Miracle-dz/UniFAR-FTUs huggingface dataset:
A literature-based method for assessing the functional coherence of a gene group

MOTIVATION Many experimental and algorithmic approaches in biology generate groups of genes that need to be examined for related functional properties. For example, gene expression profiles are frequently organized into clusters of genes that may share functional properties. We evaluate a method, neighbor divergence per gene (NDPG), that uses scientific literature to assess whether a group of genes are functionally related. The method requires only a corpus of documents and an index connecting the documents to genes. RESULTS We evaluate NDPG on 2796 functional groups generated by the Gene Ontology consortium in four organisms: mouse, fly, worm and yeast. NDPG finds functional coherence in 96, 92, 82 and 45% of the groups (at 99.9% specificity) in yeast, mouse, fly and worm respectively.
Active versus passive inhibition of activated information in long-term and working memory

The focus of this research was to investigate the possible existence of an indirect inhibitory mechanism working on activated yet unattended information in long-term memory (LTM). There exists evidence in the cognition and memory literature, specifically the retrieval-induced forgetting and negative priming literature, as well as others, that suggests indirect inhibition may be acting to moderate activation levels in conjunction with semantic activation. Participants (n=120) were given a memory load of different category exemplars and were then instructed to either recall a given dominant category membership or a novel subordinate category membership. The novel category recall instruction required a reorganization of exemplar category associations and the hypothesized inhibition of dominant categories. Following recall, a series of category comparison frames presented new exemplars from the dominant categories of the memory load. Indirect inhibition of the dominant categories would be evidenced by longer response time (RT) on subordinate relative to dominant recall trials. RTs for the category comparisons associated with subordinate recall were not significantly different from the comparisons associated with dominant category recall. These data are incongruent with the hypothesis of an indirect inhibitory mechanism acting on activated yet unattended information in LTM. Instead, they are consistent with Cowan’s (1999) model of working memory (WM) that posited active-but-unattended information in WM is subject to time-based decay but not interference.
Design and Implementation of a BCI System Based on Steady-State Visual Evoked Potentials

In recent years, Brain-computer interface (BCI) based on electroencephalogram (EEG) is an active topic in brain function research. BCI provides a direct communication and control channel for sending messages and instructions from brain to external computers or other electronic devices. However, the EEG signals are very faint and often corrupted by noises such as power line noise, EMG, EOG etc. EEG signal acquisition is very critical for the BCI system. In the paper, a circuit for EEG signal acquisition is designed. The circuit module is mainly composed of protection circuit, instrumentation amplifier, common mode rejection (CMR) circuit, gain adjustable amplifiers and filters. Finally, a BCI system based on SSVEP sets up by this hardware circuit's platform. The experimental results show that the circuit is effective with good amplification ability and high CMR, and it is very suitable for the BCI system.
Oxidative stress and hippocampus in a low‐grade hepatic encephalopathy model: protective effects of curcumin

Aim: The present study was performed on prehepatic portal hypertensive rats, a model of low‐grade hepatic encephalopathy, designed to evaluate whether oxidative stress was a possible pathway implicated in hippocampal damage and if so, the effect of an anti‐oxidant to prevent it.
Analysis of design and delivery of critical incident workshops for elementary school English as a foreign language teachers in community of practice

ABSTRACT Language teachers can uncover new understanding of the teaching and learning process through reflecting on critical incidents [Richard, J.C. , and T.S. C. Farrell. 2005. Professional Development for Language Teachers. New York, NY: Cambridge University Press]. Based on the data analysis of workshop handouts, observation notes, and interviews, this study analyses three critical incident workshops designed and delivered to 19 elementary school English teachers in Taiwan in terms of design, participants’ learning, strengths, and suggestions. The study has the following findings. First, the participants moved from knowing nothing about critical incidents or mazes to writing up, discussing, and analysing critical incidents in collaborative reflective practice. Most importantly, the workshop facilitator fostered a safe and trusting environment for participating teachers to discuss critical incidents freely and combat their isolation. Five elements are recommended to be integrated into the design and delivery of critical incident workshops.
Antimicrobial-Drug Prescription in Ambulatory Care Settings, United States, 1992–2000

