Animal-borne tags provide insights into the acoustic communication of southern right whales (Eubalaena australis) on the calving grounds

Funding: This study was supported by the Marine Mammal Commission under Grant No. MMC17-230. Additional support was provided by Cetacean Society International and VIVA Baleias, golfinhos ecia.This study investigated the repertoire, call-type variability and call rates of southern right whales on a calving ground off Brazil in the western South Atlantic. Acoustic tag data were collected from four lactating females and one juvenile. Pulsive, hybrid, and upcalls showed the greatest variability among call-types with up to 23% of non-standard forms detected. Quiet sounds (grunt, single, and double pulse) were detected for the first time in this species on the calving grounds. Although the sample size was limited, results suggest that social interaction increased call-type diversity and call rates, in line with other acoustic studies on right whales.Publisher PDFPeer reviewe

Academic motherhood and fieldwork: Juggling time, emotions and competing demands

The idea and practice of going ‘into the field’ to conduct research and gather data is a deeply rooted aspect of Geography as a discipline. For global North Development Geographers, amongst others, this usually entails travelling to, and spending periods of time in, often far-flung parts of the global South. Forging a successful academic career as a Development Geographer in the UK, is therefore to some extent predicated on mobility. This paper aims to critically engage with the gendered aspects of this expected mobility, focusing on the challenges and time constraints that are apparent when conducting overseas fieldwork as a mother, unaccompanied by her children. The paper emphasises the emotion work that is entailed in balancing the competing demands of overseas fieldwork and mothering, and begins to think through the implications of these challenges in terms of the types of knowledge we produce, as well as in relation to gender equality within the academy

Effects of Non-Aerobic Maximal Effort Exercise on Fatigue in Deconditioned Men and Women with Multiple Sclerosis

Multiple Sclerosis (MS) is a neurodegenerative disease of unknown etiology affecting women more frequently than men. Mental and physical fatigue complaints are often the most disabling symptoms for an MS patient. Both are multifactorial, potentially exacerbated by aerobic exercise, may prevent sustained physical functioning, and significantly interfere with activities of daily living1. A multi-center study was designed to investigate the effects of non-aerobic maximal effort exercise (MEE) for deconditioned persons with MS, with the expectation of minimizing fatigue. The IsoPUMP (Neuromuscular Engineering; Nashville, TN), is a specialized exercise and strength-sensing machine, designed to allow individuals to safely perform and record their non-aerobic MEE sessions. The Modified Fatigue Impact Scale (MFIS) and Multiple Sclerosis Functional Composite (MSFC) are common, accepted methods used to measure fatigue and function. The MFIS is a 21-item questionnaire which assesses the subjects’ perception of physical, cognitive, and psychosocial aspects of fatigue over a four-week period2. Each of the 21 items are scored on a scale from 0 (never) to 4 (almost always), and the total MFIS score is calculated by summing the circled number for each item. Total scores can range from 0 to 84; higher scores indicating a greater impact of fatigue on the person. The MFIS has three distinct subscales: (1) physical, (2) cognitive, and (3) psychosocial. These subscales can be scored independently by summing the questions that pertain to each subscale2. The MFIS physical subscale score can range from 0 – 36 and the MFIS cognitive subscale score can range from 0 – 40. The MSFC combines clinical measures used to assess lower limb function (Timed 25-Foot Walk [25-FW]), upper limb function (9-Hole Peg Test [9-HPT]), and cognition (Paced Auditory Serial Addition Test [PASAT-3”])3. The 25-FW is a quantitative measure of lower extremity function. The 9-HPT is a quantitative measure of arm and hand function where a subject inserts and then removes 9 pegs from a board, using one hand at a time. The time is recorded for each hand with the dominant hand trial first and the non-dominant hand trial second. The final score is recorded as the mean time for both hands. The PASAT-3” is a measure of cognitive function, specifically assessing auditory information processing speed, short-term memory, flexibility, and calculation ability. Cognitive dysfunction affects half of all MS patients; slowing ability to reason, concentrate, and recall5. In this test subjects listen to a series of 61 spoken numbers separated by 3 seconds and must add each number to the prior number. Their final PASAT-3” score is the number of correct additions in the series, with 60 reflecting a perfect score. The MSFC is then evaluated by creating Z-scores for each component, which compare each outcome with the average outcome of the study population. The three Z-scores are then averaged to create an overall composite score (the MSFC score) which represents change over time for that population of MS subjects3

