The Environmental Context and Function of Burnt-Mounds : New Studies of Irish Fulachtaí Fiadh

The authors acknowledge funding from The Leverhulme Trust (F/00144/AI) and assistance from a large number of individuals including; Margaret Gowen (access to sites and assistance throughout),A. Ames, H, Essex (pollen processing), S. Rouillard & R. Smith (illustrations), C. McDermott, S. Bergerbrandt, all the staff of Margaret Gowen & Co. Ltd, TVAS Ireland and CRDS. Excavation works and some post-excavation analysis was paid for my Bord Gáis and the National Roads Authority (now Transport Infrastructure Ireland). Thanks also to David Smith for access to the Maureen Girling collection and assistance with identifications.Peer reviewedPostprintPostprin

Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid

Post-acute sequelae of SARS-CoV-2 infection (PASC) or Long COVID is an emerging medical condition that has been observed in several patients with a positive diagnosis for COVID-19. Historical Electronic Health Records (EHR) like diagnosis codes, lab results and clinical notes have been analyzed using deep learning and have been used to predict future clinical events. In this paper, we propose an interpretable deep learning approach to analyze historical diagnosis code data from the National COVID Cohort Collective (N3C) to find the risk factors contributing to developing Long COVID. Using our deep learning approach, we are able to predict if a patient is suffering from Long COVID from a temporally ordered list of diagnosis codes up to 45 days post the first COVID positive test or diagnosis for each patient, with an accuracy of 70.48\%. We are then able to examine the trained model using Gradient-weighted Class Activation Mapping (GradCAM) to give each input diagnoses a score. The highest scored diagnosis were deemed to be the most important for making the correct prediction for a patient. We also propose a way to summarize these top diagnoses for each patient in our cohort and look at their temporal trends to determine which codes contribute towards a positive Long COVID diagnosis

Identifying barriers to help seeking for non-motor symptoms in people with Parkinson’s disease

Non-motor Symptoms (NMS) of Parkinson’s disease (PD) have a significant impact on quality of life. Despite this many NMS remain unreported by patients and consequently untreated. The present study explored barriers to help-seeking using two theoretical frameworks, the Common Sense Model of illness and Theoretical Domains Framework. 20 Participants completed semi-structured interviews to explore symptom beliefs and help-seeking behaviour. Uncertainty about the relationship of NMS to PD and lack of clarity around treatments were common. Embarrassment and communication difficulties were common for potentially sensitive symptoms such as sexual dysfunction. Symptom perceptions and beliefs about help-seeking acted as barriers to reporting NMS

The environmental context and function of Burnt-Mounds: new studies of Irish Fulachtaí Fiadh

Burnt mounds, or fulachtaí fiadh as they are known in Ireland, are probably the most common prehistoric site type in Ireland and Britain. Typically Middle–Late Bronze Age in age (although both earlier and later examples are known), they are artefact-poor and rarely associated with settlements. The function of these sites has been much debated with the most commonly cited uses being for cooking, as steam baths or saunas, for brewing, tanning, or textile processing. A number of major infrastructural development schemes in Ireland in the years 2002–2007 revealed remarkable numbers of these mounds often associated with wood-lined troughs, many of which were extremely well-preserved. This afforded an opportunity to investigate them as landscape features using environmental techniques – specifically plant macrofossils and charcoal, pollen, beetles, and multi-element analyses. This paper summarises the results from eight sites from Ireland and compares them with burnt mound sites in Great Britain. The fulachtaí fiadh which are generally in clusters, are all groundwater-fed by springs, along floodplains and at the bases of slopes. The sites are associated with the clearance of wet woodland for fuel; most had evidence of nearby agriculture and all revealed low levels of grazing. Multi-element analysis at two sites revealed elevated heavy metal concentrations suggesting that off-site soil, ash or urine had been used in the trough. Overall the evidence suggests that the most likely function for these sites is textile production involving both cleaning and/or dyeing of wool and/or natural plant fibres and as a functionally related activity to hide cleaning and tanning. Whilst further research is clearly needed to confirm if fulachtaí fiadh are part of the ‘textile revolution’ we should also recognise their important role in the rapid deforestation of the wetter parts of primary woodland and the expansion of agriculture into marginal areas during the Irish and British Bronze Ages

Clinically relevant enhancement of human sperm motility using compounds with reported phosphodiesterase inhibitor activity