During the 1990s, as antimicrobial resistance increased among pneumococci, many organizations promoted appropriate antimicrobial use to combat resistance. We analyzed data from the National Ambulatory Medical Care Survey, an annual sample survey of visits to office-based physicians, and the National Hospital Ambulatory Medical Care Survey, an annual sample survey of visits to hospital emergency and outpatient departments, to describe trends in antimicrobial prescribing from 1992 to 2000 in the United States. Approximately 1,100–1,900 physicians reported data from 21,000–37,000 visits; 200–300 outpatient departments reported data for 28,000–35,000 visits; ~400 emergency departments reported data for 21,000–36,000 visits each year. In that period, the population- and visit-based antimicrobial prescribing rates in ambulatory care settings decreased by 23% and 25%, respectively, driven largely by a decrease in prescribing by office-based physicians. Antimicrobial prescribing rates changed as follows: amoxicillin and ampicillin, –43%; cephalosporins, –28%; erythromycin, –76%; azithromycin and clarithromycin, +388%; quinolones, +78%; and amoxicillin/clavulanate, +72%. This increasing use of azithromycin, clarithromycin, and quinolones warrants concern as macrolide- and fluoroquinolone-resistant pneumococci are increasing.
A Quadtree-Based Lightweight Data Compression Approach to Processing Large-Scale Geospatial Rasters

Huge amounts of geospatial rasters, such as remotely sensed imagery and environmental modeling output, are being generated with increasingly finer spatial, temporal, spectral and thematic resolutions. Given that CPUs on modern computer systems are three orders of magnitude faster than disk I/O speed and two orders of magnitude faster than network bandwidth, it becomes more and more beneficial to allocate computing power for real time compression and decompression to reduce I/O times in streaming large-scale geospatial rasters among CPU memory, disks and distributed computing nodes and file systems. In this study, we aim at developing a lightweight lossless data compression technique that balances the performance between compression and decompression for large-scale geospatial rasters. Our Bitplane bitmap Quadtree (or BQ-Tree) based technique encodes the bitmaps of raster bitplanes as compact quadtrees which can compress and index rasters simultaneously. The technique is simple by design and lightweight by implementations. Apart from computing Z-order codes for cache efficiency, only bit level operations are required. Extensive experiments using 36 rasters of the NASA Shuttle Range Topography Mission (SRTM) 30 meter resolution elevation data with 20 billion raster cells have shown that our BQ-Tree technique is more than 4X faster for compression and 36% faster for decompression than zlib using a single CPU core while achieving very similar compression ratios. Our technique further has achieved 10-13X speedups for compression and 4X speedups for decompression using 16 CPU cores. On the experiment machine equipped with dual Intel Xeon 8-core E5-2650V2 CPUs, our technique is able to compress the SRTM raster dataset in about 35 seconds and decompress back in 29 seconds. The performance compares favorably with the best known technique with respect to both compression and decompression throughputs. We have made the source code package and a subset of the SRTM raster publically available to facilitate validations and cross-comparisons.
Multiple fault diagnosis using n-detection tests

We study the relationship between multiple fault diagnosability and fault detection count. Instead of developing a complex diagnostic algorithm for multiple fault behavior, we change the test sets used in test and diagnosis. This allows us to apply a simple single-fault based diagnostic algorithm, and yet achieve very good diagnosability for the failure test cases caused by multiple faults. We have verified experimentally the effectiveness of n-detection tests for multiple-fault cases and explained the results in probabilistic terms.
Multi-institutional trial of preoperative chemoradiotherapy in patients with potentially resectable gastric carcinoma.

