Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparison of Different Machine Transliteration Models

Machine transliteration is a method for automatically converting words in one language into phonetically equivalent ones in another language. Machine transliteration plays an important role in natural language applications such as information retrieval and machine translation, especially for handling proper nouns and technical terms. Four machine transliteration models - grapheme-based transliteration model, phoneme-based transliteration model, hybrid transliteration model, and correspondence-based transliteration model - have been proposed by several researchers. To date, however, there has been little research on a framework in which multiple transliteration models can operate simultaneously. Furthermore, there has been no comparison of the four models within the same framework and using the same data. We addressed these problems by 1) modeling the four models within the same framework, 2) comparing them under the same conditions, and 3) developing a way to improve machine transliteration through this comparison. Our comparison showed that the hybrid and correspondence-based models were the most effective and that the four models can be used in a complementary manner to improve machine transliteration performance.
Identification and classification of silks using infrared spectroscopy

ABSTRACT Lepidopteran silks number in the thousands and display a vast diversity of structures, properties and industrial potential. To map this remarkable biochemical diversity, we present an identification and screening method based on the infrared spectra of native silk feedstock and cocoons. Multivariate analysis of over 1214 infrared spectra obtained from 35 species allowed us to group silks into distinct hierarchies and a classification that agrees well with current phylogenetic data and taxonomies. This approach also provides information on the relative content of sericin, calcium oxalate, phenolic compounds, poly-alanine and poly(alanine-glycine) β-sheets. It emerged that the domesticated mulberry silkmoth Bombyx mori represents an outlier compared with other silkmoth taxa in terms of spectral properties. Interestingly, Epiphora bauhiniae was found to contain the highest amount of β-sheets reported to date for any wild silkmoth. We conclude that our approach provides a new route to determine cocoon chemical composition and in turn a novel, biological as well as material, classification of silks. Summary: FTIR analysis performed on unspun silks and cocoons from 35 different species provides information regarding the biochemical diversity and evolution of this group of materials.
Chaperone use amongst UK urological surgeons - an evaluation of current practice and opinion.

Introduction Intimate examinations are routinely performed by urologists as part of clinical practice. To protect patients and doctors, the General Medical Council offers guidance on the use of chaperones for intimate examinations. We assessed the opinions and use of chaperones amongst members of the British Association of Urological Surgeons (BAUS). Methods An online questionnaire comprising 12 questions on the use of chaperones in clinical practice was sent to all full, trainee and speciality doctor members of BAUS. Results The questionnaire had a response rate of 26% (n=331). The majority of respondents were consultant urologists, comprising 78.8% (n=261), with a wide range of years of experience. Of the respondents, 38.9% were not aware of the GMC guidance on chaperones. While 72.5% always used a chaperone. , 22.9% never use a chaperone when the patient was of the same sex. Chaperones were most commonly used for intimate examinations (64.6%), and for examinations involving members of the opposite sex (77.3%). A majority of respondents felt that chaperones protect both the patient (77.3%), and the doctor (96.6%). However, 42.5% did not feel that using a chaperone assists the doctor's examination, and some (17.2%) participants felt that chaperones were unnecessary. Conclusions This study shows considerable variability amongst urologists in their use of chaperones. A significant proportion of respondents were not aware of the GMC guidelines and did not regularly use a chaperone during an intimate examination. In addition, practice appears to be gender biased. Further study and education is suggested.
Efficient Team Formation Based on Learning and Reorganization and Influence of Communication Delay

We propose a method of distributed team formation that uses reinforcement learning and dynamic reorganization by taking into account communication delay in multi-agent systems (MAS). A task in a distributed environment is usually achieved by doing a number of subtasks that require different functions and resources. These subtasks have to be processed cooperatively in the appropriate team of agents that have the required functions with sufficient resources, but it is difficult to anticipate what kinds of tasks will be requested in the dynamic and open environment during the design stage of the system. It is also unknown whether or not their inter-agent network (that is, the organization of agents) is appropriate to form teams for the given tasks. In addition, communication delay between the agents always occurs in the actual systems, and this often causes a failure or delay of tasks. Therefore, both appropriate team formation and (re)organization suitable for the request patterns of incoming tasks and the environment where agents are deployed are required. The proposed method combines the learning for team formation and reorganization in a way that is adaptive to the environment. This includes task generation patterns and communication delay that may change dynamically. We show that it can improve the overall performance and increase the success rate of team formation in a dynamic environment.
Ethnic-specific relationships between haemostatic and oxidative stress markers in black and white South Africans: The SABPA study

