Evaluation of a deep neural network for acoustic classification using simulated echo sounder data

An important part of fisheries acoustics is the classification of fish species. Sound waves are transmitted through water to detect fish species, and the echoes returning from the fish are categorized to be used for fish abundance estimates. These estimates are import for fishery management. Recently, it has been shown that a deep learning model performs well on the task of classifying acoustic data. However, these models are often criticized for being “black boxes” and hard to interpret. We have created a pipeline to test a neural network model, in order to shed light on what features of the data impact the predictions of the model. In this pipeline, simulated data is utilized, created by a model that emulates the performance of a multi-frequency echo sounder. The simulated data enables the possibility of adjusting one feature of the data at a time. We have concentrated on two features: the relative frequency response, an energetic characteristic of the data, and the shape of the fish schools. A neural network is trained to recognize two types of fish schools, dissimilar only in shape and relative frequency response. The network is then tested on data where either shape or relative frequency is changed, to evaluate the importance of each feature. From these tests we conclude that the relative frequency response affects the model's performance more than shape.Masteroppgåve i anvend og utrekningsorientert matematikkMAB399MAMN-MA

The association between cognitive impairment, gait speed, and Walk ratio

Background: Gait speed has been found to be associated with cognitive function. However, gait speed is an unspecific measure that may not be informative about gait patterns. The Walk ratio (step length divided by step frequency) can be measured without specialized equipment, and has been suggested as an indicator of central gait control. However, the association with cognitive function is unknown. Research question: Is there a relationship between Walk ratio and cognitive function, and gait speed and cognitive function? Methods: This was a systematic literature review of studies where spatiotemporal gait parameters was reported in populations with cognitive impairment. The search was performed through PubMed, PEDro, AMED, Cochrane, Embase, MEDLINE, and PsycINFO. The studies had to contain either the Walk ratio, or report average step length and average step frequency. In the latter case, the average step length was divided by the average step frequency. The studies also had to report gait speed and the minimal mental state examination (MMSE). Studies testing patients on treadmills or that did not state the exclusion of patients with neurologic or orthopedic diseases, possible affecting gait ability, were excluded. Results: A total of 24 studies were included, consisting of 909 patients with cognitive impairment and 4,108 healthy controls. The patient group had a lower Walk ratio (mean difference 0.07, p ≤ 0.001) and gait speed (mean difference 0.26, p ≤ 0.001) than the healthy controls. Using linear regression models, we found an association between the MMSE and the Walk ratio (R2 = 0.29, p < 0.001) and gait speed (R2 = 0.41, p < 0.001) in separate, unadjusted models. In a final model with Walk ratio, gait speed and age, Walk ratio was not significantly associated with MMSE, while gait speed was. Significance: Our results suggest that preferred gait speed may be preferable to the Walk ratio when assessing older adults with cognitive impairment.publishedVersio

Global transcriptome response in Lactobacillus sakei during growth on ribose

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus sakei </it>is valuable in the fermentation of meat products and exhibits properties that allow for better preservation of meat and fish. On these substrates, glucose and ribose are the main carbon sources available for growth. We used a whole-genome microarray based on the genome sequence of <it>L. sakei </it>strain 23K to investigate the global transcriptome response of three <it>L. sakei </it>strains when grown on ribose compared with glucose.</p> <p>Results</p> <p>The function of the common regulated genes was mostly related to carbohydrate metabolism and transport. Decreased transcription of genes encoding enzymes involved in glucose metabolism and the L-lactate dehydrogenase was observed, but most of the genes showing differential expression were up-regulated. Especially transcription of genes directly involved in ribose catabolism, the phosphoketolase pathway, and in alternative fates of pyruvate increased. Interestingly, the methylglyoxal synthase gene, which encodes an enzyme unique for <it>L. sakei </it>among lactobacilli, was up-regulated. Ribose catabolism seems closely linked with catabolism of nucleosides. The deoxyribonucleoside synthesis operon transcriptional regulator gene was strongly up-regulated, as well as two gene clusters involved in nucleoside catabolism. One of the clusters included a ribokinase gene. Moreover, <it>hprK </it>encoding the HPr kinase/phosphatase, which plays a major role in the regulation of carbon metabolism and sugar transport, was up-regulated, as were genes encoding the general PTS enzyme I and the mannose-specific enzyme II complex (EII^man). Putative catabolite-responsive element (<it>cre</it>) sites were found in proximity to the promoter of several genes and operons affected by the change of carbon source. This could indicate regulation by a catabolite control protein A (CcpA)-mediated carbon catabolite repression (CCR) mechanism, possibly with the EII^manbeing indirectly involved.</p> <p>Conclusions</p> <p>Our data shows that the ribose uptake and catabolic machinery in <it>L. sakei </it>is highly regulated at the transcription level. A global regulation mechanism seems to permit a fine tuning of the expression of enzymes that control efficient exploitation of available carbon sources.</p

