Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving software text retrieval using conceptual knowledge in source code

A large software project usually has lots of various textual learning resources about its API, such as tutorials, mailing lists, user forums, etc. Text retrieval technology allows developers to search these API learning resources for related documents using free-text queries, but it suffers from the lexical gap between search queries and documents. In this paper, we propose a novel approach for improving the retrieval of API learning resources through leveraging software-specific conceptual knowledge in software source code. The basic idea behind this approach is that the semantic relatedness between queries and documents could be measured according to software-specific concepts involved in them, and software source code contains a large amount of software-specific conceptual knowledge. In detail, firstly we extract an API graph from software source code and use it as software-specific conceptual knowledge. Then we discover API entities involved in queries and documents, and infer semantic document relatedness through analyzing structural relationships between these API entities. We evaluate our approach in three popular open source software projects. Comparing to the state-of-the-art text retrieval approaches, our approach lead to at least 13.77% improvement with respect to mean average precision (MAP).
A Mitochondrial Paradigm of Metabolic and Degenerative Diseases, Aging, and Cancer: A Dawn for Evolutionary Medicine

Life is the interplay between structure and energy, yet the role of energy deficiency in human disease has been poorly explored by modern medicine. Since the mitochondria use oxidative phosphorylation (OXPHOS) to convert dietary calories into usable energy, generating reactive oxygen species (ROS) as a toxic by‐product, it is hypothesized that mitochondrial dysfunction plays a central role in a wide range of age‐related disorders including metabolic deficiencies like diabetes, neurodegenerative diseases like Alzheimer and Parkinson disease, aging and various forms of cancer. The mitochondrial energy system is assembled from the products of both nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) genes. Since the mtDNA is present in thousands of copies per cell and encodes essential genes for energy production, it is further proposed that the delayed‐onset and progressive course of the age‐related diseases results from the accumulation of somatic mutations in the mtDNAs of post‐mitotic tissues. The tissue‐specific manifestations of these diseases are envisioned to result from the varying energetic roles and needs of the different tissues which are the result of differential expression of key nuclear regulatory factors. The variation in individual and regional predisposition to degenerative diseases and cancer is hypothesized to result from the interaction of modern dietary caloric intake and ancient mitochondrial genetic polymorphisms that permitted ancestral humans to adapt to the various environments that they encountered as they migrated around the globe. Therefore the mitochondria provide a direct link between our environment and our genes and the mtDNA variants that permitted our forbearers to energetically adapt to their ancestral homes are influencing our health today.
Efficacy and safety of enoxaparin versus unfractionated heparin during percutaneous coronary intervention: systematic review and meta-analysis

Objective To determine the efficacy and safety of enoxaparin compared with unfractionated heparin during percutaneous coronary intervention. Design Systematic review and meta-analysis. Data sources Medline and Cochrane database of systematic reviews, January 1996 to May 2011. Study selection Randomised and non-randomised studies comparing enoxaparin with unfractionated heparin during percutaneous coronary intervention and reporting on both mortality (efficacy end point) and major bleeding (safety end point) outcomes. Data extraction Sample size, characteristics, and outcomes, extracted independently and analysed. Data synthesis 23 trials representing 30 966 patients were identified, including 10 243 patients (33.1%) undergoing primary percutaneous coronary intervention for ST elevation myocardial infarction, 8750 (28.2%) undergoing secondary percutaneous coronary intervention after fibrinolysis, and 11 973 (38.7%) with non-ST elevation acute coronary syndrome or stable patients scheduled for percutaneous coronary intervention. A total of 13 943 patients (45.0%) received enoxaparin and 17 023 (55.0%) unfractionated heparin. Enoxaparin was associated with significant reductions in death (relative risk 0.66, 95% confidence interval 0.57 to 0.76; P<0.001), the composite of death or myocardial infarction (0.68, 0.57 to 0.81; P<0.001), and complications of myocardial infarction (0.75, 0.6 to 0.85; P<0.001), and a reduction in incidence of major bleeding (0.80, 0.68 to 0.95; P=0.009). In patients who underwent primary percutaneous coronary intervention, the reduction in death (0.52, 0.42 to 0.64; P<0.001) was particularly significant and associated with a reduction in major bleeding (0.72, 0.56 to 0.93; P=0.01). Conclusion Enoxaparin seems to be superior to unfractionated heparin in reducing mortality and bleeding outcomes during percutaneous coronary intervention and particularly in patients undergoing primary percutaneous coronary intervention for ST elevation myocardial infarction.
Crystal Structure of the Eukaryotic Ribosome

