Miracle-dz/UniFAR-FTUs huggingface dataset:
The ManyBugs and IntroClass Benchmarks for Automated Repair of C Programs

The field of automated software repair lacks a set of common benchmark problems. Although benchmark sets are used widely throughout computer science, existing benchmarks are not easily adapted to the problem of automatic defect repair, which has several special requirements. Most important of these is the need for benchmark programs with reproducible, important defects and a deterministic method for assessing if those defects have been repaired. This article details the need for a new set of benchmarks, outlines requirements, and then presents two datasets, ManyBugs and IntroClass, consisting between them of 1,183 defects in 15 C programs. Each dataset is designed to support the comparative evaluation of automatic repair algorithms asking a variety of experimental questions. The datasets have empirically defined guarantees of reproducibility and benchmark quality, and each study object is categorized to facilitate qualitative evaluation and comparisons by category of bug or program. The article presents baseline experimental results on both datasets for three existing repair methods, GenProg, AE, and TrpAutoRepair, to reduce the burden on researchers who adopt these datasets for their own comparative evaluations.
Generalized clustering coefficients and Milgram condition for q-th degrees of separation

We introduce a series of generalized clustering coefficients based on String formalism given by Aoyama, using adjacent matrix in networks. We numerically evaluate Milgram condition proposed in order to explore q-th degrees of separation in scale free networks and small world networks. We find that scale free network with exponent 3 just shows 6-degrees of separation. Moreover we find some relations between separation numbers and generalized clustering coefficient in both networks.
Periplasmic phosphorylation of lipid A is linked to the synthesis of undecaprenyl phosphate

One‐third of the lipid A found in the Escherichia coli outer membrane contains an unsubstituted diphosphate unit at position 1 (lipid A 1‐diphosphate). We now report an inner membrane enzyme, LpxT (YeiU), which specifically transfers a phosphate group to lipid A, forming the 1‐diphosphate species. 32P‐labelled lipid A obtained from lpxT mutants do not produce lipid A 1‐diphosphate. In vitro assays with Kdo2‐[4′‐32P]lipid A as the acceptor shows that LpxT uses undecaprenyl pyrophosphate as the substrate donor. Inhibition of lipid A 1‐diphosphate formation in wild‐type bacteria was demonstrated by sequestering undecaprenyl pyrophosphate with the cyclic polypeptide antibiotic bacitracin, providing evidence that undecaprenyl pyrophosphate serves as the donor substrate within whole bacteria. LpxT‐catalysed phosphorylation is dependent upon transport of lipid A across the inner membrane by MsbA, a lipid A flippase, indicating a periplasmic active site. In conclusion, we demonstrate a novel pathway in the periplasmic modification of lipid A that is directly linked to the synthesis of undecaprenyl phosphate, an essential carrier lipid required for the synthesis of various bacterial polymers, such as peptidoglycan.
Algebraic Aspects of the Supersymmetric Minimal Surface Equation

In this paper, a supersymmetric extension of the minimal surface equation is formulated. Based on this formulation, a Lie superalgebra of infinitesimal symmetries of this equation is determined. A classification of the one-dimensional subalgebras is performed, which results in a list of 143 conjugacy classes with respect to action by the supergroup generated by the Lie superalgebra. The symmetry reduction method is used to obtain invariant solutions of the supersymmetric minimal surface equation. The classical minimal surface equation is also examined and its group-theoretical properties are compared with those of the supersymmetric version.
Introduction and establishment of tadpole shrimp Triops newberryi (Notostraca: Triopsidae) in a date garden for biological control of mosquitoes in the Coachella Valley, Southern California.