Pain pressure threshold algometry in knee osteoarthritis: intra- and inter-rater reliability

Introduction: Synovitis and effusion can cause pain sensitization in persons with knee osteoarthritis (KOA). Pain Pressure Threshold (PPT) algometry is a means to quantify somatosensory abnormalities, including inflammatory-mediated pressure hyperalgesia. We investigated the reliability of PPT algometry with three raters. Methods: Twenty-seven persons (50 knees) with KOA, according to the American College of Rheumatology criteria, were included. The PPT of the most tender spot in the joint line of each knee, identified by palpation, was assessed using a digital pressure algometer with a round 1 cm2 rubber tip. The algometer was applied three times with at least twenty-second intervals by three physiotherapists each in a single session. Two of the physiotherapists had no experience with the procedure prior to the study. We estimated the Intraclass Correlation Coefficient (ICC) model 2.1, 95% within-subject standard deviation (sw), and Minimal Detectable Difference (MDD). Results: The mean PPTs ranged from 39.94 to 41.81 Newton (N), the intra-rater ICC ranged from 0.909 to 0.956, the sw ranged from 6.44 to 10.77 N, and the related MDD ranged from 9.11 to 15.23 N. The three raters achieved an inter-rater ICC of 0.707, an sw of 17.68 N, and an MDD of 25.01 N. The results were homoscedastic. Conclusions: Our results indicate that PPT algometry is a suitable method for assessment of pain in osteoarthritic knees. After a short session of PPT procedure training, good intra-rater and acceptable inter-rater ICCs were achieved.publishedVersio

Primary metabolism in Lactobacillus sakei food isolates by proteomic analysis

<p>Abstract</p> <p>Background</p> <p><it>Lactobacillus sakei </it>is an important food-associated lactic acid bacterium commonly used as starter culture for industrial meat fermentation, and with great potential as a biopreservative in meat and fish products. Understanding the metabolic mechanisms underlying the growth performance of a strain to be used for food fermentations is important for obtaining high-quality and safe products. Proteomic analysis was used to study the primary metabolism in ten food isolates after growth on glucose and ribose, the main sugars available for <it>L. sakei </it>in meat and fish.</p> <p>Results</p> <p>Proteins, the expression of which varied depending on the carbon source were identified, such as a ribokinase and a D-ribose pyranase directly involved in ribose catabolism, and enzymes involved in the phosphoketolase and glycolytic pathways. Expression of enzymes involved in pyruvate and glycerol/glycerolipid metabolism were also affected by the change of carbon source. Interestingly, a commercial starter culture and a protective culture strain down-regulated the glycolytic pathway more efficiently than the rest of the strains when grown on ribose. The overall two-dimensional gel electrophoresis (2-DE) protein expression pattern was similar for the different strains, though distinct differences were seen between the two subspecies (<it>sakei </it>and <it>carnosus</it>), and a variation of about 20% in the number of spots in the 2-DE gels was observed between strains. A strain isolated from fermented fish showed a higher expression of stress related proteins growing on both carbon sources.</p> <p>Conclusions</p> <p>It is obvious from the data obtained in this study that the proteomic approach efficiently identifies differentially expressed proteins caused by the change of carbon source. Despite the basic similarity in the strains metabolic routes when they ferment glucose and ribose, there were also interesting differences. From the application point of view, an understanding of regulatory mechanisms, actions of catabolic enzymes and proteins, and preference of carbon source is of great importance.</p

