Miracle-dz/UniFAR-FTUs huggingface dataset:
Data Mining in MEDLINE for Disease-Disease Associations Via Second Order Co-Occurrence

DDMiner, a new method for mining disease-disease associations in MEDLINE, is presented together with its first results. DDMiner searches for co-occurrences of gene names and disease terms, and finds relationships between diseases by word vector-similarity calculations. All records in PubMed were labeled with around 40,000 gene and protein names, and around 4,000 disease terms. Each disease term was described by a word vector from which the length equals the number of gene names. Each field in the vector represented a gene or a protein. The value in the field was derived from the number of publications in which this gene occurred together with the disease term. Disease-disease associations were calculated by vector-similarity calculation. Five diseases were examined together with their closest neighbor diseases to show the validity of our approach. All five examples showed only disease-disease associations that could be validated by medical literature. These results show that mining for disease-disease associations by second order co-occurrence is a powerful tool for medical science.
2‐Week Triple Therapy for Helicobacter pylori Infection is Better Than 1‐Week in Clinical Practice: a Large Prospective Single‐Center Randomized Study

Background: Proton pump inhibitor (PPI)‐based triple therapies are considered the standard regimens for Helicobacter pylori eradication, but the optimal duration of these regimens is still controversial. The aim of this study was to compare the efficacy of 1‐week versus 2‐week triple therapies in H. pylori‐positive patients.
Routine neonatal examination: effectiveness of trainee paediatrician compared with advanced neonatal nurse practitioner

OBJECTIVE To compare the effectiveness of routine neonatal examination performed by senior house officers (SHOs) and advanced neonatal nurse practitioners (ANNPs). DESIGN A prospective study of all infants referred to specialist orthopaedic, ophthalmology, and cardiology clinics. A standardised proforma was used to record details of the professional performing the neonatal check, any abnormalities discovered, source of ultimate referral to the specialist clinic, and specialist findings. RESULTS 527 eligible infants were recruited. For hip abnormalities, ANNPs displayed greater sensitivity than SHOs (96% v 74%; p < 0.05). Similarly for eye abnormalities, ANNPs were more sensitive (100% v 33%; p < 0.05). There were no significant differences between ANNPs and SHOs in terms of positive predictive values or effectiveness of detecting cardiac abnormalities. There was no difference in underlying incidence of abnormalities between the two hospitals. CONCLUSION ANNPs are significantly more effective in detecting abnormalities during the neonatal check. This has implications both for future workforce planning and current methods of medical training.
On the Probability Distribution of the Minimal Number of Hops Between any Pair of Nodes in a Bounded Wireless Ad-Hoc Network Subject to Fading

We investigate an ad hoc network where node locations are distributed according to a homogeneous Poisson process with intensity λn. We assume that all the nodes are equipped with an identical wireless transceiver capable of operating satisfactorily up to a certain maximal link loss. Our link model depends on the length of the link and on random lognormal fading. Each node functions as a source and destination of data packets, and may also serve as a repeater to transport packets over multi-hop routes as determined by the network router. We focus on the probability distribution of the minimum number of hops between a source and a destination node known to be at distance D from the source. When the distribution of source-todestination distances is known, the distribution of the minimal number of hops between any arbitrary pair of nodes can also be found. Many variations of this same problem have been studied in the literature. However, as far as we know, no exact closedform analytic results for fading environments have been presented before.
Synthesis of Software Programs for Embedded Control Applications

Software components for embedded reactive real-time applications must satisfy tight code size and run-time constraints. Cooperating Finite State Machines provide a convenient intermediate format for embedded system co-synthesis, between high-level specification languages and software or hardware implementations. We propose a software generation methodology that takes advantage of the very restricted class of specifications and allows for tight control over the implementation cost. The methodology exploits several techniques from the domain of Boolean function optimization. We also describe how the simplified control/data-flow graph used as an intermediate representation can be used to accurately estimate the size and timing cost of the final executable code.
Effect of levetiracetam on DNA oxidation and glutathione content in a temporal lobe epilepsy model