Abstract Haemostatic- and oxidative stress markers are associated with increased cardiovascular risk. In the black population, evidence exists that both an imbalance in the haemostatic system and oxidative stress link with the development of hypertension. However, it is unclear whether these two risk components function independently or are related, specifically in the black population, who is known to have a high prevalence of stroke. We aimed to investigate associations between the haemostatic system and oxidative stress in black and white South Africans. We performed a cross-sectional study including 181 black (mean age, 44; 51.4% women) and 209 white (mean age, 45; 51.7% women) teachers. Several markers of the haemostatic- (von Willebrand factor, fibrinogen, plasminogen activator inhibitor-1, d-dimer and clot lysis time) and oxidant–antioxidant (serum peroxides, total glutathione, glutathione peroxidase- and glutathione reductase activities) systems were measured. Along with a worsened cardiovascular profile, the black group had higher haemostatic-, inflammation- and oxidative stress markers as well as decreased glutathione peroxidase activity. In multiple regression analyses, fibrinogen was positively associated with serum peroxides (p < 0.001) in both ethnic groups. In the black population, we found negative associations of von Willebrand factor and clot lysis time with glutathione peroxidase activity (p ≤ 0.008), while a positive association existed between clot lysis time and serum peroxides (p = 0.011) in the white population. We conclude that in the black population, decreased GPx activity accompanies an altered haemostatic profile, while in the white population associations may suggest that serum peroxides impair fibrin clot lysis.
Preoperative Evaluation of Prostate Cancer Aggressiveness: Using ADC and ADC Ratio in Determining Gleason Score.

OBJECTIVE The objective of our study was to evaluate apparent diffusion coefficient (ADC) and various ADC ratios in determining aggressiveness of prostate cancer. MATERIALS AND METHODS One hundred sixty-five patients with biopsy-proven prostate cancer underwent 3-T MRI followed by radical prostatectomy. ADC and ADC ratios were calculated using the peripheral zone, transition zone, same zone as the tumor, and urinary bladder as references. ADC and ADC ratios were correlated with Gleason score using the Spearman correlation coefficient (ρ) and were compared between low-grade (Gleason score = 6) and high-grade (Gleason score ≥ 7) prostate cancer using the unpaired t test. ROC curves were used to compare diagnostic accuracies of ADC and ADC ratios in determining high-grade prostate cancer. RESULTS Fifty-six (33.9%) and 109 (66.1%) patients had low- and high-grade prostate cancer, respectively. ADC (ρ = -0.476) and all ADC ratios (ρ = -0.397, -0.412, -0.381, and -0.474, respectively) correlated significantly with Gleason score (p < 0.001) and were significantly lower in patients with high-grade prostate cancer (p < 0.001). For predicting high-grade prostate cancer, tumor ADC and tumor-to-urinary bladder ADC ratio showed the highest AUC (0.794 and 0.790, respectively) but without statistically significant difference (p = 0.803). AUC of tumor ADC (0.794) was statistically significantly higher than those of the tumor-to-peripheral zone and tumor-to-transition zone ADC ratios (0.746, p = 0.039; 0.751, p = 0.027; respectively). AUC of tumor ADC was not statistically significantly higher than that of the tumor-to-tumor zone ADC ratio (0.763, p = 0.193). AUC calculated using the tumor-to-urinary bladder ADC ratio was statistically significantly higher than that using the tumor-to-transition zone ADC ratio (p = 0.028) and marginally higher than that from tumor-to-peripheral zone ADC ratio (p = 0.080). Otherwise, no significant differences were seen in the AUCs (p = 0.193-0.828). CONCLUSION Both ADC and various ADC ratios correlated significantly with Gleason score and were significant predictors of high-grade prostate cancer. However, no benefit was found in using ADC ratio over ADC.
Antifungal and proteolytic activities of endophytic fungi isolated from Piper hispidum Sw