En kvalitativ studie om hvordan osteopater tilnærmer seg pasienter med akillestendinopati

Bakgrunn: Bakgrunnen for valg av tema er at det finnes få studier som omhandler hvordan osteopater tilnærmer seg pasienter med akillestendinopati. En stor del av befolkningen rammes av denne tilstanden, og opp mot halvparten av disse er idrettsutøvere. Målet med denne studien er derfor å øke kunnskapen rundt den kliniske resonneringsprosessen osteopater gjør i møte med pasienter med akillestendinopati. Problemstilling: Hvordan tilnærmer osteopater seg pasienter med akillestendinopati? Metode: I denne kvalitative studien benyttet vi semistrukturerte intervjuer av fire osteopater for innhenting av informasjon. Intervjuene ble transkribert, analysert og deretter knyttet opp mot relevant teori. Resultater og konklusjon: Under anamnesen og den kliniske undersøkelsen er informantene opptatt av å dekke områder som risikofaktorer, varighet, smertebilde, palpasjonsømhet i akillessenen, samt aktive og passive bevegelser. De gjennomfører også en osteopatisk undersøkelse av hele kroppen til pasienten. På denne måten kan de få et overblikk over mulige medvirkende faktorer til akillestendinopatien og hvilken fase den befinner seg i. Tre av informantene bruker belastningsøvelser og manuell behandling, og tilpasser dette individuelt for hver pasient. Det er likevel nødvendig med flere studier for å kunne konkludere om manuell behandling sammen med belastningsøvelser gir effekt. Den siste informanten skiller seg ut ved å kun benytte manuell behandling. Flere kvalitative studier kan gi et større innblikk rundt den osteopatiske tilnærmingen til pasienter med akillestendinopati. Alle informantene opplever en langvarig, men god prognose for tilstanden

Measuring pressure pain threshold in the cervical region of dizzy patients-The reliability of a pressure algometer

Objectives: A tool for measuring neck pain in patients with dizziness is needed to further investigate the relationship between the two symptoms. The objective of this study was to examine the reliability and validity of a hand‐held pressure algometer in measuring pressure pain threshold (PPT) in different cervical regions of dizzy patients. Methods: PPT was measured at two bilateral standardized sites of the neck by a trained physiotherapist in 50 patients with dizziness. Intraclass correlation coefficients (ICC) were calculated for intrarater and test–retest reliability. Concurrent validity was assessed by measuring the association between PPT and the American College of Rheumatology (ACR) tender points at each site and with the numeric pain rating scale (NPRS). Results: Almost perfect intrarater (ICC = 0.815–0.940) and within‐session test–retest (ICC = 0.854–0.906) reliability was found between the measures. On each site, a low PPT predicted a positive ACR tender point at each site (OR = 0.864–0.922). Last, we found a statistical inverse relationship between the PPT and the NPRS (R = −0.52 to −0.66). Conclusion: The study shows that a pressure algometer is a reliable tool for measuring PPT in the neck of dizzy patients. Further, the PPT correlates significantly with other subjective measures of pain indicating that it may be a useful tool for further research.publishedVersio

Effectiveness of Low-Level Laser Therapy Associated with Strength Training in Knee Osteoarthritis: Protocol for a Randomized Placebo-Controlled Trial

Physical activity and low-level laser therapy (LLLT) can reduce knee osteoarthritis (KOA) inflammation. We are conducting a randomized placebo-controlled trial to investigate the long-term effectiveness of LLLT combined with strength training (ST) in persons with KOA, since it, to our knowledge, has not been investigated before. Fifty participants were enrolled. LLLT and ST was performed 3 times per week over 3 and 8 weeks, respectively. In the LLLT group, 3 Joules of 904 nm wavelength laser was applied to 15 spots per knee (45 Joules/knee/session). The primary outcomes are pain during movement, at night and at rest (Visual Analogue Scale) and global pain (Knee injury and Osteoarthritis Outcome Score, KOOS) pain subscale. The secondary outcomes are KOOS disability and quality-of-life, analgesic usage, global health change, knee active range of motion, 30 s chair stand, maximum painless isometric knee extension strength, knee pain pressure threshold and real-time ultrasonography-assessed suprapatellar effusion, meniscal neovascularization and femur cartilage thickness. All the outcomes are assessed 0, 3, 8, 26 and 52 weeks post-randomization, except for global health change, which is only evaluated at completed ST. This study features the blinding of participants, assessors and therapists, and will improve our understanding of what occurs with the local pathophysiology, tissue morphology and clinical status of persons with KOA up to a year after the initiation of ST and a higher 904 nm LLLT dose than in any published trial on this topic.publishedVersio

