Miracle-dz/UniFAR-FTUs huggingface dataset:
How do Java methods grow?

Overly long methods hamper the maintainability of software - they are hard to understand and to change, but also difficult to test, reuse, and profile. While technically there are many opportunities to refactor long methods, little is known about their origin and their evolution. It is unclear how much effort should be spent to refactor them and when this effort is spent best. To obtain a maintenance strategy, we need a better understanding of how software systems and their methods evolve. This paper presents an empirical case study on method growth in Java with nine open source and one industry system. We show that most methods do not increase their length significantly; in fact, about half of them remain unchanged after the initial commit. Instead, software systems grow by adding new methods rather than by modifying existing methods.
The effect of an acute fast on human head and neck carcinoma xenograft. Growth effects on an 'isolated tumor vascular pedicle' in the nude rat.

The effects of nutritional state on tumor growth are poorly understood. Most animal studies to date suggest an inhibitory effect of nutritional depletion on tumor growth and a stimulatory effect of nutritional repletion or overfeeding. We have modified an "isolated tumor vascular pedicle" model in the nude rat to study the growth and tumor-specific nutrient utilization of the FaDu cell line of human hypopharyngeal squamous carcinoma. Two weeks after tumor implantation, rats were randomized to either a fed or fasted study group for an additional 7 days. Tumors were significantly larger in the fasted group (0.602 +/- 0.215 g vs 0.362 +/- 0.104 g; P < .02). Whole blood nutrient gradients were determined across the tumor and systemic tissues in both groups. The nutrient gradients across these tissues were significantly different in the fed animals and approached statistical significance in the fasted animals. In addition, there appeared to be a greater utilization of glucose in the fed group (-0.401 +/- 0.904 mmol/L vs -0.298 +/- 0.589 mmol/L), while there was a greater production of lactate in the fasted group (0.798 +/- 0.518 mmol/L vs 0.046 +/- 0.639 mmol/L; P < .1). Flow cytometric analysis revealed no difference in the percentage of cells in any particular stage of the cell cycle between the two groups. These results suggest that the maintenance of adequate body weight may be beneficial not only to the nutrition of the cachectic tumor-bearing host but may also prevent a ketotic state or state of lipolysis that may be preferential to the tumor.
A stream computing approach towards scalable NLP

Computational power needs have grown dramatically in recent years. This is also the case in many language processing tasks, due to overwhelming quantities of textual information that must be processed in a reasonable time frame. This scenario has led to a paradigm shift in the computing architectures and large-scale data processing strategies used in the NLP field. In this paper we describe a series of experiments carried out in the context of the NewsReader project with the goal of analyzing the scaling capabilities of the language processing pipeline used in it. We explore the use of Storm in a new approach for scalable distributed language processing across multiple machines and evaluate its effectiveness and efficiency when processing documents on a medium and large scale. The experiments have shown that there is a big room for improvement regarding language processing performance when adopting parallel architectures, and that we might expect even better results with the use of large clusters with many processing nodes.
Ginsenoside Rb1 protects the intestinal mucosal barrier following peritoneal air exposure

Ginsenoside Rb1 (GRb1), which is one of the main ingredients derived from Panax ginseng, has been widely used to treat various gastrointestinal disorders. The present study aimed to determine whether GRb1 was able to prevent intestinal mucosal barrier damage in rats following peritoneal air exposure for 3 h. GRb1 (5, 10, and 20 mg/kg) was orally administrated via gavage four times prior to and following surgery. Blood and terminal ileum were sampled 24 h following surgery. Levels of serum D-lactate (D-LA) were detected using an enzyme-linked immunosorbent assay kit. Intestinal permeability was assessed by determining the intestinal clearance of fluorescein isothiocyanate-dextran (FD4). Activity of intestinal myeloperoxidase was measured to assess intestinal inflammation, and intestinal histopathology was assessed by light microscopy. The results showed that GRb1 reduced the level of serum D-LA, intestinal clearance of FD4, and the activity of intestinal myeloperoxidase. Intestinal edema and inflammation were also ameliorated by GRb1, and the Chiu's scores employed for assessing intestinal mucosal damage were also reduced in the GRb1-treated peritoneal air exposure group. In addition, GRb1 induced a significant difference at 10 and 20 mg/kg, indicating a dose-dependent effect. The results of the present study suggest that GRb1 may be able to protect the intestinal mucosal barrier against damage induced by peritoneal air exposure, which may be associated with its anti-inflammatory action.
Hybrid evolutionary algorithm based fuzzy logic controller for automatic generation control of power systems with governor dead band non-linearity

