This paper is organised as follows: in section 2 we discuss the essential ideas behind vector-based call-routing and describe two variants of the technique experimented with here.Section 2.3 outlines how latent semantic analysis (LSA) has previously been used for information retrieval and section 2.4 gives some arguments for why a different approach to the use of LSA may be appropriate for call-routing.Section 3 describes the routing scenario used and the experiments performed, and

Objective: The diagnosis of vertigo is challenging, particularly as patients usually present while asymptomatic. We have developed an ambulatory medical device that allows vestibular telemetry to record eye movements over a 30-day period to aid the diagnosis of vertigo. We have undertaken proof-of-concept work to identify unique properties of nystagmus that could be used to differentiate between three of the most common causes of vertigo: Ménière's disease, vestibular migraine, and Benign Paroxysmal Positional Vertigo. Patients: We analyze the nystagmus from patients with a diagnosis of Ménière's disease, vestibular migraine, and Benign Paroxysmal Positional Vertigo. Intervention(s): Our vestibular telemetry system includes a wearable, ambulatory monitor which continuously records horizontal and vertical eye-movements, as well as three-axis movements of the head. Main Outcome Measure(s): Horizontal and vertical eye-movement data, and three-axis head positioning data. Results: Sixteen participants were enrolled onto the study and three reported experiencing rotatory vertigo during their 30-day trial, confirmed by the presence of nystagmus in their eye-movement traces. Vestibular telemetry revealed distinct differences between the nystagmus produced during an acute Ménière's attack, and attacks of vestibular migraine and Benign Paroxysmal Positional Vertigo. Attack frequency, nystagmus duration, whether the nystagmus onset was motion provoked, nystagmus direction, slow phase velocity, and slow phase duration were found to be discriminatory features that could be exploited to allow an automated diagnosis to be made. Conclusions: The data provided by vestibular telemetry can be used to differentiate between different inner-ear causes of dizziness.

We describe efforts towards getting better resources for English-Arabic machine translation of spoken text. In particular, we look at movie subtitles as a unique, rich resource, as subtitles in one language often get translated into other languages. Movie subtitles are not new as a resource and have been explored in previous research; however, here we create a much larger bi-text (the biggest to date), and we further generate better quality alignment for it. Given the subtitles for the same movie in different languages, a key problem is how to align them at the fragment level. Typically, this is done using length-based alignment, but for movie subtitles, there is also time information. Here we exploit this information to develop an original algorithm that outperforms the current best subtitle alignment tool, subalign. The evaluation results show that adding our bi-text to the IWSLT training bi-text yields an improvement of over two BLEU points absolute.

A table summarizing each of the experiments included in this study.

Objectives: There is evidence that symptoms of maldigestion or malabsorption in autistic individuals are related to changes in the indigenous microbiota. Analysis of colonic bacteria has revealed microbial dysbiosis in children with autism; however, characteristics of the duodenal microbiome are not well described. In the present study the microbiome of the duodenal mucosa of subjects with autism was evaluated for dysbiosis, bacteria overgrowth, and microbiota associated with carbohydrate digestion. The relationship between the duodenal microbiome and disaccharidase activity was analyzed in biopsies from 21 autistic subjects and 19 children without autism. Methods: Microbiota composition was determined by 16S ribosomal RNA gene sequencing, and disaccharidase activity via biochemical assays. Results: Although subjects with autism had a higher frequency of constipation (P < 0.005), there was no difference in disaccharidase activity between groups. In addition, no differences in microbiome diversity (species richness and evenness) were observed. Bacteria belonging to the genus Burkholderia were more abundant in subjects with autism, whereas members of the genus Neisseria were less abundant. At the species level, a relative decrease in abundance of 2 Bacteroides species and Escherichia coli was found in autistic individuals. There was a positive correlation between the abundance of Clostridium species, and disaccharidase activity, in autistic individuals. Conclusions: There are a variety of changes at the genus and species level in duodenal microbiota in children with autism that could be influenced by carbohydrate malabsorption. These observations could be affected by variations in individual diets, but also may represent a more pervasive dysbiosis that results in metabolites that affect the behavior of autistic children.

