Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring Bug Signatures to Detect Real Bugs

Static tools like Findbugs allow their users to manually define bug patterns, so they can detect more types of bugs, but due to the complexity and variety of programs, it is difficult to manually enumerate all bug patterns, especially for those related to API usages or project-specific rules. Therefore, existing bug-detection tools (e.g., Findbugs) based on manual bug patterns are insufficient in detecting many bugs. Meanwhile, with the rapid development of software, many past bug fixes accumulate in software version histories. These bug fixes contain valuable samples of illegal coding practices. The gap between existing bug samples and well-defined bug patterns motivates our research. In the literature, researchers have explored techniques on learning bug signatures from existing bugs, and a bug signature is defined as a set of program elements explaining the cause/effect of the bug. However, due to various limitations, existing approaches cannot analyze past bug fixes in large scale, and to the best of our knowledge, no previously unknown bugs were ever reported by their work. The major challenge to automatically analyze past bug fixes is that, bug-inducing inputs are typically not recorded, and many bug fixes are partial programs that have compilation errors. As a result, for most bugs in the version history, it is infeasible to reproduce them for dynamic analysis or to feed buggy/fixed code directly into static analysis tools which mostly depend on compilable complete programs. In this paper, we propose an approach, called DePa, that extracts bug signatures based on accurate partial-code analysis of bug fixes. With its support, we conduct the first large scale evaluation on 6,048 past bug fixes collected from four popular Apache projects. In particular, we use DePa to infer bug signatures from these fixes, and to check the latest versions of the four projects with the inferred bug signatures. Our results show that DePa detected 27 unique previously unknown bugs in total, including at least one bug from each project. These bugs are not detected by their developers nor other researchers. Among them, three of our reported bugs are already confirmed and repaired by their developers. Furthermore, our results show that the state-of-the-art tools detected only two of our found bugs, and our filtering techniques improve our precision from 25.5 to 51.5 percent.
The effect of solid‐phase composition on the drying behavior of Markermeer sediment

We studied the drying behavior of slurries of Markermeer sediments in the Netherlands having different solid compositions. Natural processes such as sand–mud segregation and oxidation of organic matter were mimicked to analyze the effect of changes in sediment composition. Evaporation experiments were performed with soft slurry samples using the Hyprop setup. Soil water retention curves (SWRCs) and hydraulic conductivity curves (HCCs) were determined as a function of the water ratio (WR, defined as volume of water/volume of solids). The sediment remained close to saturation until the end of the experiments. The Atterberg limits reduced significantly after sediment treatment involving drying at 50 °C, rewetting, and chemical oxidation. Furthermore, the oxidized sediment lost capacity to retain water. The SWRCs of sandy and oxidized clays were steeper, and fine‐textured sediments showed large water ratios. At low matric suctions, the water retention capacity of the upper sediment samples containing more labile organic matter was larger than that of the sediment underneath. Clear correlations were found between van Genuchten parameters and the degree of degradation of the organic matter. The hydraulic conductivity of fine‐textured samples with less labile organics was larger. The results give insight into the drying behavior of Markermeer sediment, currently used to build wetlands.
Temporal patterns in diversification rates