Endophytes are being considered for use in biological control, and the enzymes they secrete might facilitate their initial colonization of internal plant tissues and direct interactions with microbial pathogens. Microbial proteases are also biotechnologically important products employed in bioremediation processes, cosmetics, and the pharmaceutical, photographic and food industries. In the present study, we evaluated antagonism and competitive interactions between 98 fungal endophytes and Alternaria alternata, Colletotrichum sp. , Phyllosticta citricarpa and Moniliophthora perniciosa. We also examined the proteolytic activities of endophytes grown in liquid medium and conducted cup plate assays. The results showed that certain strains in the assemblage of P. hispidum endophytes are important sources of antifungal properties, primarily Lasiodiplodia theobromae JF766989, which reduced phytopathogen growth by approximately 54 to 65%. We detected 28 endophytes producing enzymatic halos of up to 16.40 mm in diameter. The results obtained in the present study highlight the proteolytic activity of the endophytes Phoma herbarum JF766995 and Schizophyllum commune JF766994, which presented the highest enzymatic halo diameters under at least one culture condition tested. The increased activities of certain isolates in the presence of rice or soy flour as a substrate (with halos up to 17.67 mm in diameter) suggests that these endophytes have the potential to produce enzymes using agricultural wastes.
An Empirical Study of Differences between Conversion Schemes and Annotation Guidelines

We establish quantitative methods for comparing and estimating the quality of dependency annotations or conversion schemes. We use generalized tree-edit distance to measure divergence between annotations and propose theoretical learnability, derivational perplexity and downstream performance for evaluation. We present systematic experiments with treeto-dependency conversions of the PennIII treebank, as well as observations from experiments using treebanks from multiple languages. Our most important observations are: (a) parser bias makes most parsers insensitive to non-local differences between annotations, but (b) choice of annotation nevertheless has significant impact on most downstream applications, and (c) while learnability does not correlate with downstream performance, learnable annotations will lead to more robust performance across domains.
Change-point Detection Methods for Body-Worn Video

Body-worn video (BWV) cameras are increasingly utilized by police departments to provide a record of police-public interactions. However, large-scale BWV deployment produces terabytes of data per week, necessitating the development of effective computational methods to identify salient changes in video. In work carried out at the 2016 RIPS program at IPAM, UCLA, we present a novel two-stage framework for video change-point detection. First, we employ state-of-the-art machine learning methods including convolutional neural networks and support vector machines for scene classification. We then develop and compare change-point detection algorithms utilizing mean squared-error minimization, forecasting methods, hidden Markov models, and maximum likelihood estimation to identify noteworthy changes. We test our framework on detection of vehicle exits and entrances in a BWV data set provided by the Los Angeles Police Department and achieve over 90% recall and nearly 70% precision -- demonstrating robustness to rapid scene changes, extreme luminance differences, and frequent camera occlusions.
On the Capacity of the Finite Field Counterparts of Wireless Interference Networks

This paper explores how degrees of freedom (DoF) results from wireless networks can be translated into capacity or linear capacity results for their finite field counterparts that arise in network coding applications. The main insight is that scalar (SISO) finite field channels over Fpn are analogous to n × n vector (MIMO) channels in the wireless setting, but with an important distinction-there is additional structure due to finite held arithmetic, which enforces commutativity of matrix multiplication and limits the channel diversity to n, making these channels similar to diagonal channels in the wireless setting. Within the limits imposed by the channel structure, the DoF optimal precoding solutions for wireless networks can be translated into capacity or linear capacity optimal solutions for their finite held counterparts. This is shown through the study of capacity of the 2-user X channel and linear capacity of the 3-user interference channel. Besides bringing the insights from wireless networks into network coding applications, the study of finite held networks over Fpn also touches upon important open problems in wireless networks (finite SNR, finite diversity scenarios) through interesting parallels between p and SNR, and n and diversity.
A Randomized, Controlled, Observer-Blinded Phase 1 Study of the Safety and Immunogenicity of a Respiratory Syncytial Virus Vaccine With or Without Alum Adjuvant