PURPOSE In the West, curative (R0) resection is achieved in approximately 50% of patients with localized gastric carcinoma, and more than 60% die of cancer following an R0 resection. A multi-institutional study of preoperative chemoradiotherapy was done to assess the R0 resection rate, pathologic complete response (pathCR) rate, safety, and survival in patients with resectable gastric carcinoma. PATIENTS AND METHODS Operable patients with localized gastric adenocarcinoma were eligible. Staging also included a laparoscopy and endoscopic ultrasonography (EUS). Patients received up to two 28-day cycles of induction chemotherapy of fluorouracil, leucovorin, and cisplatin, followed by 45 Gy of radiation plus concurrent fluorouracil. Patients were then staged and surgery was attempted. RESULTS Thirty-four patients were registered at three institutions. One ineligible patient was excluded. Most patients had a promixal cancer and EUST3N1 designation. Twenty-eight (85%) of 33 patients underwent surgery. The R0 resection rate was 70% and pathCR rate was 30%. A pathologic partial response (< 10% residual carcinoma in the primary) occurred in eight patients (24%). EUS T plus N and postsurgery T plus N correlation showed significant downstaging (P = <.01). The median survival time for 33 patients was 33.7 months. Patients achieving a pathCR or pathPR had a significantly longer median survival time (63.9 months) than those achieving less than pathPR (12.6 months; P =.03). There were two treatment-related deaths. CONCLUSION Our data suggest that the three-step strategy of preoperative induction chemotherapy followed by chemoradiotherapy resulted in substantial pathologic response that resulted in durable survival time. This strategy is worthy of a direct comparison with postoperative adjuvant chemoradiotherapy.
Estimaciones de la prevalencia del trastorno por déficit de atención-hiperactividad en niños marabinos

Summary. Aims. This study reports the findings of research aimed at determining the rate of prevalence of attention deficit hyperactivity disorder (ADHD) in children of school age. Subjects and methods. The epidemiological study was conducted using a community sample extracted by means of multi-stage stratified sampling according to socio-economic level and schooling and consisted in 1,141 children of both sexes of school age from the city of Maracaibo. The revised Conners scales were used to col lect data. Results. The estimated prevalence of ADHD was 7.19% and we also obtained 0.35% for the hyperactive subtype, 1.14% for the disattentional subtype, and 5.70% for the combined subtype. Contrary to what was expected, prevalence was higher for females. It was found that 7.45% of the general sample scored higher on the academic problems scales, whereas for the sample identified as having ADHD, academic problems were 50% and the comorbidity between ADHD and academic problems was confirmed. Conclusions. The estimates for prevalence found in this study are consistent with those reported in the literature, which suggests that ADHD is a valid diagnosis for Marabino children. (REV NEUROL 2002; 35: 1019-24)
Listening to old wives’ tales: small stories and the (re)making and (re)telling of research in HE/FE practitioner education

In this paper we share the outcomes of a project that sought to take up Nutbrown’s challenge to ‘push out from the safe(er) boundaries of established methodologies’ in early years research. We explore the value of auto-ethnographic storytelling, Lyotard’s ‘petit récit’, to the processes of doing and learning about research in the context of practitioner education. We offer a rationale for the use of creative methods in (post? ) professional learning and describe the process of working with identity boxes and symbolic objects, to produce a collection of auto-ethnographic narratives, the old wives’ tales of the title, through which to explore practitioners’ experiences of professional identity formation. We consider the opportunities such methods offer for reflexive learning about practitioner positionality within the knowledge-making practices of research and attempt to (re)position ourselves differently as writers and makers of research. Towards a conclusion we review and theorise meanings participant-researchers make about their career trajectories and proffer auto-ethnography as a dynamic modality for practitioner learning. We mobilise Patti Lather’s notion of methodological proliferation to re-think practitioner education as a wild profusion of post-professional possibilities.
Motion detection using 3D-FFT spectrum