Abstract A new intelligent Automatic Generation Control (AGC) scheme based on Evolutionary Algorithms (EAs) and Fuzzy Logic concept is developed for a multi-area power system. EAs i.e. Genetic Algorithm–Simulated Annealing (GA–SA) are used to optimize the gains of Fuzzy Logic Algorithm (FLA)-based AGC regulators for interconnected power systems. The multi-area power system model has three different types of plants i.e. reheat, non-reheat and hydro and are interconnected via Extra High Voltage Alternate Current transmission links. The dynamic model of the system is developed considering one of the most important Governor Dead Band (GDB) non-linearity. The designed AGC regulators are implemented in the wake of 1% load perturbation in one of the control areas and the dynamic response plots are obtained for various system states. The investigations carried out in the study reveal that the system dynamic performance with hybrid GA–SA-tuned Fuzzy technique (GASATF)-based AGC controller is appreciably superior as compared to that of integral and FLA-based AGC controllers. It is also observed that the incorporation of GDB non-linearity in the system dynamic model has resulted in degraded system dynamic performance.
Planning with Problems Requiring Temporal Coordination

We present the first planner capable of reasoning with both the full semantics of PDDL2.1 (level 3) temporal planning and with numeric resources. Our planner, CRIKEY3, employs heuristic forward search, using the start-and-end semantics of PDDL2.1 to manage temporal actions. The planning phase is interleaved with a scheduling phase, using a Simple Temporal Network, in order to ensure that temporal constraints are met. To guide search, we introduce a new temporal variant of the Relaxed Planning Graph heuristic that is capable of reasoning with the features of this class of domains, along with the Timed Initial Literals of PDDL2.2. CRIKEY3 extends the state-of-the-art in handling the full temporal expressive power of PDDL2.1, including numeric temporal domains.
Interactive-Predictive Translation Based on Multiple Word-Segments

Current machine translation systems require human revision to produce high-quality translations. This is achieved through a post-editing process or by means of an interactive human–computer collaboration. Most protocols belonging to the last scenario follow a left-to-right strategy, where the preﬁx of the translation is iteratively increased by successive validations and corrections made by the user. In this work, we propose a new interactive protocol which allows the user to validate all correct word sequences in the translation generated by the system, breaking the left-to-right barrier. We evaluated our proposal through simulated experiments, obtaining large reductions of the human effort.
Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica

The Shanghai RAPESEED Database (RAPESEED, http://rapeseed.plantsignal.cn/) was created to provide the solid platform for functional genomics studies of oilseed crops with the emphasis on seed development and fatty acid metabolism. The RAPESEED includes the resource of 8462 unique ESTs, of which 3526 clones are with full length cDNA; the expression profiles of 8095 genes and the Serial Analysis of Gene Expression (SAGE, 23 895 unique tags) and tag-to-gene data during seed development. In addition, a total of ∼14 700 M3 mutant populations were generated by ethylmethanesulfonate (EMS) mutagenesis and related seed quality information was determined using the Foss NIR System. Further, the TILLING (Targeting Induced Local Lesions IN Genomes) platform was established based on the generated EMS mutant population. The relevant information was collected in RAPESEED database, which can be searched through keywords, nucleotide or protein sequences, or seed quality parameters, and downloaded.
Stable and robust walking with compliant legs

Bipedal walking could be implemented into a robot by mimicking spring-like leg behaviour. The fundamental model, describing human-like leg function in walking is the bipedal spring-mass model which was investigated in this study. We identified several types of walking patterns, e.g. symmetric and asymmetric walking, that accounts for high variability of gait. The aim of this study is the identification of a stiffness range which allows for stable walking with comparatively large robustness against perturbations. Walking with compliant legs was tested with the bipedal PogoWalker, demonstrating advantages of the underlying leg mechanics, i.e. walking without the necessity of precise leg adjustments, and acceptable impact forces.
Breaking through the thresholds: an analysis for iterative reweighted ℓ1 minimization via the Grassmann angle framework

It is now well understood that the ℓ<inf>1</inf> minimization algorithm is able to recover sparse signals from incomplete measurements [2], [1], [3] and sharp recoverable sparsity thresholds have also been obtained for the ℓ<inf>1</inf> minimization algorithm. However, even though iterative reweighted ℓ<inf>1</inf> minimization algorithms or related algorithms have been empirically observed to boost the recoverable sparsity thresholds for certain types of signals, no rigorous theoretical results have been established to prove this fact. In this paper, we try to provide a theoretical foundation for analyzing the iterative reweighted ℓ<inf>1</inf> algorithms. In particular, we show that for a nontrivial class of signals, the iterative reweighted ℓ<inf>1</inf> minimization can indeed deliver recoverable sparsity thresholds larger than that given in [1], [3]. Our results are based on a high-dimensional geometrical analysis (Grassmann angle analysis) of the null-space characterization for ℓ<inf>1</inf> minimization and weighted ℓ<inf>1</inf> minimization algorithms.
The effect of desferrioxamine on antigen‐induced inflammation in the rat air pouch