Tadpole shrimp (TPS), Triops newberryi (Packard), has been reported to have a potential as a biocontrol agent for larval mosquitoes breeding in intermittently flooded habitats. To develop and promote this predator for controlling mosquitoes, a date garden devoid of preexisting TPS populations was chosen in the Coachella Valley, southern California in 2000 to receive introductions of TPS eggs and mature TPS. Mosquito control by TPS was assessed in the plots one year after their introductions. In a selected block on this ranch, 2 rows were stocked with TPS eggs, where soil containing approximately 2,000 eggs was spread over the surface of dry ground in each row before flooding. Another 2 rows were used for mature TPS introduction, where about 400 mature TPS were released into standing water in each row 1 day after flooding. After a single egg or mature TPS introduction, active TPS in water and viable eggs in dry surface soil were noted in increasing numbers during the 3-4 subsequent irrigations. Disking before irrigation, which turned the eggs over and mixed them into the soil column, reduced TPS egg populations at the soil surface and subsequent active TPS populations in standing water after irrigation. After one or two irrigations, viable eggs and active shrimp were found in centers adjacent to the introduced plots in the stocked rows. Ample evidence is presented to show that TPS populations were established after a single introduction of eggs or mature TPS. TPS eggs and/or newly hatched TPS were also carried into the neighboring rows across the borders by the overflowing irrigation water, and TPS populations became established there too, as active TPS were noted after each irrigation in the adjacent unstocked rows. Considering the ease and economical storage, transportation and handling, dessication--resistant eggs have advantages over mature TPS for field introductions. Mosquito control by TPS was assessed in rows with and without TPS in July 2001, one year after TPS introductions. Production of Psorophora columbiae Dyar and Knab and TPS populations were determined 4-5 days after each of 2 irrigations, when there was no or little vegetation inside the rows. As compared with the row without TPS, the presence of relatively high numbers of TPS reduced Ps. columbiae by 73 to 99% as based on the average numbers of larvae, pupae and exuviae per dip in the rows with versus without TPS.
Post-menopausal oestrogen-progestogen therapy.

Post-menopausal oestrogen–progestogen therapy involves administration of the oestrogens described in the monograph on ‘Post-menopausal oestrogen therapy’ accompanied by a progestogen or progesterone to women around the time of the menopause, primarily for the treatment of menopausal symptoms but also for the prevention of conditions that become more common after the menopause, such as osteoporosis and ischaemic heart disease. The progestogen can be administered orally or transdermally and either continuously or at various intervals. Intermittent progestogen administration causes withdrawal uterine bleeding, while continuous therapy generally does not. In ‘peri-menopausal hormonal therapy’, the components are not specified but are usually oestrogen with or without a progestogen. Annex 2 (Table 5) gives examples of brands of post-menopausal oestrogen– progestogen therapy. Progestogens that can be given in combination with the oestrogens are listed in Annex 1, with their constituents, doses, routes of administration and the names of some countries in which the brands are available; Annex 1 also gives the chemical formulae and some information on indications for use.
Cloning and characterization of dnaA(Cs), a mutation which leads to overinitiation of DNA replication in Escherichia coli K-12

The product of the dnaA gene is essential for the initiation of chromosomal DNA replication in Escherichia coli K-12. A cold-sensitive mutation, dnaA(Cs), was originally isolated as a putative intragenic suppressor of the temperature sensitivity of a dnaA46 mutant (G. Kellenberger-Gujer, A. J. Podhajska, and L. Caro, Mol. Gen. Genet. 162:9-16, 1978). The cold sensitivity of the dnaA(Cs) mutant was attributed to a loss of replication control resulting in overinitiation of DNA replication. We cloned and sequenced the dnaA gene from the dnaA(Cs) mutant and showed that it contains three point mutations in addition to the original dnaA46(Ts) mutation. The dnaA(Cs) mutation was dominant to the wild-type allele. Overproduction of the DnaA(Cs) protein blocked cell growth. In contrast, overproduction of wild-type DnaA protein reduced the growth rate of cells but did not stop cell growth. Thus, the effect of elevated levels of the DnaA(Cs) protein was quite different from that of the wild-type protein under the same conditions.
Genetics of bovine respiratory disease in cattle: can breeding programs reduce the problem?