Macromolecular Message Translation The ribosome is a macromolecular machine that translates the sequence of messenger RNA into proteins in all living cells. Structures of prokaryotic ribosomes have supplied insight into the conserved features of such protein synthesis; however, eukaryotic translation has additional levels of complexity. Ben-Shem et al. (p. 1203) have determined the crystal structure of the yeast 80S ribosome at 4.15 angstrom resolution. The ribosome is in a ratcheted conformation, which is a state that is an intermediate in the translocation of messenger RNA and transfer RNA. The crystal structure provides the molecular underpinning for existing biochemical and genetic data and will inform the design of functional experiments. The structure of the 80S ribosome from yeast has been determined at 4.15 angstrom resolution. Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.
Pathophysiology of depression and innovative treatments: remodeling glutamatergic synaptic connections

Despite the complexity and heterogeneity of mood disorders, basic and clinical research studies have begun to elucidate the pathophysiology of depression and to identify rapid, efficacious antidepressant agents. Stress and depression are associated with neuronal atrophy, characterized by loss of synaptic connections in key cortical and limbic brain regions implicated in depression. This is thought to occur in part via decreased expression and function of growth factors, such as brain-derived neurotrophic factor (BDNF), in the prefrontal cortex (PFC) and hippocampus. These structural alterations are difficult to reverse with typical antidepressants. However, recent studies demonstrate that ketamine, an N-methyl-D-aspartate (NMDA) receptor antagonist that produces rapid antidepressant actions in treatment-resistant depressed patients, rapidly increases spine synapses in the PFC and reverses the deficits caused by chronic stress. This is thought to occur by disinhibition of glutamate transmission, resulting in a rapid but transient burst of glutamate, followed by an increase in BDNF release and activation of downstream signaling pathways that stimulate synapse formation. Recent work demonstrates that the rapid-acting antidepressant effects of scopolamine, a muscarinic receptor antagonist, are also associated with increased glutamate transmission and synapse formation. These findings have resulted in testing and identification of additional targets and agents that influence glutamate transmission and have rapid antidepressant actions in rodent models and in clinical trials. Together these studies have created tremendous excitement and hope for a new generation of rapid, efficacious antidepressants.
Fabrication of a three-dimensional photonic band-gap crystal of air-spheres in a titania matrix

A three-dimensional (3D) colloidal crystal have been grown from an aqueous colloidal solution of highly monodisperse submicrometer-sized polystyrene spheres using a self-assembly processing technique. The electromagnetic waves diffracted by this crystal can interfere and give rise to a photonic band-gap. However, due to the low refractive index contrast within this material the band-gap is incomplete. By filling the voids between the spheres of the colloidal crystal with titania and removing the polystyrene beads by sublimation, we obtained an inverse-opal structure with an increased refractive index contrast showing strong opalescence.
Exploitation of semantic similarity for adaptation of existing terminologies within biomedical area

We present a novel method for adaptation of existing terminologies. Within biomedical domain and when no textual corpora for building terminologies are available, we exploit UMLS metathesaurus which merges over a hundred existing biomedical terminologies and ontologies. We exploit also algorithms for measuring the semantic similarity in order to limit, within UMLS, a semantically homogeneous space. In order to make possible such measure, we transform symbolic and semantic information associated to UMLS relations into numeric values. Evaluation performed by experts indicates that extracted concepts are relevant and their coverage satisfying. Additional semantic filters allow to improve the precision of the obtained terminology.
Variable-frequency electric drive with a function of compensation for induction motor asymmetry

Operation of a variable-frequency electric drive with damages in power electric circuit of the motor stator results in asymmetry of the motor phase current charge, increase of heating losses in certain phases, occurrence of variable components of electromagnetic torque and consumed power. Such operation modes significantly influence both motor operation and frequency converter operation, as long operation of a semiconductor energy converter under such conditions results in considerable overheat of certain switches, and later — in complete breakdown. The paper presents results of research of two devised vector-control systems with a function of compensation for motor broken windings influence on the characteristics of the variable-frequency electric drive. The first case deals with a possibility of compensation for electromagnetic torque variable component that causes additional vibrations of the motor. In the second case a possibility of compensation for consumed active power variable component is demonstrated; it results in reduction of heat overload of both separate phases of the motor and semiconductor switches of the frequency converter.
The Proximal Pedicled Anterolateral Thigh Flap for Lower Limb Coverage

Although primarily considered as a versatile free-flap donor site, the anterolateral thigh can also be a source of a local muscle perforator flap. This attribute has previously been rarely considered for lower limb coverage. This small series of 3 additional cases demonstrates the usefulness of a proximal pedicled anterolateral thigh flap for medial and lateral thigh wounds. This flap can also be part of a combined flap, in particular when transferred with the vastus lateralis muscle as a local chimeric flap. The peninsular version of the anterolateral thigh local flap avoids venous congestion and is very reliable. The orthograde pedicled anterolateral thigh muscle perforator flap should be considered as another useful alternative for any upper thigh wound if a flap is essential.
An efficient multi channel, 425µW QPSK transmitter with tuning for process variation in the Medical Implantable Communications Service (MICS) band of 402–405MHz