Levetiracetam (LEV) is a drug commonly used as an anticonvulsant. However, recent evidence points to a possible role as an antioxidant. We previously demonstrated the antioxidant properties of LEV by significantly increasing catalase and superoxide dismutase activities and decreasing the hydrogen peroxide (H2O2) levels in the hippocampus of rats with temporal lobe epilepsy (TLE) showing scavenging properties against the hydroxyl radical. The aim of the present work was to evaluate, the effect of LEV on DNA oxidation, by determining 8‑hydroxy‑2‑deoxyguanosine (8‑OHdG) levels, and glutathione content, through reduced (GSH) and oxidized (GSSG) glutathione levels, in the hippocampus of rats with TLE. Male Wistar rats were assigned to the control (CTRL), CTRL+LEV, epileptic (EPI) and EPI+LEV groups. TLE was induced using the lithium‑pilocarpine model. Thirteen weeks after TLE induction, LEV was administered for one week through osmotic pumps implanted subcutaneously. The determination of 8‑OHdG, GSH and GSSG levels were measured using spectrophotometric methods. We showed that LEV alone significantly increased 8‑OHdG and GSSG levels in the hippocampus of control rats compared to those in epileptic condition. No significant differences in GSH levels were observed. LEV could induce changes in the hippocampus increasing DNA oxidation and GSSG levels under nonepileptic condition but not protecting against the mitochondrial dysfunction observed in TLE probably by mechanisms related to changes in chromatin structure, neuroinflammation and alterations in redox components.
Experimental Crystallization of a High-K Arc Basalt: the Golden Pumice, Stromboli Volcano (Italy)

The near-liquidus crystallization of a high-K basalt (PST-9 golden pumice, 49·4 wt % SiO2, 1·85 wt % K2O, 7·96 wt % MgO) from the present-day activity of Stromboli (Aeolian Islands, Italy) has been experimentally investigated between 1050 and 1175°C, at pressures from 50 to 400 MPa, for melt H2O concentrations between 1·2 and 5·5 wt % and {Delta}NNO ranging from –0·07 to +2·32. A drop-quench device was systematically used. AuPd alloys were used as containers in most cases, resulting in an average Fe loss of 13% for the 34 charges studied. Major crystallizing phases include clinopyroxene, olivine and plagioclase. Fe–Ti oxide was encountered in a few charges. Clinopyroxene is the liquidus phase at 400 MPa down to at least 200 MPa, followed by olivine and plagioclase. The compositions of all major phases and glass vary systematically with the proportion of crystals. Ca in clinopyroxene sensitively depends on the H2O concentration of the coexisting melt, and clinopyroxene Mg-number shows a weak negative correlation with {Delta}NNO. The experimental data allow the liquidus surface of PST-9 to be defined. When used in combination with melt inclusion data, a consistent set of pre-eruptive pressures (100–270 MPa), temperatures (1140–1160°C) and melt H2O concentrations is obtained. Near-liquidus phase equilibria and clinopyroxene Ca contents require melt H2O concentrations <2·7–3·6 and 3 ± 1 wt %, respectively, overlapping with the maximum frequency of glass inclusion data (2·5–2·7 wt % H2O). For olivine to crystallize close to the liquidus, pressures close to 200 MPa are needed. Redox conditions around {Delta}NNO = +0·5 are inferred from clinopyroxene compositions. The determined pre-eruptive parameters refer to the storage region of golden pumice melts, which is located at a depth of around 7·5 km, within the metamorphic arc crust. Golden pumice melts ascending from their storage zone along an adiabat will not experience crystallization on their way to the surface.
Carotenoid Pigments in Tubers of the Katahdin Variety of Irish Potato.