The effect of desferrioxamine, a relatively specific iron chelating drug, has been examined in an allergic air pouch model of inflammation in the rat. The model has both an acute and chronic phase and allows quantitative measurements of the cellular and exudative response within the pouch fluid and the tissue response in the membrane that develops around the preformed cavity. Desferrioxamine given as a single bolus injection, directly into the cavity, stimulated the acute inflammatory phase, increasing both the exudative and leukocyte response, in a dose-dependent fashion. In marked contrast, repeated injections during the acute to chronic phase or during the established chronic reaction, led to a reduction in both leukocyte numbers within the cavity and the amount of granulation tissue surrounding it. The exudative response was, however, unaltered. These results are discussed in relation to the potential role of iron in promoting an acute and chronic inflammatory reaction.
Improving English-Czech Tectogrammatical MT

Improving English-Czech Tectogrammatical MT The present paper summarizes our recent results concerning English-Czech Machine Translation implemented in the TectoMT framework. The system uses tectogrammatical trees as the transfer medium. A detailed analysis of errors made by the previous version of the system (considered as the baseline) is presented first. Then several improvements of the system are described that led to better translation quality in terms of BLEU and NIST scores. The biggest performance gain comes from applying Hidden Tree Markov Model in the transfer phase, which is a novel technique in the field of Machine Translation.
ProcessFast, a Java Framework for Development of Concurrent and Distributed Applications

Today, any application that requires processing information gathered from the Web will likely require a parallel processing approach to be able to scale. While writing such applications, the developer should be able to exploit several types of parallelism paradigms in a natural way. Most of the available development tools are focused on just one of these parallelism types, e.g. the data parallelism, stream processing, etc. In this paper, we introduce ProcessFast, a Java framework for the development of concurrent/distributed applications, designed to allow the developer to integrate both stream/task parallelism and data parallelism in the same application and to seamlessly combine solutions to sub-problems where each solution exploits a specific programming model.
PERFORMANCE ANALYSIS OF NON COOPERATIVE SPECTRUM SENSING USING SEARCH BASED ENERGY DETECTION

Almost 80 to 90 percent of the radio spectrum is left unutilized at any period of time, while at the same time some other regions of spectrum experience overcrowding. We consider a dynamic spectrum access system in which Secondary Users (SUs) choose to either acquire dedicated spectrum or to use spectrum-holes (white spaces) which belong to Primary Users (PUs). The tradeoff incorporated in this decision is between immediate yet costly transmission and free but delayed transmission (a consequence of both the possible appearance of PUs and sharing the spectrum holes with multiple SUs). Cognitive radio is a smart radio that can identify the idle frequencies (also termed as spectral holes or white spaces) and allot them for the use of unlicensed secondary users. The basic functionality of a cognitive radio is to sense the spectrum accurately by avoiding any chances for interfering with primary or licensed users. Spectrum sensing can be performed either in cooperative or non-cooperative method. This paper performs Non cooperative spectrum sensing, using search based energy detection technique (SB-ED). The idea is to utilize nodes to convey the signal transmitted from primary user to the fusion center and then estimate the presence or absence of primary activities in the spectrum.
Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers

Significance Seasonality in disease incidence is ubiquitous among infectious diseases. Seasonal drivers include weather variables, such as temperature and humidity, and social factors (e.g., contact patterns). Attempts to make long-term predictions of infectious diseases are hampered by the inability to understand the complex interplay of these factors. Here, we model the dynamics of seasonal influenza based on a high-quality 12-year Israeli dataset. The dynamics are completely explainable by the time evolution of the model equations, the antigenic jumps of the virus, and the climatic forcing, yielding high-correlation fits to the data (r = 0.94). The forecasting ability is greatly increased through the predictability of the system’s transient dynamics, resulting in accurate predictions (r = 0.93) that have not yet been found elsewhere. Human influenza occurs annually in most temperate climatic zones of the world, with epidemics peaking in the cold winter months. Considerable debate surrounds the relative role of epidemic dynamics, viral evolution, and climatic drivers in driving year-to-year variability of outbreaks. The ultimate test of understanding is prediction; however, existing influenza models rarely forecast beyond a single year at best. Here, we use a simple epidemiological model to reveal multiannual predictability based on high-quality influenza surveillance data for Israel; the model fit is corroborated by simple metapopulation comparisons within Israel. Successful forecasts are driven by temperature, humidity, antigenic drift, and immunity loss. Essentially, influenza dynamics are a balance between large perturbations following significant antigenic jumps, interspersed with nonlinear epidemic dynamics tuned by climatic forcing.
Fatal cardiovascular collapse of infants receiving large amounts of chloramphenicol.