A truly Medical Implantable Communications Service (MICS) band compliant transmitter for biomedical applications, covering all ten channels in 402-405MHz is presented in this paper. The transmitter consists of a Phase Locked Loop(PLL) with rail to rail quadrature output, a passive mixer and a power amplifier (PA). The power consumption of the transmitter is 425μW at 1.2 V, and consumes only 7.1 nJ of energy per bit transmitted. The overall global efficiency of the transmitter is 19.3 %. This transmitter can account for PVT variations. The proposed transmitter meets all the federal communications commission (FCC) requirements for the MedRadio band. This proposed work is implemented in a 180nm CMOS process.
Carrier dynamics of composite and nanolayered films of zinc phthalocyanine and C60 measured by time-resolved terahertz spectroscopy

We present a study of charge transfer and carrier dynamics in films of zinc phthalocyanine (ZnPc) and buckmisnsterfullerene (C60) investigated by time-resolved terahertz spectroscopy (TRTS). These films are model structures for charge generation layers in organic photovoltaics and their intrinsic properties are therefore of interest. We compare two classes of films: composite films of ZnPc and C60 prepared by co-evaporation and layered ZnPc/C60 films prepared by alternating deposition. We find evidence for a short-lived charge transfer state of C60 that decays within several picoseconds of excitation. In contrast, both composite and multi-layered films have a long-lived THz absorption that depends on the composition and structure of the fims. The optimum composition for charge transfer within composite films is a 1:1 blend of ZnPc and C60. Amongst the layered films, there is an increase in charge photogeneration with decreasing layer thickness with a sample having ultrathin (2 nm) exhibiting the strongest THz absorption. A much stronger THz absorption signal was obtained from the layered structure than for the best composite film, even both structures contain similar fractions of ZnPc and C60 .
Polyamide 12 modified with nanoparticles: Effect on impact behaviour and on the electrical conductivity of carbon fibre-reinforced epoxy composites

Modifying the impact toughness of carbon composite by means of introducing thermoplastic inserts in the interlaminar layer is state of the art. However, these inlayers reduce the electrical conductivity through the thickness of the composite. Because the combination of good electrical conductivity and high fracture toughness is desirable, a detailed investigation was carried out into additive-enhanced polyamide 12 compound. The modification consisted in compounding graphite, graphene and carbon nanotubes with polyamide 12 in various proportions. After it was introduced into the interlaminar layer, the samples' electrical conductivity was measured and their mechanical properties assessed. Afterwards, these results were compared with various inserts made with unmodified polyamide 12. It turned out that the coarse-mesh laid scrim showed only a slight fall in conductivity. Furthermore, it provided promising results regarding the increase of the interlaminar toughness. Thus, the expensive modification of polyamide 12 can be avoided by using discrete laid scrim.
An Iteration-Based Variable Step-Size Algorithm for Joint Explicit Adaptation of Time Delay

By using an adaptive technique similar to the joint explicit time delay estimator, a novel variable step-size algorithm is derived. This algorithm employs the iteration time to control the step-size update and its respective performance analysis is also given. It is also proved that the proposed algorithm efficiently improves the convergence speed and the delay variance with only increasing a little computational cost compared to the conventional adaptive time delay estimation algorithm.
Nonlocal similarity regularization for sparse hyperspectral unmixing

This paper is concerned with semisupervised hyperspectral unmixing using a nonlocal similarity prior on the abundance images. To this end, the nonlocal self-similarity regularization is incorporated into the classical sparse regression formula to propose a new model for hyperspectral sparse unmixing. The rationale is the idea that there are many nonlocal similar patches to the given patch in the abundance images. The effectiveness of the proposed algorithm is illustrated using the synthetic and real data sets.
The Economic Benefits of the Dokdo Seals Restoration Project in Korea: A Contingent Valuation Study