Flesh color in Irish potato varieties ranges from almost pure white to a deep canary yellow. The yellowish tinge of "white-fleshed'' varieties is intensified after dehydration, becoming a definite yellow if the tubers have been harvested in an immature state, as is the case with material grown in the south (1, 2). This residual yellow color, when it occurred, was at one time considered by the Army Quartermaster Corps to be due to a faulty technique in dehydration and as a result such material was graded downward. It was soon recognized, however, that this yellow color was due to the presence of naturally occurring carotenoid pigments. Caldwell, Brunstetter, Culpepper, and Ezell (3) showed that 19 "white-fleshed'' varieties, representing fully-matured material, averaged 0.021 mg. of total carotenoid pigments per 100 gm. fresh weight, while 3 normally yellow-fleshed varieties averaged 0.138 mg. per 100 gm. fresh weight. This means that when the total concentration of carotenoid pigments is about 1 p.p.m. on a dry weight basis, the yellow color of the dried product will be slight. When the total pigment concentration is about 7 p.p.m. dry weight, the dried product will have a marked yellow color. One of the findings of the present paper is that in the case of the Katahdin variety, harvested in an immature state, there was still a pronounced yellow color in the dried product when the concentration of carotenoid pigments was 3 p.p.m. dry weight. This paper reports an intensive study of the carotenoid pigments in three samples of the Katahdin variety, with the purpose of separating and identifying as many of the pigments as possible.
Synchronization Stability Analysis and Research on Parameters Stability Region in Renewable Energy Grid-Connected Converter System

Renewable energy grid-connected converters (GCCs) employing phase-locked loops (PLLs) have become the prevailing control scheme in wind and photovoltaic power generation systems, owing to their efficiently, controllability, and flexibility. However, the susceptibility to synchronization stability issues arises from weak grid characteristics associated with long-distance transmission lines. To precisely delineate the synchronous stability boundary concerning control and operating parameters in the renewable energy GCC system, the small-signal linearization model of the system is firstly established in this paper. Subsequently, a synchronization stability criterion is derived by considering the static stability conditions of the system and the operating range of the point of common coupling (PCC) voltage. The parameter stability regions for system operating parameters, encompassing active output power and short-circuit ratio (SCR), along with system control parameters, namely PLL proportion and integral coefficient, are provided. The mutual constraints among the system operating parameters and the system control parameters are elucidated from a mechanistic perspective. Validation of the theoretical derivation is achieved through case study examples, finally, highlighting the impact of system operating parameters and control parameters on the stability of the new energy GCC system based on the stability region of parameters. And the application of the stability region of parameters is demonstrated in the planning and operation of grid-connected new energy systems.
Removal of cryptic poxvirus transcription termination signals from the human immunodeficiency virus type 1 envelope gene enhances expression and immunogenicity of a recombinant vaccinia virus

The in vivo role of the proposed poxvirus early transcription termination signal TTTTTNT was confirmed by analysis of the RNA species made by recombinant vaccinia viruses. Premature transcription termination occurred following each of two TTTTTNT sequences present naturally within the coding region of the human immunodeficiency virus type 1 envelope gene. Alteration of the TTTTTNT sequences, without changing the encoded amino acids, resulted in production of full-length early mRNAs, improved protein expression, and a more consistent immune response.
Scaling MapReduce Vertically and Horizontally

Glass wing is a MapReduce framework that uses OpenCL to exploit multi-core CPUs and accelerators. However, compute device capabilities may vary significantly and require targeted optimization. Similarly, the availability of resources such as memory, storage and interconnects can severely impact overall job performance. In this paper, we present and analyze how MapReduce applications can improve their horizontal and vertical scalability by using a well controlled mixture of coarse- and fine-grained parallelism. Specifically, we discuss the Glass wing pipeline and its ability to overlap computation, communication, memory transfers and disk access. Additionally, we show how Glass wing can adapt to the distinct capabilities of a variety of compute devices by employing fine-grained parallelism. We experimentally evaluated the performance of five MapReduce applications and show that Glass wing outperforms Hadoop on a 64-node multi-core CPU cluster by factors between 1.2 and 4, and factors from 20 to 30 on a 23-node GPU cluster. Similarly, we show that Glass wing is at least 1.5 times faster than GPMR on the GPU cluster.
BasiLex: An 11.5 million words corpus of Dutch texts written for children