Abstract Genetics is responsible for approximately half the observed change in performance internationally in well-structured cattle breeding programs. Almost all, if not all, individual characteristics, including animal health, have a genetic basis. Once genetic variation exists then breeding for improvement is possible. Although the heritability of most health traits is low to moderate, considerable exploitable genetic variation does exist. From the limited studies undertaken, and mostly from limited datasets, the direct heritability of susceptibility to BRD varied from 0.07 to 0.22 and the maternal heritability (where estimated) varied from 0.05 to 0.07. Nonetheless, considerable genetic variation clearly exists; the genetic standard deviation for the direct component (binary trait), although differing across populations, varied from 0.08 to 0.20 while the genetic standard deviation for the maternal component varied from 0.04 to 0.07. Little is known about the genetic correlation between genetic predisposition to BRD and animal performance; the estimation of these correlations should be prioritized. (Long-term) Breeding strategies to reduce the incidence of BRD in cattle should be incorporated into national BRD eradication or control strategies.
Interannual and Interdecadal Variations of the East Asian Summer Monsoon and Tropical Pacific SSTs. Part II: Meridional Structure of the Monsoon

Abstract The relationship between the interannual variations of the East Asian summer monsoon and that of the tropical SST shows considerable variations. In this study, rainfall in the southeastern coastal area of China (SEC) during 1951–96 is used to composite the tropical SST, 850-hPa wind, and 500-hPa height. The results relative to the May–June rainfall, which represents most of the SEC summer monsoon rainfall, are compared to the Yangtze River Valley (YRV) rainfall composites. It is shown that strong interdecadal changes in the Pacific may account for the observed variations in the meridional structure of the monsoon–SST relationship. The western Pacific 500-hPa subtropical ridge, which is influenced by the equatorial eastern Pacific SST, is crucial to these variations. During 1951–77 the SEC wet phase is produced by an anomalous anticyclone in the northern South China Sea, which tends to make the monsoon pre-Mei-yu and Mei-yu fronts quasi-stationary in the general area of both SEC and YRV, and also .
Thermal-reliable 3D clock-tree synthesis considering nonlinear electrical-thermal-coupled TSV model

3D physical design needs accurate device model of through-silicon vias (TSVs). In this paper, physics-based electrical-thermal model is introduced for both signal and dummy thermal TSVs with the consideration of nonlinear electrical-thermal dependence. Taking thermal-reliable 3D clock-tree synthesis as a case-study to verify the effectiveness of the proposed TSV model, one nonlinear programming-based clock-skew reduction problem is formulated to allocate thermal TSVs for clock-skew reduction under non-uniform temperature distribution. With a number of 3D clock-tree benchmarks, experiments show that under the nonlinear electrical-thermal TSV model, insertion of thermal TSVs can effectively reduce temperature-gradient introduced clock-skew by 58.4% on average, and has 11.6% higher clock-skew reduction than the result under linear electrical-thermal model.
Sensory and electromyographic mapping during delayed-onset muscle soreness.

PURPOSE The aim of this human study was to apply novel topographical mapping techniques to investigate sensory and EMG manifestations of delayed-onset muscle soreness (DOMS) in multiple locations of the quadriceps. METHODS Bipolar surface EMG signals were recorded from 11 healthy men with 15 pairs of electrodes located at 10, 20, 30, 40, and 50% of the distance from the medial, superior, and lateral border of the patella to the anterior superior iliac spine. Subjects performed sustained isometric knee extensions at 40% of the maximal force (MVC) until task failure before, 24 h, and 48 h after eccentric exercise. Pressure-pain thresholds (PPT) were assessed at the 15 locations where the EMG was recorded. RESULTS Time to task failure was reduced after the eccentric exercise (mean +/- SD, 56.6 +/- 23 s before the eccentric exercise; 34.3 +/- 18.9 s at 24 h after exercise; and 34.3 +/- 14.4 s at 48 h after exercise). During the postexercise sustained contractions, EMG average rectified value (ARV) significantly decreased over time (P < 0.001), but it did not change over time before the eccentric exercise. Moreover, the decrease in ARV over time during postexercise contractions was greatest in the distal region of the quadriceps, where the PPT were most reduced (P < 0.05). CONCLUSION Novel topographical mapping of both surface EMG and PPT of the quadriceps showed site-dependent effects of eccentric exercise, probably attributable to variations in the morphological and architectural characteristics of the muscle fibers. Greater manifestations of DOMS in the distal region of the quadriceps may indicate a greater susceptibility of this region to further injury after eccentric exercise.
A new histogram modification based robust image data hiding technique