Background. Respiratory syncytial virus (RSV) is a leading cause of childhood bronchiolitis and pneumonia, particularly in early infancy. Immunization of pregnant women could boost preexisting immune responses, providing passive protection to newborns through placental transfer of anti-RSV antibody. Methods. In this first-in-humans clinical trial of a purified recombinant RSV protein F vaccine engineered to preferentially maintain prefusion conformation (RSV-PreF), 128 healthy men 18–44 years old were randomized to one dose of a RSV-PreF vaccine containing 10, 30, or 60 µg of RSV-PreF antigen, with or without alum adjuvant, or control, and followed for one year for safety and immunogenicity outcomes. Results. Injection site pain was the most common adverse event, reported by up to 81.3% of participants. The highest RSV neutralizing antibody responses were in the 30 µg RSV-PreF/alum, 60 µg RSV-PreF/alum, and 60 µg RSV-PreF/nonadjuvant groups. Responses were evident on day 7, and 30 days after vaccination these participants had RSV-A neutralizing antibody titers of ≥1:512, and >70% had titers of 1:1024, with titers increasing by 3.2–4.9 fold. Responses remained high on day 60 but waned on days 180 and 360. Conclusions. The RSV-PreF vaccine elicited rapid RSV neutralizing antibody responses in healthy young men, with an acceptable adverse event profile.
Use of stereotactic body radiotherapy for prostate cancer in the United States from 2004 through 2012

Stereotactic body radiotherapy (SBRT) is a newer treatment option for patients with localized prostate cancer. The rates of diffusion of this technology across the United States are unknown. The goal of the current study was to describe the use of SBRT among patients with prostate cancer based on different risk groups (low, intermediate, or high risk) and by type of facility (community cancer program, comprehensive community cancer program, or academic program) in which patients were treated.
Gene Family Evolution by Duplication, Speciation, and Loss

We consider two algorithmic questions related to the evolution of gene families. First, given a gene tree for a gene family, can the evolutionary history of this family be explained with only speciation and duplication events? Such gene trees are called DS-trees. We show that this question can be answered in linear time, and that a DS-tree induces a single species tree. We then study a natural extension of this problem: what is the minimum number of gene losses involved in an evolutionary history leading to an observed gene tree or set of gene trees? Based on our characterization of DS-trees, we propose a heuristic for this problem, and evaluate it on a dataset of plants gene families and on simulated data.
Four quadrant FGMOS analog multiplier

A novel four-quadrant analog multiplier using floating gate MOS (FGMOS) transistors operating in the saturation region is presented. The drain current is proportional to the square of the weighted sum of the input signals. This square law characteristic of the FGMOS transistor is used to implement the quarter square identity by utilizing only six FGMOS transistors. The main features of this remarkably simple multiplier circuit configuration are the large input signal range equal to 100% of the supply voltage, nonlinearity of 0.0081%, bandwidth of 1.4--1.5 Ghz and THD of maximum 2.67% (while the inputs are at their maximum values).
Improved carotid intraplaque hemorrhage imaging using a slab‐selective phase‐sensitive inversion‐recovery (SPI) sequence