Death of three newborn infants (without obvious immediate cause of death at necropsy) followed administration of moderately large amounts of chloramphenicol. The recommended intramuscular dose of the microcrystalline suspension of chloramphenicol in aqueous vehicle was 100 to 150 mg. per kilogram of body weight per day for children of 15 kg. or less. 1-3 One death occurred after administration of 220 mg. per kilogram per day for 60 hours. Another death occurred after administration of 230 mg. per kilogram per day for 72 hours. The recommended oral dose of the suspension of chloramphenicol palmitate for children of 15 kg. or less was 50 to 100 mg. per kilogram per day 4 up to 100 to 150 mg. per kg. per day. 3,5 One death occurred after 50 mg. per kilogram per day for 56 hours and 10 hours after a single inadvertent oral dose of 400 mg. The use of
Development of a novel larynx pacemaker multichannel array electrode: In vivo animal analysis

Electrical stimulation of posterior cricoarytenoid muscle offers a physiological approach to retain the function of the paralyzed larynx muscle after paralysis. The aim of this study was to develop and evaluate a durable, biocompatible, and atraumatic array electrode for inclusion in a larynx pacemaker. In addition to developing the electrode array, an evaluation methodology using in vivo multichannel electromyography was assessed.
Closing the gap in a generation: Health equity through action on the social determinants of health

Committees often figure in the punch lines of jokes about inefficiency and lack of productivity sometimes for good reason. Ideological stalemates can grind work to a halt, or lack of agreement on substantive items can produce documents that cater only to the very least common denominator. When confronted with ‘Closing the gap in a generation’, produced by a committee appointed by the embattled World Health Organization, a reader might feel authorised to be cynical before even opening it. But the jaded reader is in for a surprise. The Commission on Social Determinants of Health, chaired by Michael Marmot, includes 19 participants from several countries and diverse academic backgrounds, among them heavyweights such as Giovanni Berlinguer, one of the most relevant intellectuals in the international field of public health, and Nobel Prize-winning economist Amartya Sen. Part manual, part manifesto, ‘Closing the gap in a generation’, the product of their collaboration, is a powerful proposal of sound health policies, with a broad, intersectoral approach, founded in solid evidence and pulling no punches in putting forward a very progressive agenda. Incidentally, such characteristics make writing a review about this book quite a challenge; among other aspects, how to summarise something that is already a summary. The key argument of the book is quite straightforward, and could be summarised by its very first sentence: ‘Social justice is a matter of life and death’. Further, ‘inequities in health, avoidable health inequalities, arise because of the circumstances in which people grow, live, work, and age, and the systems put in place to deal with illness. The conditions in which people live and die are, in turn, shaped by political, social, and economic forces’. The action plan is spelled out a couple of paragraphs after that: ‘In the spirit of social justice, the Commission on Social Determinants of Health was set up by the World Health Organization (WHO) in 2005 to marshal the evidence on what can be done to promote health equity, and to foster a global movement to achieve it’. And that, in a nutshell, is exactly what the book is about. It is organised in three parts: an executive summary that presents the overall discussion of the book in synthetic form; 17 chapters contained in six divisions (‘parts’) that flesh out the full argument in detail; and an appendix that lists again all the recommendations. This reiteration of ideas is in line with its dual characteristics of being simultaneously a reference textbook and a guide for political action. In the detailed chapters that form the bulk of the book, the arguments are structured in smaller segments, beginning with a review of pertinent literature, followed by a brief discussion on the problems and ways to face them and ending Global Public Health Vol. 6, No. 1, January 2011, 102 105
A Lightweight Buyer-Seller Watermarking Protocol

The buyer-seller watermarking protocol enables a seller to successfully identify a traitor from a pirated copy, while preventing the seller from framing an innocent buyer. Based on finite field theory and the homomorphic property of public key cryptosystems such as RSA, several buyer-seller watermarking protocols (N. Memon and P. W. Wong (2001) and C. -L. Lei et al. (2004)) have been proposed previously. However, those protocols require not only large computational power but also substantial network bandwidth. In this paper, we introduce a new buyer-seller protocol that overcomes those weaknesses by managing the watermarks. Compared with the earlier protocols, ours is n times faster in terms of computation, where n is the number of watermark elements, while incurring only O(1/lN) times communication overhead given the finite field parameter lN. In addition, the quality of the watermarked image generated with our method is better, using the same watermark strength.