Introduction The study of rates of speciation and extinction, and how these have changed over time, has traditionally mainly been the preserve of paleontology (Simpson 1953; Stanley 1979; Raup 1985). More recently, phylogenies of extant species have been shown to contain information on these rates and how they may have changed, under the assumption that the same rules have applied in all contemporaneous lineages (Harvey et al. 1994; Kubo & Iwasa 1995; see Nee 2006 for a recent review). The first section of this chapter contrasts the strengths and weaknesses of these two approaches – paleontological and phylogenetic – to the study of macroevolution in general. Moving to a specificmacroevolutionary hypothesis, we then outline some tests of the hypothesis that diversification rates have declined in the recent past, either in response to changed abiotic conditions or as a result of density-dependence or diversity-dependence. It has long been appreciated that incomplete specieslevel sampling can cause a bias in favour of this hypothesis at the expense of the null hypothesis of no change (Pybus & Harvey 2000), but we highlight a further sort of incompleteness that is likely to be very widespread and which is not widely appreciated – products of recent lineage splits are unlikely to be considered as distinct species. We reanalyze the data from a key early paper (Zink & Slowinski 1995) to show how this incompleteness, which is inevitable when taxonomy and phylogeny meet, is sufficiently strong to account for much (though not all) of the apparent tendency for rates to have declined through time. Attempts to infer the deeper history of diversification rates are relatively free of this problem but instead encounter others: in particular, the assumption that the underlying probabilities of speciation and extinction per unit time have changed in the same way in all lineages becomes increasingly unlikely as a wider and wider clade is considered. We explain how analyses of a nearcomplete species-level phylogeny of extant mammals show a complex pattern of temporal variation in the rate of effective cladogenesis (Bininda-Emonds et al. 2007), and compare the mammalian picture with that obtained some years previously for birds (Nee et al. 1992).
The Sequence of cDNA Encoding Lipoprotein Lipase

cDNA clones corresponding to the entire coding re- gion of mature lipoprotein lipase were identified by antibody screening of a mouse macrophage library and sequenced. The predicted amino acid sequence indi- cates that the mature protein contains 447 amino acids with a molecular weight of 50,314. Comparison of the nucleotide and amino acid sequence with those of rat hepatic lipase and porcine pancreatic lipase reveals extensive homology among the enzymes, indicating that they are members of a gene family of lipases. Most striking is a conservation of five disulfide bridges in all three enzymes, strongly suggesting that the en- zymes have similar overall folding patterns. Lipopro- tein lipase is also shown to be extraordinarily con- served among mouse, human, and bovine species. The mRNA for lipoprotein lipase is abundant in heart and adipose tissue but is
Regional disparities in the distribution of Sudan's health resources.

Background Equal distribution of health resources has been a core objective of both long- and medium-term strategic plans for the health sector in Sudan. However, the targets of these plans have not yet been achieved, resulting in weak performance of the whole health system. The unequal distribution of the health resources has resulted in significant regional disparities in provision of health care services. Aims This study aims to describe and analyse the inequality in geographic distribution of public sector's physical and human health resources in Sudan. In addition, the study also aims to measure the relations between density of health resources and health outcomes. Methods State-level data on health resources and health outcomes obtained from the Sudan Health Statistical Report of 2016 were used to calculate inequality indices, drawing Lorenz curves, and calculating Spearman's correlation analysis between health resource density and health-related outcomes. Results Our findings show that the distributions of health resources, based on population size, were highly unequal among the 18 states of Sudan. Conclusion There is a crucial need to improve health status in the relatively under-resourced states, particularly in Darfur, South Kordofan and Blue Nile states. Moreover, the government needs to use health resource allocation models that take into account the population size and health outcomes variables in each state in future health strategies.
Structure and habits of living branchiopod crustaceans and their bearing on the interpretation of fossil forms

ABSTRACT Branchiopods are primitive crustaceans whose history extends back at least to the Devonian, yet some are highly successful today. Most fossil branchiopods do not show many features that lead to an understanding of function, but the Devonian lipostracan Lepidocaris is an exception. Recent work on living branchiopods, especially anostracans and anomopod cladocerans, enables Lepidocaris to be considered as a living animal. Work on extant anostracan nauplii also makes it possible to deduce how its larval stages swam and collected food. Other early crustaceans are briefly considered and comments are made on the concept of “living fossils”. While rates of morphological and genomic evolution are often discordant, the concept is still useful. Some branchiopods, such as the Notostraca, display remarkable morphological stasis: on the basis of morphology, a Triassic and a present-day form appear to be conspecific. The latter may be referred to as a “living fossil”. The outstanding morphological stasis of the crustacean nauplius is noted. Its existence in Cambrian times, deducible from its distribution among modern taxa, has been confirmed by Müller's finds. Such stasis, involving part of the genome of organisms whose adults display enormous adaptive radiation, has persisted with relatively small modifications since before the commencement of the entire radiation of vertebrates.
Biogeography and Evolution of New Zealand Priasilphidae (Coleoptera: Cucujoidea)