The relationship between the host and its microbiota is challenging to understand because both microbial communities and their environments are highly variable. We have developed a set of techniques based on population dynamics and information theory to address this challenge. These methods identify additional bacterial taxa associated with pediatric Crohn disease and can detect significant changes in microbial communities with fewer samples than previous statistical approaches required. We have also substantially improved the accuracy of the diagnosis based on the microbiota from stool samples, and we found that the ecological niche of a microbe predicts its role in Crohn disease. Bacteria typically residing in the lumen of healthy individuals decrease in disease, whereas bacteria typically residing on the mucosa of healthy individuals increase in disease. Our results also show that the associations with Crohn disease are evolutionarily conserved and provide a mutual information-based method to depict dysbiosis.

Recent improvements in tracking and feature extraction mean that speaker-dependent lip-reading of continuous speech using a medium size vocabulary (around 1000 words) is realistic. However, the recognition of previously unseen speakers has been found to be a very challenging task, because of the large variation in lip-shapes across speakers and the lack of large, tracked databases of visual features, which are very expensive to produce. By adapting a technique that is established in speech recognition but has not previously been used in lip-reading, we show that error-rates for speaker-independent lip-reading can be very significantly reduced. Furthermore, we show that error-rates can be even further reduced by the additional use of Deep Neural Networks (DNN). We also find that there is no need to map phonemes to visemes for context-dependent visual speech transcription.

The extent to which microorganisms impair wound healing is an ongoing controversy in the management of chronic wounds. Because the high diversity and extreme variability of the microbiota between individual chronic wounds lead to inconsistent findings in small cohort studies, evaluation of a large number of chronic wounds using identical sequencing and bioinformatics methods is necessary for clinicians to be able to select appropriate empiric therapies. In this study, we utilized 16S rDNA pyrosequencing to analyze the composition of the bacterial communities present in samples obtained from patients with chronic diabetic foot ulcers (N = 910), venous leg ulcers (N = 916), decubitus ulcers (N = 767), and nonhealing surgical wounds (N = 370). The wound samples contained a high proportion of Staphylococcus and Pseudomonas species in 63 and 25% of all wounds, respectively; however, a high prevalence of anaerobic bacteria and bacteria traditionally considered commensalistic was also observed. Our results suggest that neither patient demographics nor wound type influenced the bacterial composition of the chronic wound microbiome. Collectively, these findings indicate that empiric antibiotic selection need not be based on nor altered for wound type. Furthermore, the results provide a much clearer understanding of chronic wound microbiota in general; clinical application of this new knowledge over time may help in its translation to improved wound healing outcomes.

Background: Emergence and spread of antibiotic resistance has become a global health threat and is often linked with overuse and misuse of clinical and veterinary chemotherapeutic agents. Modern industrial-scale animal feeding operations rely extensively on veterinary pharmaceuticals, including antibiotics, to augment animal growth. Following excretion, antibiotics are transported through the environment via runoff, leaching, and land application of manure; however, airborne transport from feed yards has not been characterized. Objectives: The goal of this study was to determine the extent to which antibiotics, antibiotic resistance genes (ARG), and ruminant-associated microbes are aerially dispersed via particulate matter (PM) derived from large-scale beef cattle feed yards. Methods: PM was collected downwind and upwind of 10 beef cattle feed yards. After extraction from PM, five veterinary antibiotics were quantified via high-performance liquid chromatography with tandem mass spectrometry, ARG were quantified via targeted quantitative polymerase chain reaction, and microbial community diversity was analyzed via 16S rRNA amplification and sequencing. Results: Airborne PM derived from feed yards facilitated dispersal of several veterinary antibiotics, as well as microbial communities containing ARG. Concentrations of several antibiotics in airborne PM immediately downwind of feed yards ranged from 0.5 to 4.6 μg/g of PM. Microbial communities of PM collected downwind of feed yards were enriched with ruminant-associated taxa and were distinct when compared to upwind PM assemblages. Furthermore, genes encoding resistance to tetracycline antibiotics were significantly more abundant in PM collected downwind of feed yards as compared to upwind. Conclusions: Wind-dispersed PM from feed yards harbors antibiotics, bacteria, and ARGs. Citation: McEachran AD, Blackwell BR, Hanson JD, Wooten KJ, Mayer GD, Cox SB, Smith PN. 2015. Antibiotics, bacteria, and antibiotic resistance genes: aerial transport from cattle feed yards via particulate matter. Environ Health Perspect 123:337–343; http://dx.doi.org/10.1289/ehp.1408555