A novel motion detection technique for multiple objects from image sequences is proposed. The algorithm is based on directional filtering in the spatiotemporal frequency domain. By using the 3-D fast Fourier transform (FFT), because of its computational efficiency, the spectrum of an object moving at constant velocity lies in several parallel planes in the frequency domain. The object's velocity is estimated by detecting the orientation of those planes. This problem can be reduced to detecting the orientation of parallel lines in the plane intersecting those planes by using direction-tuned filters. Statistical estimation is used to eliminate the uncertainty which originates from nonorthogonality of the filters. Experimental results on computer-generated images and real-life video images are also described. <<ETX>>
Fusion of multispectral palmprint images for automatic person identification

Reliability and accuracy in personal identification system is a dominant concern to the security world. Biometric has gained much attention in this subject recently. Many types of personal identification systems have been developed, and palmprint identification is one of the emerging technologies. This paper presents a novel biometric technique to automatic personal identification system using multispectral palmprint technology. In this method, each of spectrum images are aligned and then used to extract palmprint features using 1D log-Gabor filter. These features are then examined for their individual and combined performances. Finally, the hamming distance is used for matching of palmprint features. The experimental results showed that the proposed method achieve an excellent identification rate and provide more security.
Coordinated Slowing of Metabolism in Enteric Bacteria under Nitrogen Limitation: A Perspective

It is natural to ask how bacteria coordinate metabolism when depletion of an essential nutrient limits their growth, and they must slow their entire rate of biosynthesis. A major nutrient with a fluctuating abundance is nitrogen. The growth rate of enteric bacteria under nitrogen-limiting conditions is known to correlate with the internal concentration of free glutamine, the glutamine pool. Here we compare the patterns of utilization of L-glutamine and L-glutamate, the two central intermediates of nitrogen metabolism. Monomeric precursors of all of the cell's macromolecules -- proteins, nucleic acids, and surface polymers -- require the amide group of glutamine at the first dedicated step of biosynthesis. This is the case even though only a minority (~12%) of total cell nitrogen derives from glutamine. In contrast, the amino group of glutamate, which provides the remainder of cell nitrogen, is generally required late in biosynthetic pathways, e.g. in transaminase reactions for amino acid synthesis. We propose that the pattern of glutamine dependence coordinates the decrease in biosynthesis under conditions of nitrogen limitation. Hence, the glutamine pool plays a global regulatory role in the cell.
Validity of animal models for the cholesterol-raising effects of coffee diterpenes in human subjects

Cafestol and kahweol, coffee lipids present in unfiltered coffee brews, potently increase LDL-cholesterol concentration in human subjects. We searched for an animal species in which cafestol similarly increases LDL-cholesterol. Such an animal model could be used subsequently as a model to study the mechanism of action of cafestol and kahweol. Cafestol and kahweol increased serum lipids in African green monkeys (Cercopithecus aethiops), cebus (Cebus apella) and rhesus (Macaca mulatta) monkeys, hamsters, rats and gerbils differently from the increase in human subjects. In African green monkeys, the rise in total cholesterol was less pronounced than that in human subjects. In addition, the increase in total cholesterol was predominantly due to a rise in HDL-cholesterol rather than LDL-cholesterol. Thus, the rise in plasma lipids might illustrate the mechanism in these monkeys rather than the mechanism in human subjects. In other animal species, cafestol and kahweol did not raise cholesterol consistently. The variability in effects on serum lipids could not be explained by the mode of administration or dose of diterpenes, nor by the amount of cholesterol in the diet. In conclusion, we did not find an animal model in which cafestol and kahweol elevate plasma lipoproteins to the same extent as in human subjects. For the time being, therefore, studies on the mechanism of action should be done preferably in human subjects.
An acoustic measure for predicting recognition performance degradation

An acoustic measure for predicting the degradation of speech recognition performance due to noise contamination is developed. The merits of the proposed measure over using conventional SNR are that (1) the measure does not require the original clean signal as a reference signal (2) the measure takes the spectral shape of the noise into account and, (3) the measure can predict recognition performance directly. The basic idea of the measure is to utilize the dynamic range of the sub-band signals as an estimate of SNR in the corresponding subband and, to predict the degradation of the recognition performance by taking a product of the recognition accuracy of each sub-band. The proposed measure is tested through experimental evaluation using white Gaussian and human speech like (HSL) noise. In the experiment, the correlation between the predicted and the actual recognition accuracies are 0.96 and 0.99 for white and HSL noise respectively. From the results, the effectiveness of the proposed measure is confirmed.
From architecture to manufacturing: An accurate framework for optimal OTA design