Photobiomodulation Therapy is Able to Modulate PGE2 Levels in Patients With Chronic Non‐Specific Low Back Pain: A Randomized Placebo‐Controlled Trial

Background and Objectives Non-specific low back pain (LBP) is responsible for triggering increased biomarkers levels. In this way, photobiomodulation therapy (PBMT) may be an interesting alternative to treat these patients. One of the possible biological mechanisms of PBMT involved to decrease pain intensity in patients with musculoskeletal disorders is modulation of the inflammatory mediators’ levels. The aim of this study was to evaluate the effects of PBMT compared with placebo on inflammatory mediators’ levels and pain intensity in patients with chronic non-specific LBP. Study Design/Materials and Methods A prospectively registered, randomized triple-blinded (volunteers, therapists, and assessors), placebo-controlled trial was performed. Eighteen patients with chronic non-specific LBP were recruited and treated with a single session of active PBMT or placebo PBMT. The primary outcome of the study was serum prostaglandin E2 levels and the secondary outcomes were tumor necrosis factor-α, interleukin-6 levels, and pain intensity. All outcomes were measured before and after 15 minutes of treatment session. Results PBMT was able to decrease prostaglandin E2 levels at post-treatment compared with placebo, with a mean difference of −1470 pg/ml, 95% confidence interval −2906 to −33.67 in patients with LBP. There was no difference between groups in the other measured outcomes. Patients did not report any adverse events. Conclusion Our results suggest that PBMT was able to modulate prostaglandin E2 levels, indicating that this may be one of the mechanisms involved in the analgesic effects of PBMT in patients with LBP.publishedVersio

Short-and Long-Term Effectiveness of Low-Level Laser Therapy Combined with Strength Training in Knee Osteoarthritis: A Randomized Placebo-Controlled Trial

Background: Both physical activity and low-level laser therapy (LLLT) can reduce knee osteoarthritis (KOA) inflammation. We conducted a randomized clinical trial to investigate the short- and long-term effectiveness of LLLT combined with strength training in persons with KOA. Methods: Fifty participants were randomly divided in two groups, one with LLLT plus strength training (n = 26) and one with placebo LLLT plus strength training (n = 24). LLLT and strength training were performed triweekly for 3 and 8 weeks, respectively. In the laser group, 3 joules 904 nm wavelength laser was applied to fifteen points (45 joules) per knee per session. Patient-reported outcomes, physical tests, and ultrasonography assessments were performed at baseline and 3, 8, 26, and 52 weeks after initial LLLT or placebo therapy. The primary outcomes were pain on movement, at rest, at night (Visual Analogue Scale), and globally (Knee injury and Osteoarthritis Outcome Score (KOOS) subscale). Parametric data were assessed with analysis of variance using Šidák’s correction. Results: There were no significant between-group differences in the primary outcomes. However, in the laser group there was a significantly reduced number of participants using analgesic and non-steroidal anti-inflammatory drugs and increased performance in the sit-to-stand test versus placebo-control at week 52. The joint line pain pressure threshold (PPT) improved more in the placebo group than in the laser group, but only significantly at week 8. No other significant treatment effects were present. However, pain on movement and joint line PPT were worse in the placebo group at baseline, and therefore, it had more room for improvement. The short-term percentage of improvement in the placebo group was much higher than in similar trials. Conclusions: Pain was reduced substantially in both groups. LLLT seemed to provide a positive add-on effect in the follow-up period in terms of reduced pain medication usage and increased performance in the sit-to-stand test.publishedVersio