Background: In this study, the genetic substructure and morphology of the species Neusticomys monticolus was evaluated. A nuclear marker and mitochondrial maker were used to examine phylogeographic structure and to estimate genetic distances. Two statistical measurement analyses were applied to morphological data.Results: These data recovered two morphologically distinct phylogeographic groups corresponding to populations on the eastern and western slopes of the Andes. Further, these eastern and western Andean slope populations of N. monticolus are 8.5 % divergent using sequence data from cytochrome-b (0.8 % divergent in the interphotoreceptor retinoid-binding protein gene).Conclusions: Populations currently assigned to N. monticolus constitute a species complex. The name N. monticolus is here restricted to western Andean slope populations. Populations on the eastern slope of the Andes are assigned to a new species, to which the authors assign the name Neusticomys vossi sp. nov.

BACKGROUND:The role of viruses in chronic rhinosinusitis (CRS) is poorly understood. In part, this is secondary to difficulty in isolating viruses. Although traditional detection methods for respiratory viruses have had little clinical utility, modern viral screening techniques that use molecular sequencing are now both rapid and feasible, which makes analysis of the paranasal sinus microbiome more accessible.OBJECTIVE:To detect respiratory viruses in the paranasal sinuses of patients with CRS and of healthy controls as well as to correlate clinical and radiographic measures of CRS with viral presence.METHODS:In this prospective study, 13 patients with CRS with nasal polyposis (CRSwNP) and 8 patients without nasal polyposis (CRSsNP) were enrolled and compared with 14 healthy controls. Samples were obtained from the paranasal sinuses and were screened for viral DNA with polymerase chain reaction--based sequencing techniques. Typical symptoms of CRS, the Sinonasal Questionnaire, and objective measures, including the modified Lund-Mackay and modified Lund-Kennedy scores were obtained.RESULTS:Eighty percent of the positive screens (4/5) were found in patients with CRSsNP, whereas 20% of the positive tests (1/5) were in the CRSwNP group, and none of the controls tested positive (p = 0.0029). Coronavirus was the most common virus detected. Sinonasal Questionnaire scores of the patients with CRS who tested positive for viruses were higher but not statistically different than those without a positive screen (p = 0.31). Radiographic and endoscopic measures of disease were not significantly different in the setting of a positive viral screen (p = 0.12 and 0.11 respectively).CONCLUSION:Although traditionally difficult, advances in molecular sequencing enhance detection of viruses in the sinonasal tract. In this study, respiratory viruses were more commonly isolated from patients with CRS compared with healthy controls. Moreover, viral infection may play a greater role in symptom exacerbation in CRSsNP than in CRSwNP. These findings warrant further investigation into the role of the viral microbiome in CRS.