This article discusses Basilex, a 13.5-million tokens, 11.5-million Dutch words corpus of written language offered to children in the elementary school age, which was recently finalized. The corpus is automatically analyzed at the levels of part-of-speech tagging and lemmatization, and a limited amount of polysemous words has been partly automatically disambiguated. Also, a lemma-based lexicon is derived. The aim of the present article is threefold: First, to give a description of BasiLex and how it was built, and to discuss its validity. Second, to compare the BasiLex lexicon with two other lexicons regarding differences in their most frequent words: the Schrooten and Vermeer (1994) lexicon, a small and now outdated Dutch corpus of language addressed to children, and a derived lexicon of SoNaR, an adult written language corpus (Oostdijk et al. 2013). Third, we discuss some potential educational applications of BasiLex.
Smarter than Genius? Human Evaluation of Music Recommender Systems

Genius is a popular commercial music recommender system that is based on collaborative filtering of huge amounts of user data. To understand the aspects of music similarity that collaborative filtering can capture, we compare Genius to two canonical music recommender systems: one based purely on artist similarity, the other purely on similarity of acoustic content. We evaluate this comparison with a user study of 185 subjects. Overall, Genius produces the best recommendations. We demonstrate that collaborative filtering can actually capture similarities between the acoustic content of songs. However, when evaluators can see the names of the recommended songs and artists, we find that artist similarity can account for the performance of Genius. A system that combines these musical cues could generate music recommendations that are as good as Genius, even when collaborative filtering data is unavailable.
Rhythmic parsing

Abstract A controlled reading experiment reveals that stress-based linguistic rhythm impinges on syntactic ambiguity resolution in silent and oral reading. The results suggest that, at points of syntactic underspecification, the accruing prosodic representation may affect even the earliest stages of structure building, viz. the analysis of syntactic features of an ambiguous word. Such an effect remains inexplicable in the context of (psycho-)linguistic theories that assume a strictly unidirectional relationship between syntactic and phonological processes, the latter merely interpreting the conditions the syntactic component imposes on it. Here, a performance compatible grammar in the framework of Optimal Parsing is presented that is capable of capturing the reading data. The model integrates syntactic parsing and prosodification in reading and predicts that, at points of syntactic indetermination, weak prosodic constraints alone may guide syntactic structure assignment. This suggests a bidirectional relationship between syntax and phonology in grammar and processing while, at the same time, confirming a tight coupling of language production and comprehension.
EMG Processing Based Measures of Fatigue Assessment during Manual Lifting

Manual lifting is one of the common practices used in the industries to transport or move objects to a desired place. Nowadays, even though mechanized equipment is widely available, manual lifting is still considered as an essential way to perform material handling task. Improper lifting strategies may contribute to musculoskeletal disorders (MSDs), where overexertion contributes as the highest factor. To overcome this problem, electromyography (EMG) signal is used to monitor the workers' muscle condition and to find maximum lifting load, lifting height and number of repetitions that the workers are able to handle before experiencing fatigue to avoid overexertion. Past researchers have introduced several EMG processing techniques and different EMG features that represent fatigue indices in time, frequency, and time-frequency domain. The impact of EMG processing based measures in fatigue assessment during manual lifting are reviewed in this paper. It is believed that this paper will greatly benefit researchers who need a bird's eye view of the biosignal processing which are currently available, thus determining the best possible techniques for lifting applications.
A Convolution Neural Network based QPSK and 16QAM Modulations Simulator for a Multiuser MIMO-OFDM Transmission Simulation over a Nakagami-m Fading Channel