The phylogenetic relationships of the seven species of the endemic New Zealand genus Priasilpha were reconstructed by a cladistic analysis of 22 adult characters. One fully resolved tree was produced that was rooted with the Tasmanian species Priastichus megathorax with the following relationships among Priasilpha (distributions in square brackets): (P. aucklandicus [Auckland Island] + P. obscura [South Island and southern North Island]) (P. angulata [Franz Joseph Glacier, Westland] (P. earlyi [Kellys Creek, Arthurs Pass] (P. carinata [Mt. Arthur, Northwest Nelson] (P. bufonia [Richmond Range, Northwest Nelson, Marlborough] + P. embersoni [Paparoa Range, Buller Region])))). The only winged species, P. obscura, is placed as a sister taxon to P. aucklandicus, both of which are in a basal clade that is a sister group to the remaining species. Aptery evolved early in the genus and there is a statistically significant morphological trend towards body roundness, with basal species elongate in shape and derived species progressively more rounded. The P. angulata clade is found to the west of the Alpine Fault and is part of the Challenger Plateau, a cratonic fragment forming the southernmost limit of the Melanesian Rift. Priasilpha obscura is found mainly on Torlesse and Waipapa terranes and is of east Gondwanan origin. Priasilpha aucklandicus is restricted to the Campbell Plateau, a cratonic fragment derived from west Gondwana. The phylogeny of Priasilpha suggests that the Melanesian Rift-Torlesse split occurred prior to the East-West Gondwanan split (hypothesis 1), which is clearly contradicted by their relative ages. If the flighted P. obscura is deleted from consideration or if it is assumed that it was once a Campbell Plateau species, then this older distribution supports a hypothesis that there is a basal East-West Gondwanan split occurring about 100 Ma. If, however, P. aucklandicus evolved from a P. obscura + P. aucklandicus ancestor some time after 20 Ma, then the derived east-west Gondwanan split is falsified and the distributions are an artefact due to faunal mixing (hypothesis 2). Examination of a 3-taxon statement for the genera of Priasilphidae (Chileosilpha [Southern Chile] (Priastichus [Tasmania] + Priasilpha [New Zealand])) supports hypothesis 2 where the East-West Gondwana split preceded one between East Gondwana and the Melanesian Rift.
Sexual differentiation and juvenile intersexuality in the European sea bass (Dicentrarchus labrax)

Sexual differentiation was studied at the histological level using a mixture of 30 families of sea bass Dicentrarchus labrax. Most of the fish (93%) differentiated into males as usually observed in farmed populations. All testes were differentiated when the males reached 12 cm and no more undifferentiated fish were found from 419 days post-fertilization (p.f.). In 28% of the males, among the biggest, sexual differentiation had already begun at 168 days p.f. (8.3–9.5 cm) and these fish started spermatogenesis in their first year of life. The other males differentiated later and remained immature at the end of their first year of life. Ovaries could be identified at the histological level from the age of 168 days p.f. (7.9–9.0 cm) and the females became significantly longer than the males from the age of 191 days p.f. , i.e. during the process of ovarian differentiation. In the studied group, 62% of the males developed intratesticular oocytes. Such intersexuality had no consequence on growth rate. Intratesticular oocytes were also recorded in testes of wild males originating from Atlantic (Britain and Gulf of Gascogne) and West Mediterranean showing that juvenile intersexuality is not restricted to farmed populations but is a widespread phenomenon in sea bass.
Characteristics of the Alarm Calls of Buff-Streaked Chat Groups and African Stonechat Pairs in Response to Increased Distances from Surrogate Raptors and Snakes