STUDY QUESTION: Can we identify compound(s) with reported phosphodiesterase inhibitor (PDEI) activity that could be added to human spermatozoa in vitro to enhance their motility without compromising other sperm functions? SUMMARY ANSWER: We have identified several compounds that produce robust and effective stimulation of sperm motility and, importantly, have a positive response on patient samples. WHAT IS KNOWN ALREADY: For >20 years, the use of non-selective PDEIs, such as pentoxifylline, has been known to influence the motility of human spermatozoa; however, conflicting results have been obtained. It is now clear that human sperm express several different phosphodiesterases and these are compartmentalized at different regions of the cells. By using type-specific PDEIs, differential modulation of sperm motility may be achieved without adversely affecting other functions such as the acrosome reaction (AR). STUDY DESIGN, SIZE, DURATION: This was a basic medical research study examining sperm samples from normozoospermic donors and subfertile patients attending the Assisted Conception Unit (ACU), Ninewells Hospital Dundee for diagnostic semen analysis, IVF and ICSI. Phase 1 screened 43 commercially available compounds with reported PDEI activity to identify lead compounds that stimulate sperm motility. Samples were exposed (20 min) to three concentrations (1, 10 and 100 µM) of compound, and selected candidates (n = 6) progressed to Phase 2, which provided a more comprehensive assessment using a battery of in vitro sperm function tests.  PARTICIPANTS/MATERIALS, SETTING, METHODS: All healthy donors and subfertile patients were recruited at the Medical Research Institute, University of Dundee and ACU, Ninewells Hospital Dundee (ethical approval 08/S1402/6). In Phase 1, poor motility cells recovered from the 40% interface of the discontinuous density gradient were used as surrogates for patient samples. Pooled samples from three to four different donors were utilized in order to reduce variability and increase the number of cells available for simultaneous examination of multiple compounds. During Phase 2 testing, semen samples from 23 patients attending for either routine diagnostic andrology assessment or IVF/ICSI were prepared and exposed to selected compounds. Additionally, 48 aliquots of prepared samples, surplus to clinical use, were examined from IVF (n = 32) and ICSI (n = 16) patients to further determine the effects of selected compounds under clinical conditions of treatment. Effects of compounds on sperm motility were assessed by computer-assisted sperm analysis. A modified Kremer test using methyl cellulose was used to assess sperm functional ability to penetrate into viscous media. Sperm acrosome integrity and induction of apoptosis were assessed using the acrosomal content marker PSA-FITC and annexin V kit, respectively. MAIN RESULTS AND THE ROLE OF CHANCE: In Phase 1, six compounds were found to have a strong effect on poor motility samples with a magnitude of response of ≥60% increase in percentage total motility. Under capacitating and non-capacitating conditions, these compounds significantly (P ≤ 0.05) increased the percentage of total and progressive motility. Furthermore, these compounds enhanced penetration into a cervical mucus substitute (P ≤ 0.05). Finally, the AR was not significantly induced and these compounds did not significantly increase the externalization of phosphatidylserine (P = 0.6, respectively). In general, the six compounds maintained the stimulation of motility over long periods of time (180 min) and their effects were still observed after their removal. In examinations of clinical samples, there was a general observation of a more significant stimulation of sperm motility in samples with lower baseline motility. In ICSI samples, compounds #26, #37 and #38 were the most effective at significantly increasing total motility (88, 81 and 79% of samples, respectively) and progressive motility (94, 93 and 81% of samples, respectively). In conclusion, using a two-phased drug discovery screening approach including the examination of clinical samples, 3/43 compounds were identified as promising candidates for further study. LIMITATIONS, REASONS FOR CAUTION: This is an in vitro study and caution must be taken when extrapolating the results. Data for patients were from one assessment and thus the robustness of responses needs to be established. The n values for ICSI samples were relatively small. WIDER IMPLICATIONS OF THE FINDINGS: We have systematically screened and identified several compounds that have robust and effective stimulation (i.e. functional significance with longevity and no toxicity) of total and progressive motility under clinical conditions of treatment. These compounds could be clinical candidates with possibilities in terms of assisted reproductive technology options for current or future patients affected by asthenozoospermia or oligoasthenozoospermia

Casein Kinase 1 Proteomics Reveal Prohibitin 2 Function in Molecular Clock

Throughout the day, clock proteins synchronize changes in animal physiology (e.g., wakefulness and appetite) with external cues (e.g., daylight and food). In vertebrates, both casein kinase 1 delta and epsilon (CK1δ and CK1ε) regulate these circadian changes by phosphorylating other core clock proteins. In addition, CK1 can regulate circadian-dependent transcription in a non-catalytic manner, however, the mechanism is unknown. Furthermore, the extent of functional redundancy between these closely related kinases is debated. To further advance knowledge about CK1δ and CK1ε mechanisms of action in the biological clock, we first carried out proteomic analysis of both kinases in human cells. Next, we tested interesting candidates in a cell-based circadian readout which resulted in the discovery of PROHIBITIN 2 (PHB2) as a modulator of period length. Decreasing the expression of PHB2 increases circadian-driven transcription, thus revealing PHB2 acts as an inhibitor in the molecular clock. While stable binding of PHB2 to either kinase was not detected, knocking down CK1ε expression increases PHB2 protein levels and, unexpectedly, knocking down CK1δ decreases PHB2 transcript levels. Thus, isolating CK1 protein complexes led to the identification of PHB2 as an inhibitor of circadian transcription. Furthermore, we show that CK1δ and CK1ε differentially regulate the expression of PHB2