The main objective of this presented research work is to implement a steganography application simply based on a new image histogram modification approach. An image histogram is a type of histogram which acts as a graphical representation of the tonal distribution in a digital image. The stego images, obtained using the proposed data hiding method, are inherently robust against main geometrical attacks such as rotation, scattered tiles and warping. The application of proposed method has comparatively higher secret data embedding capacity than its counterparts, as well as providing relatively enhanced PSNR results. Not only has it improved the data embedding capacity from 300─360 bits to 665─747 bits but also the PSNR from 53.10─55.18 dB to 56.01─62.75 dB for the well-known Lena, Baboon and Pepper images, compared to one of its important counterparts.
Entrainment and motion of coarse particles in a shallow water stream down a steep slope

We investigate the entrainment, deposition and motion of coarse spherical particles within a turbulent shallow water stream down a steep slope. This is an idealization of bed-load transport in mountain streams. Earlier investigations have described this kind of sediment transport using empirical correlations or concepts borrowed from continuum mechanics. The intermittent character of particle transport at low-water discharges led us to consider it as a random process. Sediment transport in this regime results from the imbalance between entrainment and deposition of particles rather than from momentum balance between water and particles. We develop a birth–death immigration–emigration Markov process to describe the particle exchanges between the bed and the water stream. A key feature of the model is its long autocorrelation times and wide, frequent fluctuations in the solid discharge, a phenomenon never previously explained despite its ubiquity in both nature and laboratory experiments. We present experimental data obtained using a nearly two-dimensional channel and glass beads as a substitute for sediment. Entrainment, trajectories, and deposition were monitored using a high-speed digital camera. The empirical probability distributions of the solid discharge and deposition frequency were properly described by the theoretical model. Experiments confirmed the existence of wide and frequent fluctuations of the solid discharge, and revealed the existence of long autocorrelation time, but theory overestimates the autocorrelation times by a factor of around three. Particle velocity was weakly dependent on the fluid velocity contrary to the predictions of the theoretical model, which performs well when a single particle is moving. For our experiments, the dependence of the solid discharge on the fluid velocity is entirely controlled by the number of moving particles rather than by their velocity. We also noted significant changes in the behaviour of particle transport when the bed slope or the water discharge was increased. The more vigorous the stream was, the more continuous the solid discharge became. Moreover, although 90% of the energy supplied by gravity to the stream is dissipated by turbulence for slopes lower than 10%, particles dissipate more and more energy when the bed slope is increased, but surprisingly, the dissipation rate is nearly independent of fluid velocity. A movie is available with the online version of the paper.
Mott Transition in VO2 Revealed by Infrared Spectroscopy and Nano-Imaging

Electrons in correlated insulators are prevented from conducting by Coulomb repulsion between them. When an insulator-to-metal transition is induced in a correlated insulator by doping or heating, the resulting conducting state can be radically different from that characterized by free electrons in conventional metals. We report on the electronic properties of a prototypical correlated insulator vanadium dioxide in which the metallic state can be induced by increasing temperature. Scanning near-field infrared microscopy allows us to directly image nanoscale metallic puddles that appear at the onset of the insulator-to-metal transition. In combination with far-field infrared spectroscopy, the data reveal the Mott transition with divergent quasi-particle mass in the metallic puddles. The experimental approach used sets the stage for investigations of charge dynamics on the nanoscale in other inhomogeneous correlated electron systems.
Outcome after surveillance of low‐grade and indefinite dysplasia in patients with ulcerative colitis