Many animals emit alarm calls in response to a potential predator. These calls may transmit information about predator type and response urgency. This study compared the alarm calls of the social buff-streaked chat, Oenanthe bifasciata, to the asocial African stonechat, Saxicola torquata. Spring traps were used to capture birds in the foothills of the Drakensberg Mountains, and pairs and groups were housed separately in outdoor aviaries. Both species were exposed to latex snakes and raptor models presented individually at 1 m, 5 m and 10 m respectively, while alarm calls were recorded. Analyses of the acoustic variables revealed that both call rate and duration decreased when the predator was further away. Larger groups of buff-streaked chats increased their raptor alarm call rate (39 calls in five minutes) and reduced the frequency of their end-pulses (for both predators) by 0.6 kHz. Hence, large groups present a louder, perhaps more formidable mob to discourage attack; softer end-pulses may minimize cues to the callers' location, and higher call rates during high-risk situations reflect the response urgency required to escape aerial predation. African stonechats were quieter, a strategy, perhaps, to reduce detection. Group size may therefore influence the perception of threat, where larger and louder groups become more conspicuous for aerial predation.
acidic lipids in fecal water-a potential risk factor for colon cancer13

Although there have recently been reports in the literature indicatingthat vegetarian-type diets are protective against the development ofhuman colon cancer, this is still far from clear. It was also recently indicated that the concentration ofacidic lipids in the aqueous phase of stool constitutes a risk factor for the development of colon cancer. Thus, we examined the effect ofa change from a mixed to a lactovegetarian diet on this fecal variable. The dietary change caused a decrease in the total concentration ofsoluble fecal fatty acids(43 10 ± 3020 to 1080 ± 1040 �mol/ L, p < 0.05) and deoxycholic acid (125 ± 42 to 73 ± 35 �tmol/L, p < 0.05). However, there was no change in either the total bile acid concentration in (164 ± 54 to 107 ± 41 �.�mol/L) or the cellular toxicity of (0.94 ± 0.55 to 1.60 ± 0.63 �mol/L, relative survival) the aqueous phase of stool. Thus, the consumption ofa lactovegetarian diet may reduce certain risk factors of potential significance in colon carcinogenesis. Am J C/in Nuir 1989;50:992-6.
Rootstock and Training System Affect Dry-matter and Carbohydrate Distribution in `Golden Delicious' Apple Trees

A study was conducted to quantify the effects of rootstock and training system on C allocation in apple. Dry- matter distribution was determined at harvest in 5-year-old 'Golden Delicious' apple ( Malus domestica Borkh.) trees on four rootstocks (MM.111 EMLA, M.7a, M.26 EMLA, and M.9 EMLA) and in three training systems (three-wire palmette, free-standing central leader, and nonpruned). Mobilizable carbohydrate content was determined at harvest and leaf fall in trees from the same planting on MM.111 EMLA and M.9 EMLA in all three training systems. Training system effects interacted with rootstock effects in dry weights of branches and of fruit. Nonpruned system shoot and fruit dry weights reflected known rootstock vigor; whereas, pruned system (three-wire and central leader) shoot dry weights were greatest and fruit dry weights were lowest in trees on M.7a. Rootstock affected the partitioning of dry matter between above- and below-ground tree components, with MM.111 EMLA accumulating significantly more dry matter in the root system than trees on the other rootstocks. Trees in the central leader and the three-wire palmette systems partitioned more dry weight into nonbearing 1-year shoots than trees in the nonpruned system. Root starch content at harvest was greater in trees on MM.111 EMLA than on M.9 EMLA, and root sucrose and sorbitol were less in trees on MM.111 EMLA compared to M.9 EMLA. At leaf fall, starch in young roots was equal in trees on both rootstocks, and sorbitol again was lower in trees on MM.111 EMLA. Harvest starch content of roots, shoots, and branches was lower in nonpruned than in pruned trees. At leaf fall, root, shoot, and branch starch content increased in nonpruned and central leader-trained trees but did not increase in three-wire palmette-trained trees.
Requirements for a Biologically Realistic Cancer Risk Assessment for Inorganic Arsenic