We know that an audio speech signal can be unambiguously decoded by any native speaker of the language it is uttered in, provided that it meets some quality conditions. But we do not know if this is the case with visual speech, because the process of lipreading is rather mysterious and seems to rely heavily on the use of context and non-speech cues. How much information about the speech content is there in a visual speech signal? We make some attempt to provide an answer to this question by ‘discovering’ matching segments of phoneme sequences that represent recurring words and phrases in audio and visual representations of the same speech. We use a modified version of the technique of segmental dynamic programming that was introduced by Park and Glass. Comparison of the results shows that visual speech displays rather less matching content than the audio, and reveals some interesting differences in the phonetic content of the information recovered by the two modalities.

Recently, prebiotic supplementation of infant formula has become common practice; however the impact on the intestinal microbiota has not been completely elucidated. In this study, neonatal piglets were randomized to: formula (FORM, n = 8), formula supplemented with 2 g/L each galactooligosaccharides (GOS) and polydextrose (PDX, F+GP, n = 9) or a sow-reared (SOW, n = 12) reference group for 19 days. The ileal (IL) and ascending colon (AC) microbiota were characterized using culture-dependent and -independent methods. 16S amplicon sequencing identified no differences at the genera level in the IL. Interestingly, six genera in the AC were significantly different between FORM and F+GP (P<0.05): Lactobacillus, Ruminococcus, Parabacteroides, Oscillospira, Hydrogenoanaerobacterium and Catabacter. In particular, the relative abundance of AC Lactobacillus was higher (P = 0.04) in F+GP as compared to FORM. Culture-dependent analysis of the IL and AC lactobacilli communities of FORM and F+GP revealed a Lactobacillus spp. composition similar to 16S amplicon sequencing. Additional analysis demonstrated individual Lactobacillus isolates were unable to ferment PDX. Conversely, a majority of lactobacilli isolates could ferment GOS, regardless of piglet diet. In addition, the ability of lactobacilli isolates to ferment the longer chain GOS fragments (DP 3 or greater), which are expected to be present in the distal intestine, was not different between FORM and F+GP. In conclusion, prebiotic supplementation of formula impacted the AC microbiota; however, direct utilization of GOS or PDX does not lead to an increase in Lactobacillus spp.

HIV progression is characterized by immune activation and microbial translocation. One factor that may be contributing to HIV progression could be a dysbiotic microbiome. We therefore hypothesized that the GI mucosal microbiome is altered in HIV patients and this alteration correlates with immune activation in HIV. 121 specimens were collected from 21 HIV positive and 22 control human subjects during colonoscopy. The composition of the lower gastrointestinal tract mucosal and luminal bacterial microbiome was characterized using 16S rDNA pyrosequencing and was correlated to clinical parameters as well as immune activation and circulating bacterial products in HIV patients on ART. The composition of the HIV microbiome was significantly different than that of controls; it was less diverse in the right colon and terminal ileum, and was characterized by loss of bacterial taxa that are typically considered commensals. In HIV samples, there was a gain of some pathogenic bacterial taxa. This is the first report characterizing the terminal ileal and colonic mucosal microbiome in HIV patients with next generation sequencing. Limitations include use of HIV-infected subjects on HAART therapy.

Population models have emerged as a powerful tool to better understand the ecological effects of toxicant exposure. Currently, most ecotoxicology population models are deterministic and fail to account for natural variability in biological processes and uncertainty in parameter estimates. We developed, parameterized, and analyzed a Daphnia population model with three different levels of demographic stochasticity to examine how a pesticide, pendimethalin, affects population dynamics. We conducted laboratory studies to generate the data used for the modeling process. The simplest model only included parameter uncertainty and variability. The second model included daily stochastic fecundities. The third model included stochastic fecundities and stochastic mortalities. Of the three models, the second model with stochastic fecundity best described our laboratory test system. All three models were used to test hypotheses about how pesticides would affect population dynamics. We found that pendimethalin either decreased the baseline juvenile survivorship rate or the carrying capacity. We could differentiate the two test effects with our system. Our findings demonstrate how stochastic population models may provide insight into pesticide exposure. (C) 2013 Elsevier B.V. All rights reserved.