The rehabilitation enhancing aging through connected health (REACH) study: study protocol for a quasi-experimental clinical trial

Background: Mobility limitations among older adults increase the risk for disability and healthcare utilization. Rehabilitative care is identified as the most efficacious treatment for maintaining physical function. However, there is insufficient evidence identifying a healthcare model that targets prevention of mobility decline among older adults. The objective of this study is to evaluate the preliminary effectiveness of a physical therapy program, augmented with mobile tele-health technology, on mobility function and healthcare utilization among older adults. Methods: This is a quasi-experimental 12-month clinical trial conducted within a metropolitan-based healthcare system in the northeastern United States. It is in parallel with an existing longitudinal cohort study evaluating mobility decline among community-dwelling older adult primary care patients over one year. Seventy-five older adults (≥ 65–95 years) are being recruited using identical inclusion/exclusion criteria to the cohort study. Three aims will be evaluated: the effect of our program on 1) physical function, 2) healthcare utilization, and 3) healthcare costs. Changes in patient-reported function over 1 year in those receiving the intervention (aim 1) will be compared to propensity score matched controls (N = 150) from the cohort study. For aims 2 and 3, propensity scores, derived from logistic regression model that includes demographic and diagnostic information available through claims and enrollment information, will be used to match treatment and control patients in a ratio of 1:2 or 1:3 from a Medicare Claims Registry derived from the same geographic region. The intervention consists of a one-year physical therapy program that is divided between a combination of outpatient and home visits (6–10 total visits) and is augmented on a computerized tablet using of a commercially available application to deliver a progressive home-based exercise program emphasizing lower-extremity function and a walking program. Discussion Incorporating mobile health into current healthcare models of rehabilitative care has the potential to decrease hospital visits and provide a longer duration of care. If the hypotheses are supported and demonstrate improved mobility and reduced healthcare utilization, this innovative care model would be applicable for optimizing the maintenance of functional independence among community-dwelling older adults. Trial registration ClinicalTrial.gov Identifier: NCT02580409 (Date of registration October 14, 2015)

Influence of family and friend smoking on intentions to smoke and smoking-related attitudes and refusal self-efficacy among 9-10 year old children from deprived neighbourhoods: a cross-sectional study.

BACKGROUND: Smoking often starts in early adolescence and addiction can occur rapidly. For effective smoking prevention there is a need to identify at risk groups of preadolescent children and whether gender-specific intervention components are necessary. This study aimed to examine associations between mother, father, sibling and friend smoking and cognitive vulnerability to smoking among preadolescent children living in deprived neighbourhoods. METHODS: Cross-sectional data was collected from 9-10 year old children (n =1143; 50.7% girls; 85.6% White British) from 43 primary schools in Merseyside, England. Children completed a questionnaire that assessed their smoking-related behaviour, intentions, attitudes, and refusal self-efficacy, as well as parent, sibling and friend smoking. Data for boys and girls were analysed separately using multilevel linear and logistic regression models, adjusting for individual cognitions and school and deprivation level. RESULTS: Compared to girls, boys had lower non-smoking intentions (P = 0.02), refusal self-efficacy (P = 0.04) and were less likely to agree that smoking is 'definitely' bad for health (P < 0.01). Friend smoking was negatively associated with non-smoking intentions in girls (P < 0.01) and boys (P < 0.01), and with refusal self-efficacy in girls (P < 0.01). Sibling smoking was negatively associated with non-smoking intentions in girls (P < 0.01) but a positive association was found in boys (P = 0.02). Boys who had a smoking friend were less likely to 'definitely' believe that the smoke from other people's cigarettes is harmful (OR 0.57, 95% CI: 0.35 to 0.91, P = 0.02). Further, boys with a smoking friend (OR 0.38, 95% CI: 0.21 to 0.69, P < 0.01) or a smoking sibling (OR 0.45, 95% CI: 0.21 to 0.98) were less likely to 'definitely' believe that smoking is bad for health. CONCLUSION: This study indicates that sibling and friend smoking may represent important influences on 9-10 year old children's cognitive vulnerability toward smoking. Whilst some differential findings by gender were observed, these may not be sufficient to warrant separate prevention interventions. However, further research is needed