Wireless communication has been a widespread method of data transfer in the modern era. Various modulation techniques have been found and among them 16QAM has proven to be the most efficient. This study provides a Convolutional Neural Network (CNN) approach for simulating 16QAM and QPSK modulation schemes over a multiuser MIMO-OFDM using the Keras library over Nakagami-m fading. It then examines the two modulation schemes to determine if QPSK might be a viable alternative to 16QAM. In this paper two analysis have been done, a realistic MIMO OFDM system simulation and weighted belief propagation decoding.
Matching People across Camera Views using Kernel Canonical Correlation Analysis

Matching people across views is still an open problem in computer vision and in video surveillance systems. In this paper we address the problem of person re-identification across disjoint cameras by proposing an efficient but robust kernel descriptor to encode the appearance of a person. The matching is then improved by applying a learning technique based on Kernel Canonical Correlation Analysis (KCCA) which finds a common subspace between the proposed descriptors extracted from disjoint cameras, projecting them into a new description space. This common description space is then used to identify a person from one camera to another with a standard nearest-neighbor voting method. We evaluate our approach on two publicly available datasets for re-identification (VIPeR and PRID), demonstrating that our method yields state-of-the-art performance with respect to recent techniques proposed for the re-identification task.
Distributed Training of Deep Neural Networks: Theoretical and Practical Limits of Parallel Scalability

This paper presents a theoretical analysis and practical evaluation of the main bottlenecks towards a scalable distributed solution for the training of Deep Neural Networks (DNNs). The presented results show, that the current state of the art approach, using data-parallelized Stochastic Gradient Descent (SGD), is quickly turning into a vastly communication bound problem. In addition, we present simple but fixed theoretic constraints, preventing effective scaling of DNN training beyond only a few dozen nodes. This leads to poor scalability of DNN training in most practical scenarios.
Retrospective: on the inclusion properties for multi-level cache hierarchies

vv hen we wrote this paper, it had been over 20 years since caches had been introduced and they had become a regular feature in most computer systems. As applications were demanding more main memory and as the gap between processor speed and memory access time was widening (a familiar story today), the need for larger caches was clear. Like today though, increasing cache capacity was not a sufficient answer to the problem since as cache sizes grew, so did the cache access time. The need for a hierarchy of caches was apparent. Proposals for on-chip caches were burgeoning but, quite often, these caches were specialpurpose: instruction caches only, top-of-stack caches etc. Shared second level caches for multiprocessor systems had also been proposed and even been implemented in one Japanese machine (Facom). However, the placement of second level caches in shared-bus multiprocessors, the parallel processing architecture of choice in the late 80’s, and the impact of the cache hierarchy on snoopy coherence protocols had not been investigated thoroughly.
Productivity and cost of a small-scale cable yarder in an uphill and downhill area: a case study in South Korea

ABSTRACT Tree diameter, topography, and stand accessibility have been major factors to consider when selecting the optimal equipment to extract logs from stump to landing area. In Korea, forest land has 6.4 million ha of forest, comprising 64% of its total land area. Small and medium (15–30 cm in diameter at breast height [DBH]) size of trees located on steep slopes (> 30°) is approximately 80% of total forest area. Therefore, there has been an increasing interest in the application of a small-scale cable yarding system. We performed uphill and downhill yarding experiments using an 80 hp farm tractor mounted tower yarder (HAM300) to evaluate productivities and costs associated with primary transportation of tree length logs in mixed conifer stands. In addition, sensitivity analyses were performed to find the effects of different yarding directions and distances on yarding productivities and costs. Results showed that uphill and downhill yarding productivities were 9.04 m3/PMH (Productivity Machine Hours) and 7.87 m3/PMH at a cost of US$9.06 and US$10.04/m3, respectively. The yarding direction greatly affected productivity and cost: decreasing productivity may be significantly affected by working conditions. Our results support the effectiveness of an HAM300 yarder in extracting logs for small-scale cable yarding operations.