A remarkable feature of the carcinogenicity of inorganic arsenic (As,) is the observation that human exposures to Asi have been strongly associated with increases in skin, lung, and internal cancers, but As, does not typically cause tumors in standard laboratory animal test protocols. Considerable controversy has centered on whether there is epidemiological evidence of a “threshold” for the carcinogenic effects of Asi, or at least of a highly nonlinear dose–response. Saturation of metabolism in the dose-range associated with tumors does not appear to be adequate to produce a major impact on the dose-response for carcinogenicity. If there is a strong nonlinearity, it results from the nature of the carcinogenic mechanism(s) of Asi. However, no single hypothesis for the mechanism of Asi carcinogenicity has widespread support. A biologically realistic cancer risk assessment for Asi would requirea quantitative description of the dose of active arsenic species in target tissues, the interactions between active arsenic and tissue constituents, and the manner in which these interactions result in tumor formation in multiple organs in humans, but not in experimental animals. Although Asi has only infrequently been associated with tumors in animal studies, it has repeatedly been shown to act as a comutagen in vitro and as a cocarcinogen in vivo. Asi is clastogenic, producing chromatid aberrations, but does not produce point mutations at single gene loci. Of particular interest, Asi has been shown to inhibit repair of DNA single-strand breaks, a possible mechanism for its observed comutagenicity and cocarcinogenicity. We propose a cocarcinogenic mode of action in which Asi acts primarily on intermediate cells deficient in cell cycle control at a late stage in a preexisting carcinogenic process. This interaction enhances ge-nomic fragility and accelerates conversion of premalignant lesions to more aggressive, clinically observable tumors. An indirect effect of As, on DNA repair is consistent with the expectation of a nonlinear dose-response rather than the linear dose-response traditionally assumed for mutagenic carcinogens. However, defining the exact nature of this tumor dose-response will require further experimental data on the dose-response for the cellular effects of Asi. Because Asi carcinogenicity is unlikely to be observed in normal experimental animals not exposed to other carcinogens, studies in animals and cell lines deficient in cell cycle control should also be considered. Experimental studies specifically designed to address the key mechanistic and dose-response issues for Asi carcinogenicity are critically needed to support public health policy decisions regarding current environmental exposures to Asi.
Habitat factors differentiating the occurrence of Ostracoda (Crustacea) in the floodplain of a small lowland River Krąpiel (N-W Poland)

We analysed the occurrence of ostracods in a small river, taking into account all the types of water bodies in the floodplain − these included helocrenes, oxbow lakes, and ponds, as well as the main river channel. The objective of the study was to investigate the variation in ostracod communities and identify those factors determining species distribution. The environmental factors considered were the type of water body, responsible for 17% of the variance, the physical and chemical water properties (29%), and the biotic and abiotic factors associated with the substrate type (23%). Among the factors associated with the substrate, sediment sorting, plant coverage and insolation were the most important. The ostracod fauna of the helocrenes differed from that of the other water bodies in the floodplain. In the water bodies of the Krąpiel valley and in the main river channel, 33 ostracod species were recorded, of which 26 were found in the main river channel. Refugia in the floodplain were the main source of the diversity and abundance of ostracods in the main river channel. The mean density in the main river channel was very low, at 330 indiv. m−2, while in the water bodies of the floodplain it was the greatest, reaching up to 5568 indiv. m−2.
Species diversity of bats (Mammalia: Chiroptera) in forest fragments, primary forests, and savannas in central Amazonia, Brazil

The exact number of species of bats in Brazilian Amazonia is not precisely known because relatively few sites have been surveyed in detail. Here we present an updated species list of the bats of Alter do Chao at the delta of the Tapajos River in Para State. Using mist nets and acoustic monitoring of echolocation calls we systematically surveyed 5 forest sites, 14 natural forest fragments, and 12 savanna sites. We captured 3978 bats representing 70 species, 40 genera, and 7 families. Fifty species were recorded in savannas, 44 in forest sites, and 41 in forest fragments. The mean capture rate was higher in savanna and forest sites (0.747 and 0.741 bats/mist-net-hour (mnh), respectively) than in forest fragments (0.483 bats/mnh). Our list includes new records for Brazil and extends knowledge of the distribution of some species. Species-accumulation curves and species-richness estimators indicate that 75100 bat species occur at Alter do Chao, suggesting that our inventory recorded approximately 6789% of th.