Intraplaque hemorrhage in atherosclerotic plaques has been associated with accelerated plaque growth as well as exacerbation of clinical symptoms. The identification of intraplaque hemorrhage using magnetic resonance imaging primarily relies on the detection of methemoglobin on T1 weighted images. Current techniques are limited by insufficient intraplaque hemorrhage‐wall contrast and poor blood suppression. In this study, a slab‐selective phase‐sensitive inversion‐recovery (SPI) technique is proposed by combining a phase‐sensitive reconstruction with a T1 weighted sequence specifically designed to achieve improved intraplaque hemorrhage imaging. The SPI sequence was optimized and then used on ex vivo plaque specimens for histology based validation and intraplaque hemorrhage‐wall contrast‐to‐noise ratio comparison with magnetization‐prepared 3D rapid acquisition gradient echo MP‐RAGE. SPI and MP‐RAGE were also tested on a group of atherosclerosis patients to compare in vivo intraplaque hemorrhage‐wall contrast‐to‐noise ratio and blood suppression effectiveness. On ex vivo specimens SPI had better intraplaque hemorrhage identification accuracy and a significantly higher intraplaque hemorrhage‐wall contrast‐to‐noise ratio (P = 0.01) than MP‐RAGE. Similar results were found in the in vivo test: Slab‐selective phase‐sensitive inversion‐recovery provided a significantly improved intraplaque hemorrhage‐wall contrast‐to‐noise ratio (P < 0.01) and blood suppression efficiency (P < 0.01). In conclusion, SPI is a novel technique optimized for intraplaque hemorrhage detection and validated against histology. It has demonstrated its capability for improved in vivo intraplaque hemorrhage identification and blood suppression in atherosclerosis patients. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Complementary and Overlapping Expression of Glial Cell Line-Derived Neurotrophic Factor (GDNF), c-ret Proto-Oncogene, and GDNF Receptor-α Indicates Multiple Mechanisms of Trophic Actions in the Adult Rat CNS

Glial cell line-derived neurotrophic factor (GDNF), the most potent trophic factor yet described for both dopaminergic neurons of the substantia nigra and spinal motorneurons, has recently been shown to signal through a multireceptor complex composed of a novel glycosylphosphatidylinositol-anchored GDNF receptor-α (GDNFR-α) and the receptor tyrosine kinase product of the c-ret proto-oncogene (RET). Despite its importance, the individual expression patterns and the relationships between domains of expression of the different components of this trophic system are not understood. We show here by in situ hybridization that GDNF mRNA is expressed in the normal adult rat brain in several targets of substantia nigra neurons, including striatum, nucleus accumbens, thalamic nuclei, olfactory tubercle, hippocampus, cerebellum, and cingulate cortex as well as in the internal granular cell layer of the olfactory bulb. Within the basal ganglia we observe a pronounced segregation of regions expressing GDNF from those expressing GDNF receptors, suggesting that within these structures GDNF is functioning in its anticipated role as a target-derived trophic factor. In addition, the expression of GDNF and both GDNF receptors within the cerebellum, hippocampus, and olfactory bulb may indicate a paracrine mode of action. Importantly, we also see expression of RET mRNA in cellular populations within the cerebellum and the glomerular layer of the olfactory bulb, as well as in the subthalamic nucleus, which lack GDNFR-α expression, indicating that RET functions either independently of GDNFR-α or with GDNFR-α presented in trans. Conversely, GDNFR-α is widely expressed in many regions in which RET expression is absent, suggesting that GDNFR-α may associate with additional signaling receptors. Finally, RET and GDNFR-α show distinct patterns of regulated expression in the brain after kainic acid stimulation and in the sciatic nerve after nerve transection. Taken together these findings indicate that GDNF, RET, and GDNFR-α utilize multiple mechanisms to comprise physiologically relevant trophic circuits for different neuronal populations.
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

Chlamydia trachomatis is an obligate intracellular pathogenic bacterium that has been refractory to genetic manipulations. Although the genomes of several strains have been sequenced, very little information is available on the gene structure of these bacteria. We used deep sequencing to define the transcriptome of purified elementary bodies (EB) and reticulate bodies (RB) of C. trachomatis L2b, respectively. Using an RNA-seq approach, we have mapped 363 transcriptional start sites (TSS) of annotated genes. Semi-quantitative analysis of mapped cDNA reads revealed differences in the RNA levels of 84 genes isolated from EB and RB, respectively. We have identified and in part confirmed 42 genome- and 1 plasmid-derived novel non-coding RNAs. The genome encoded non-coding RNA, ctrR0332 was one of the most abundantly and differentially expressed RNA in EB and RB, implying an important role in the developmental cycle of C. trachomatis. The detailed map of TSS in a thus far unprecedented resolution as a complement to the genome sequence will help to understand the organization, control and function of genes of this important pathogen.