Design in the “Aeneid. ” Leiden. Nelis, D. 2001. Vergil’s “Aeneid” and the “Argonautica” of Apollonius Rhodius. Leeds. Pease, A. S. , ed. 1935. Virgil: “Aeneidos” Liber Quartus. Cambridge, Mass. Prescott, H. 1927. The Development of Virgil’s Art. Chicago. Rehm, R. 1994. Marriage to Death: The Conflation of Wedding and Funeral Rituals in Greek Tragedy. Princeton, N.J. Rudd, N. 1976. Lines of Enquiry: Studies in Latin Poetry. Cambridge. Seaford, R. 1987. The Tragic Wedding. JHS 107: 106–30. Starr, R. 1991. Explaining Dido to Your Son: Tiberius Claudius Donatus on Vergil’s Dido. CJ 87: 25–34. Syed, Y. 2005. Vergil’s “Aeneid” and the Roman Self: Subject and Nation in Literary Discourse. Ann Arbor, Mich. Thornton, M. 1985. The Adaptation of Homer’s Artemis-Nausicaa Simile in the Aeneid. Latomus 44: 615–22. Treggiari, S. 1991. Roman Marriage: Iusti Coniuges from Cicero to Ulpian. Oxford. Williams, G. 1968. Tradition and Originality in Roman Poetry. Oxford.
RESEARCH ON HARICOT BEAN IN ETHIOPIA AN ASSESSMENT OF STATUS, PROGRESS, PRIORITIES AND STRATEGIES

Haricot bean is one of the major crops in the middle Rift Valley of Ethiopia. It contributes about 60X of haricot bean production in the country. Haricot bean area is increasing in the wet zone and decreasing in the dry zone, • but yield is declining in both zones. Haricot bean is the first or the second■ cash crop in the regiont and is mostly of the white peabean type, The principal constraints to increasing bean production are shortage of labort moisture stressf weeds and the low potential of existing varieties. Farmers use high seed rates to suppress weeds, since the crop receives the least priority in weeding. The use of chemical fertilizer on bean is increasing. Farmers have been reluctant to accept a complete package because of resource limitations* Introduction According to official statistics* the central cone accounts for 48% of haricot bean area and 60% of haricot bean production in the country. About 92% of bean production in the region cones from the private sector. Producer cooperatives and state farms produce only 8% (CSA, 1987). [Subsequent discussion in this workshop indicated that official statistics are particularly unreliable for haricot bean. ] In this paper, the results of various diagnostic surveys and on-farm research related to haricot bean are assembled. The results of package testing in beans is also discussed. Fara Survey Results
Word formation process of terms in COVID-19 pandemic

The objectives of this research are to know the type and examples of the word-formation process of the terms that appear during pandemic Covid-19. This research uses qualitative research. From the result analysis, some types of word-formation processes include borrowing, compounding, blending, acronym, clipping, and multiple processes. In borrowing, for example, the words “Rapid test” and “Swab test”. In compounding, for example, the words “handsanitizer, lockdown, coronacoma, coronaspeck and self-quarantine”. In blending, for example, the words ‘covid, covidiot, covidient, quarantini, infodemic, quaranteam, coronials, covexit, covidivorce, quaranteen and coroncation”. In clipping, for example, the words ‘sanny” and “iso”. The word “sanny’ comes from “hand sanitizer” and “Iso” comes from “isolation”. In the acronym, for example, the initials WFH (Work from Home), PPE (Personal Protective Equipment), WFO (Work from Office), and PUI (Person Under Investigation). In multiple processes for example the words “handwashing”, zoomboombing, coronababies, self-isolation”.
Improved generalization bounds of group invariant / equivariant deep networks via quotient feature spaces

Numerous invariant (or equivariant) neural networks have succeeded in handling invariant data such as point clouds and graphs. However, a generalization theory for the neural networks has not been well developed, because several essential factors for the theory, such as network size and margin distribution, are not deeply connected to the invariance and equivariance. In this study, we develop a novel generalization error bound for invariant and equivariant deep neural networks. To describe the effect of invariance and equivariance on generalization, we develop a notion of a \textit{quotient feature space}, which measures the effect of group actions for the properties. Our main result proves that the volume of quotient feature spaces can describe the generalization error. Furthermore, the bound shows that the invariance and equivariance significantly improve the leading term of the bound. We apply our result to specific invariant and equivariant networks, such as DeepSets (Zaheer et al. (2017)), and show that their generalization bound is considerably improved by $\sqrt{n! }$, where $n! $ is the number of permutations. We also discuss the expressive power of invariant DNNs and show that they can achieve an optimal approximation rate. Our experimental result supports our theoretical claims.
Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene

Abstract. Basith A, Abinawanto, Kusrini E, Yasman. 2021. Genetic diversity analysis and phylogenetic reconstruction of groupers Epinephelus spp. from Madura Island, Indonesia based on partial sequence of CO1 gene. Biodiversitas 22: 4282-4290. Groupers populations in Indonesia, particularly from Madura Island, East Java are indicated to be over-fished, thereby requiring data collection of more accurate genetic resources as an important step for grouper conservation. A total of 14 samples of the Epinepheplus groupers were obtained from the fish landing port on Madura Island. The 617 bp CO1 gene sequence was utilized for genetic diversity analysis and phylogenetic tree reconstruction. Genetic diversity is based on the value of haplotype diversity (Hd) and nucleotide diversity (? ). Reconstruction of the phylogenetic tree includes neighbor-joining (NJ) implementing K2P substitution model, while maximum likelihood (ML) is conducted by implementing HKY+G+I substitution model, both of which were evaluated by employing a bootstrap of 1000 replications. Analysis of genetic distance between species indicated that the farthest distance between E. heniochus and E. fasciatus was 0.189, while the closest distance between E. erythrurus and E. ongus was 0.099. Intrapopulation genetic diversity indicated a high value with details of Hd=0.978 and ? =0.12107. Furthermore, NJ and ML phylogenetic tree demonstrated similar topology in the observed Epinephelus spp. obtained from Madura Island grouped into 7 clades, that is Epinephelus coioides, E. bleekeri, E. areolatus, E. erythrurus, E. heniochus, E. fasciatus, and E. ongus.
Dietary Antioxidants in Age-Related Macular Degeneration and Glaucoma

Age-related macular degeneration (AMD) and glaucoma are ophthalmic neurodegenerative diseases responsible for irreversible vision loss in the world population. Only a few therapies can be used to slow down the progression of these diseases and there are no available treatment strategies for reversing the degeneration of the neural retina. In AMD, the pathological process causes the malfunction and damage of the retinal pigmented epithelium and photoreceptors in the macula. In glaucoma, damage of the retinal ganglion cells and their axons is observed and treatment strategies are limited to intraocular pressure lowering. Therefore, other prophylactic and/or therapeutic methods are needed. Oxidative stress is involved in the neurodegenerative process accompanying both AMD and glaucoma; therefore, the use of antioxidant agents would clearly be beneficial, which is supported by the decreased prevalence and progression of AMD in patients adherent to a diet naturally rich in antioxidants. Dietary antioxidants are easily available and their use is based on the natural route of administration. Many preclinical studies both in vitro and using animal models of retinal degeneration showed the efficacy of dietary antioxidants, which was further proved in clinical trials. Resveratrol is beneficial both in AMD and glaucoma animal models, but confirmed only among AMD patients. For AMD, carotenoids and omega-3 fatty acids were also proved to be sufficient in preventing neurodegeneration. For glaucoma, coenzyme Q10 and alpha-lipoic acid showed efficacy for decreasing retinal ganglion cell loss and inhibiting the accompanying destructive processes. Interestingly, the benefits of vitamins, especially vitamin E was not confirmed, neither in preclinical nor in clinical studies.
Chiral Flavonoids as Antitumor Agents

Flavonoids are a group of natural products with a great structural diversity, widely distributed in plant kingdom. They play an important role in plant growth, development and defense against aggressors. Flavonoids show a huge variety of biological activities such as antioxidant, anti-inflammatory, anti-mutagenic, antimicrobial and antitumor, being able to modulate a large diversity of cellular enzymatic activities. Among natural flavonoids, some classes comprise chiral molecules including flavanones, flavan-3-ols, isoflavanones, and rotenoids, which have one or more stereogenic centers. Interestingly, in some cases, individual compounds of enantiomeric pairs have shown different antitumor activity. In nature, these compounds are mainly biosynthesized as pure enantiomers. Nevertheless, they are often isolated as racemates, being necessary to carry out their chiral separation to perform enantioselectivity studies. Synthetic chiral flavonoids with promising antitumor activity have also been obtained using diverse synthetic approaches. In fact, several new chiral bioactive flavonoids have been synthesized by enantioselective synthesis. Particularly, flavopiridol was the first cyclin-dependent kinase (CDK) inhibitor which entered clinical trials. The chiral pool approaches using amino acid as chiral building blocks have also been reported to achieve small libraries of chrysin derivatives with more potent in vitro growth inhibitory effect than chrysin, reinforcing the importance of the introduction of chiral moieties to improve antitumor activity. In this work, a literature review of natural and synthetic chiral flavonoids with antitumor activity is reported for the first time.
Characterizing the genetic basis of trait evolution in the Mexican cavefish

Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabits the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism and enhanced mechanosensory function. The interfertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of behavioral and morphological traits. Taken together, this approach provides a novel system to identify genes that underlie naturally occurring genetic variation in morphological and behavioral traits.