Northern fur seals (Callorhinus ursinus), especially those that live in Dokdo, Korea, represent an endangered species in Korea. Thus, the government is considering the implementation of the Dokdo Seals (DS) restoration project. This article looks at the economic benefits for implementing the project, which includes making habitats for the DS, such as an artificial sea ranch, and training DS rescued from fishing nets and wounded in the wild to adapt to the wild so that they can be released into the Dokdo Sea. To this end, we looked at the willingness to pay (WTP) for the implementation of the project by conducting a contingent valuation (CV) survey of 1000 Korean households. We employed a one-and-one-half-bounded dichotomous choice question format. Furthermore, we used a spike model to model the WTP responses with zero observations. The mean yearly WTP for the project implementation was computed to be KRW 4923 (USD 4.86) for next ten years per household, which is statistically significant at the 1% level. The national annual value amounts to KRW 90.9 billion (USD 89.8 million). This value can be taken as an indication of the economic benefits of restoring the endangered species.
Neurochemical modulation of ingestive behavior in the ventral pallidum

The nucleus accumbens and its related circuitry have been shown to play an important role in promoting the intake of hedonically desirable food. A previous report has demonstrated that the blockade of GABAA receptors in the ventral pallidum (VP), a target of GABAergic projection from the nucleus accumbens, greatly increases food, but not water, intake in satiated rats [ Stratford et al. (1999)Brain Research, 825, 199–203]. The present study examined which neurotransmission in the VP is specifically involved in the intake of normally preferred taste stimuli. Microinjections of the GABAA antagonist bicuculline selectively increased the intake of saccharin solution but not that of water and quinine solution in water‐deprived rats. In contrast, the facilitation of GABAA receptors by microinjections of muscimol in the VP generally suppressed the intake of saccharin, water and quinine. The same injections induced strong aversive taste reactivity responses to oral stimulation with not only quinine but also water and saccharin. The local administration of d‐Ala2,N‐Me‐Phe4,Glyol5‐enkephalin, a selective µ‐opioid receptor agonist, into the VP had time‐dependent effects, decreasing saccharine intake early and increasing intake late. Microinjections of SCH‐23390, a dopamine D1 receptor antagonist, in the VP suppressed the intake of saccharin but not water or quinine. Microinjections of sulpiride, the dopamine D2 receptor antagonist, and 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione, the AMPA/kainate glutamate receptor antagonist, had no effect on fluid intake. These results reveal that GABA, opioid and D1 receptors in the VP are involved in the consumption of hedonically positive taste stimuli.
Five-year outcome of concurrent radiotherapy and chemotherapy in Saudi women with locally advanced cervical cancer: single-institution experience

BACKGROUND AND OBJECTIVES We aimed to evaluate long-term treatment outcomes and toxicity profile of combined radiotherapy and chemotherapy in Saudi women with locally advanced cervical cancer. DESIGN AND SETTINGS Retrospective study in a tertiary care cancer center in Riyadh, Saudi Arabia. METHODS AND MATERIALS The medical records of patients with histopathologically proven, locally advanced cervical cancer were analyzed. These patients received three-dimensional conformal radiotherapy with concurrent chemotherapy followed by high dose rate brachytherapy in our center between July 2007 and April 2012. The data regarding the safety profile, response rates, occurrence of locoregional or distant failure, disease-free survival, and overall survival rates were recorded. RESULTS The median follow-up period was 60 months (range, 8–66) for 74 patients. The median age of study population was 52.3 years (32–78), and the stage IIB was the predominant stage (49 patients [66.2%]). A total of 45 patients (60.9%) had radiologic-positive pelvic ± para-aortic lymphadenopathy. The 5-year locoregional and distant control rates were 84.3% and 78.5%, respectively. The 5-year disease-free and overall survival rates were 75.7% and 64.5%, respectively. Stage, nodal status, and hemoglobin levels were found to be important prognostic factors for locoregional and distant control. Acute grade 3 hematological and nonhematological toxicities were seen in 4 (5.4%) and 4 (5.4%) patients. Late toxicities were mild, and only 1 (1.4%) patient presented with subacute intestinal obstruction. CONCLUSION Concurrent chemoradiation in Saudi women with locally advanced cervical cancer showed better locoregional and distant control and survival rates with minimal toxicity.
μs-Scale time synchronization for energy-constrained mission-critical DTSNs

It is generally considered a trivial task to synchronize time in a distributed sensor network having a GPS module on board for each sensor node. This is not quite true depending on the application at hand. Commissioned to implement YuShanNet, a delay-tolerant sensor network (DTSN) enabling encounter information collection for hiker search and rescue, we find that the naive use of standard GPSs time acquisition functionalities gives a synchronization error at the scale of 10-100s milliseconds, which is not sufficient given two application-specific considerations: (1) data goodput and (2) energy efficiency. The two requirements are crucial in that the matter is life or death and the hiking trips usually take days. Towards efficient use of the intermittent connectivity in YuShanNet, we design, implement, and evaluate a time synchronization mechanism that improves the synchronization accuracy by approximately two orders of magnitude. This enables TDMA-fashioned MAC for high-goodput data transmission while the GPS is duty-cycled for energy efficiency.