Background: The management of low‐grade (LGD) and indefinite dysplasia (IND) in patients with ulcerative colitis (UC) remains controversial, as outcomes after a diagnosis of LGD or IND in previous studies vary widely. Methods: All patients evaluated were from a single institution referral center who had a history of UC and a diagnosis of either LGD or IND between 1994 and 2008 as confirmed by 2 expert gastrointestinal (GI) pathologists. Data were collected by chart review of electronic and paper medical records. All patients who did not undergo a colectomy within 90 days of their dysplasia diagnosis were included in the final analysis. Hazard ratios for risk factors as well as incidence rates and Kaplan–Meier estimates were used to calculate the progression to high‐grade dysplasia (HGD) or colorectal cancer (CRC). Results: Thirty‐five patients were included in the analysis, of whom 2 patients with IND and 2 patients with LGD developed HGD or CRC over a mean duration of 49.8 months. In total, the incident rate for advanced neoplasia for all patients was 2.7 cases of HGD or CRC per 100 person‐years at risk. For flat and polypoid LGD the incident rate of advanced neoplasia was 4.3 and 1.5 cases per 100 person‐years at risk, respectively. Patients with primary sclerosing cholangitis (PSC) had an incident rate of 10.5 cases per 100 years of patient follow‐up. Conclusions: We report a low rate of progression to HGD or CRC in patients who underwent surveillance for LGD or IND; polypoid dysplasia showed less risk of progression than flat dysplasia. (Inflamm Bowel Dis 2010)
Structural Analysis of Monomeric RNA-Dependent Polymerases: Evolutionary and Therapeutic Implications

The crystal structures of monomeric RNA-dependent RNA polymerases and reverse transcriptases of more than 20 different viruses are available in the Protein Data Bank. They all share the characteristic right-hand shape of DNA- and RNA polymerases formed by the fingers, palm and thumb subdomains, and, in many cases, “fingertips” that extend from the fingers towards the thumb subdomain, giving the viral enzyme a closed right-hand appearance. Six conserved structural motifs that contain key residues for the proper functioning of the enzyme have been identified in all these RNA-dependent polymerases. These enzymes share a two divalent metal-ion mechanism of polymerization in which two conserved aspartate residues coordinate the interactions with the metal ions to catalyze the nucleotidyl transfer reaction. The recent availability of crystal structures of polymerases of the Orthomyxoviridae and Bunyaviridae families allowed us to make pairwise comparisons of the tertiary structures of polymerases belonging to the four main RNA viral groups, which has led to a phylogenetic tree in which single-stranded negative RNA viral polymerases have been included for the first time. This has also allowed us to use a homology-based structural prediction approach to develop a general three-dimensional model of the Ebola virus RNA-dependent RNA polymerase. Our model includes several of the conserved structural motifs and residues described in other viral RNA-dependent RNA polymerases that define the catalytic and highly conserved palm subdomain, as well as portions of the fingers and thumb subdomains. The results presented here help to understand the current use and apparent success of antivirals, i.e. Brincidofovir, Lamivudine and Favipiravir, originally aimed at other types of polymerases, to counteract the Ebola virus infection.
Practical Compact Indexes for Top-k Document Retrieval

We present a fast and compact index for top-k document retrieval on general string collections, in which given a string pattern, the index returns the k documents where it appears most often. We adapt a linear-space and optimal-time theoretical solution, whose implementation poses various algorithm engineering challenges. Although a naive implementation of the optimal solution is estimated to require around 80n bytes for a text collection of n symbols, our implementation requires 2.5n to 3.0n bytes, text included, and answers queries within microseconds. This outperforms all previous practical indexes by orders of magnitude; the only index using less space is hundreds of times slower. Our index can be built on collections of hundreds of gigabytes and on tokenized text collections.