The Effect of Progressive Non-Aerobic High-Intensity Maximal Effort Exercise (MEE) on the Health-Related Quality of Life in Patients with Multiple Sclerosis

Background: Studies indicate that Multiple Sclerosis (MS) patients are less satisfied with the quality of their lives than healthy individuals in similar circumstances. Common symptoms experienced include fatigue, cognitive dysfunction, pain, spasticity, depression, bladder/bowel dysfunction and sexual dysfunction. Several pharmacological and non-pharmacological methods have been employed for such symptoms to try to increase quality of life and reduce the mortality rate. Non-pharmacological methods recommended for MS patients include lifestyle modifications, exercise programs and physical therapy. MS patients easily fatigue during aerobic exercise but a non-aerobic progressive maximal effort exercise (MEE) protocol consisting of a few short, duration isometric and eccentric leg press and whole body lunges was previously seen to increase strength without increasing fatigue. The IsoPUMP® (Neuromuscular Engineering, Nashville TN) exercise system permitted safe conduct and measurement of muscle strength and duration during each exercise repetition

An Analysis of Functional Status in Multiple Sclerosis Patients after Progressive Non-Aerobic High-Intensity Maximal Effort Exercise (MEE)

Background: Multiple Sclerosis (MS) is a disease with a wide-ranging impact on functional status. MS patient function has been assessed using Multiple Sclerosis Functional Composite Score (MSFCS). The MSFCS includes the standardized scores (Z-score) of three functional tests: the Paced Auditory Serial Addition Test (PASAT-3”) for cognitive function, 9-Hole Peg Test (9-HPT) for upper extremity function, and timed 25-foot walk (25-TW) for lower extremity function. One of the most common symptoms experienced by MS patients is severe fatigue, often brought on suddenly by aerobic exercise. Non-aerobic maximal effort exercise (MEE) is thought to increase strength without increasing fatigue. The IsoPUMP® (Neuromuscular Engineering; Nashville, TN) is a stationary exercise device designed for patient use to safely perform MEE leg presses and whole body lunges using isometric and eccentric exercises. The progressive functional changes of the MS patients were tracked using the MSFCs at specific intervals during the study

Characterization of LINE-1 Ribonucleoprotein Particles

The average human genome contains a small cohort of active L1 retrotransposons that encode two proteins (ORF1p and ORF2p) required for their mobility (i.e., retrotransposition). Prior studies demonstrated that human ORF1p, L1 RNA, and an ORF2p-encoded reverse transcriptase activity are present in ribonucleoprotein (RNP) complexes. However, the inability to physically detect ORF2p from engineered human L1 constructs has remained a technical challenge in the field. Here, we have employed an epitope/RNA tagging strategy with engineered human L1 retrotransposons to identify ORF1p, ORF2p, and L1 RNA in a RNP complex. We next used this system to assess how mutations in ORF1p and/or ORF2p impact RNP formation. Importantly, we demonstrate that mutations in the coiled-coil domain and RNA recognition motif of ORF1p, as well as the cysteine-rich domain of ORF2p, reduce the levels of ORF1p and/or ORF2p in L1 RNPs. Finally, we used this tagging strategy to localize the L1–encoded proteins and L1 RNA to cytoplasmic foci that often were associated with stress granules. Thus, we conclude that a precise interplay among ORF1p, ORF2p, and L1 RNA is critical for L1 RNP assembly, function, and L1 retrotransposition

SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

<p>Abstract</p> <p>Background</p> <p>Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma (<it>σ</it>) Factor Binding Sites (SFBSs) usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations.</p> <p>Results</p> <p>We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data), performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds (of which one is possibly gapped), allowing a variable-length spacer between them. Next, the motifs are extended guided by statistical considerations, a feature that ensures a selection of motifs with statistically relevant properties. We applied our method to the pair of related bacterial genomes of <it>Streptomyces coelicolor </it>and <it>Streptomyces avermitilis</it>. Cross-check with the well-defined SFBSs of the SigR regulon in <it>S. coelicolor </it>is detailed, validating the algorithm. SFBSs for HrdB and BldN were also found; and the results suggested some new targets for these <it>σ </it>factors. In addition, consensus motifs for BldD and new SFBSs binding sites were defined, overlapping previously proposed consensuses. Relevant tests were carried out also on bacteria with moderate GC content (i.e. <it>Escherichia coli</it>/<it>Salmonella typhimurium </it>and <it>Bacillus subtilis</it>/<it>Bacillus licheniformis </it>pairs). Motifs of house-keeping <it>σ </it>factors were found as well as other SFBSs such as that of SigW in <it>Bacillus </it>strains.</p> <p>Conclusion</p> <p>We demonstrate that our approach combining statistical and biological criteria was successful to predict SFBSs. The method versatility autorizes the recognition of other kinds of two-box regulatory sites.</p

SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

<p>Abstract</p> <p>Background</p> <p>Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma (<it>σ</it>) Factor Binding Sites (SFBSs) usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations.</p> <p>Results</p> <p>We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data), performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds (of which one is possibly gapped), allowing a variable-length spacer between them. Next, the motifs are extended guided by statistical considerations, a feature that ensures a selection of motifs with statistically relevant properties. We applied our method to the pair of related bacterial genomes of <it>Streptomyces coelicolor </it>and <it>Streptomyces avermitilis</it>. Cross-check with the well-defined SFBSs of the SigR regulon in <it>S. coelicolor </it>is detailed, validating the algorithm. SFBSs for HrdB and BldN were also found; and the results suggested some new targets for these <it>σ </it>factors. In addition, consensus motifs for BldD and new SFBSs binding sites were defined, overlapping previously proposed consensuses. Relevant tests were carried out also on bacteria with moderate GC content (i.e. <it>Escherichia coli</it>/<it>Salmonella typhimurium </it>and <it>Bacillus subtilis</it>/<it>Bacillus licheniformis </it>pairs). Motifs of house-keeping <it>σ </it>factors were found as well as other SFBSs such as that of SigW in <it>Bacillus </it>strains.</p> <p>Conclusion</p> <p>We demonstrate that our approach combining statistical and biological criteria was successful to predict SFBSs. The method versatility autorizes the recognition of other kinds of two-box regulatory sites.</p

MRI Indices of Cortical Development in Young People With Psychotic Experiences: Influence of Genetic Risk and Persistence of Symptoms

Background Psychotic experiences (PEs) are considered part of an extended psychosis phenotype and are associated with an elevated risk of developing a psychotic disorder. Risk of transition increases with persistence of PEs, and this is thought to be modulated by genetic and environmental factors. However, it is unclear if persistence is associated with progressive schizophrenia-like changes in neuroanatomy. Methods We examined cortical morphometry using MRI in 247 young adults, from a population-based cohort, assessed for the presence of PEs at ages 18 and 20. We then incorporated a polygenic risk score for schizophrenia (PRS) to elucidate the effects of high genetic risk. Finally, we used atlas-based tractography data to examine the underlying white matter. Results Individuals with persisting PEs showed reductions in gyrification (local gyrification index: lGI) in the left temporal gyrus as well as atypical associations with brain volume (TBV) in the left occipital and right prefrontal gyri. No main effect was found for the PRS, but interaction effects with PEs were identified in the orbitofrontal, parietal, and temporal regions. Examination of underlying white matter did not provide strong evidence of further disturbances. Conclusions Disturbances in lGI were similar to schizophrenia but findings were mostly limited to those with persistent PEs. These could reflect subtle changes that worsen with impending psychosis or reflect an early vulnerability associated with the persistence of PEs. The lack of clear differences in underlying white matter suggests our findings reflect early disturbances in cortical expansion rather than progressive changes in brain structure