The operational transconductance amplifier (OTA) is one of the most important basic blocks used in the design of analog integrated circuits (ICs). However, its optimization involves a large number of parameters and specifications that have to be accurately adjusted during the simulation process to appropriately achieve the design goals. This work addresses the whole framework required to the automatic design of an OTA, from its architecture to manufacturing. We propose and implement a computational tool based on Genetic Algorithms to the optimization and simulation tasks as well as a measurement system that covers the layout and manufacturing of the designed OTAs in order to perform the experimental electrical characterization. Our experimental results show that this analog IC design framework allows the creation of practical solutions with remarkable accuracy (maximum error about 10%, considering all specifications investigated) regarding OTAs with 0.35 micrometer Bulk CMOS technology from ON semiconductor. We believe that the proposed framework might be a helpful design tool to manufacture OTAs with high accuracy and low design time, particularly in situations where such complex optimization task must be performed routinely by beginners.
The design of an 80 GHz stacked patch antenna on LTCC substrate

A new approach of using stacked patches rather than the one used in previous work of embedding an air cavity in Low Temperature Co-fired Ceramic (LTCC) substrate for increasing bandwidth for antenna operating at 80 GHz is proposed. The simulated S11 results show a minimum of -33 dB at 82 GHz with a 8.3% bandwidth calculated at -10 dB. The simulated radiation patterns show a maximum gain of 6.7 dBi.
Antispasmodic Activity of Persea cordata Vell. Mez. (Lauraceae) Fractions on Guinea Pig Ileum Induced by 5-Hydroxytryptamine and Bradykinin

Problem statement: Persea cordata previously demonstrated antispasmodic action against two neurotransmitters. It is important confirm such action against other neurotransmitters. Approach: Present study described the antispasmodic activity of polar (EtOAc; n-BuOH) and non polar (n-hexane; dichloromethane) fractions from the bark of Persea cordata, against guinea pig ileum contracted by 5-hydroxytryptamine (5-HT) and bradykinin (BK). Results: The results indicated that hexane and dichloromethane fractions caused the most significant relaxant activity against both neurotransmitters tested. Conclusion: The effects seem to be related to the evidenced presence of steroids and terpenes, but additional studies were in progress to identify the active principles of this plant.
Form reading based on form-type identification and form-data recognition

Form reading technology based on form-typeidentification and form-data recognition is proposed. Thistechnology can solve difficulties in variety for readingdifferent items on fairly large number of different types offorms. The form-type identification consists of two parts:(i) extraction of targets such as important keywords in aform by matching between recogised characters and wordstrings in a keyword dictionary, and (ii) analysis ofpositional or semantic relationship between the targets byconstellation matching between these targets and wordlocation information in the keyword dictionary. The formdatarecognition consists of two parts: (i) extraction of aregion of interest (ROI) contained a character string of theitem by using a layout knowledge of the very form-type,and (ii) character string recognition of the item by usingthe linguistic constraint which can be obtained from acontent knowledge of the form-type. A experiment using642 sample forms with 107 different types in totalconfirmed that the form-type identification method cancorrectly identify 97% of 642 form samples at a rejectionrate 3%. Another experiment confirmed that the form-data recognition method can correctly read 95% of thenumber of items on the form samples.
Service curves in Network Calculus: dos and don'ts

This report is a survey about service curves used in envelope-based models for worst-case performance evaluation, like Network Calculus or Real-Time Calculus. In a first part, we compare different models and their notions of service curves by establishing a hierarchy and similarities between different types of service curves and in a second part, we compare the behaviours of simple and strict service curves for concatenation and residual service curves.