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Data from: Oral Cancer: clinical presentation and associated risk factors in a high risk population presenting to a major tertiary care center in Pakistan
<p>Oral squamous cell carcinoma (OSCC) has the highest prevalence in head and neck cancers and is the first and second most common cancer in males and females of Pakistan respectively. Major risk factors include peculiar chewing habits like areca nut, betel quid, and tobacco. The majority of OSCC presents at an advanced stage with poor prognosis. On the face of such a high burden of this preventable cancer, there is a relative lack of recent robust data and its association with known risk factors from Pakistan. The aim of this study was to identify the socioeconomic factors and clinicopathological features that may contribute to the development of OSCC. A total of 186 patients diagnosed and treated at a tertiary care hospital, Karachi Pakistan were recruited. Clinicopathological and socioeconomic information was obtained on a structured questionnaire. Descriptive analysis was done for demographics and socioeconomic status (SES) while regression analysis was performed to evaluate the association between SES and chewing habits, tumor site, and tumor stage. The majority of patients were males and the mean age of OSCC patients was 47.62±12.18 years. Most of the patients belonged to low SES (68.3%) and 77.4% were habitual of chewing. Gender (male) and SES were significantly associated with chewing habits (p<0.05). Odds of developing buccal mucosa tumors in chewers (of any type of substance) and gutka users were 2 and 4 times higher than non-chewers respectively. Middle age, chewing habits, and occupation were significantly associated with late stage presentation of OSCC (p<0.05). In conclusion, male patients belonging to low SES in their forties who had chewing habits for years constituted the bulk of OSCC. Buccal mucosa was the most common site in chewers and the majority presented with late stage tumors.</p>
Data from: Effects of hay provision and presentation on cognitive development in dairy calves
<p>In the dairy industry, young dairy calves are often housed individually in restrictive environments. There is limited understanding of how approaches to increase complexity of individual rearing, such as through dietary complexity and accommodating more varied feeding behavior, may affect cognitive development in young calves. The objective of this study was to evaluate effects of provision and presentation of hay on cognitive ability of pre-weaned dairy calves. Individually-housed Holstein heifer calves were assigned at birth to 1 of 3 treatments: pelleted starter only (n = 10), hay and starter provided in separate buckets (n = 12), or hay and starter offered as a mixture (n = 11). During week 5 of age, calves were tested daily in a procedural learning task consisting of a T-maze with a milk reward (0.2 L milk) placed in one arm. Calves were subjected to an initial learning and reversal learning stage, where the reward location was changed to the opposite arm of the maze. Calves received 5 sessions/d until they met learning criteria (moving directly to correct side in 3 consecutive sessions) for initial and reversal learning. Dietary treatment did not affect pass rate or the number of sessions required to pass the initial learning stage. During the reversal learning stage, calves provided only starter tended to require more sessions to meet the learning criteria. Provision of hay also affected behavior during the reversal learning stage of the cognitive task, where calves provided hay separately spent more time exploring the testing area. The results of this experiment provide the first evidence that dietary factors alone may affect cognitive performance in dairy calves.</p>
Figure 2 in The role of female cephalopod researchers: past and present
Figure 2. Female cephalopod scientists. (A) Jeanne (Jeanette) Villepreux-Power (1794–1871). Detail from original photograph taken by A. E. E. Disdéri in 1861. (B) Julia Arsent'evna Filippova (1934- present). (C) Zulma Judith Ageitos de Castellanos (1922–2010). (D) Martina Compagno Roeleveld (1943–2006) (left) with María Edith Ré, currently of the National Patagonic Institute in Puerto Madryn, Argentina (right). Photo taken during the 1997 CIAC meeting in Capetown by Angel Guerra. (E) Nancy A. Voss (1929 – present). (F) Katharina Maria Mangold-Wirz (1922–2003). Photo by Eric Hochberg. (G) Joyce Wells (1930 – present). Photo by Angel Guerra, 1987. (H) Renata Boucher-Rodoni (1942 – present). (I) Eve Boucaud-Camou (1939-present). (J) Marion Nixon (1930 – present). Photo by Angel Guerra, 1992, Aberdeen.
Statistical prediction of the future impairs episodic encoding of the present
<p>The following submission contains the behavioral data reported from the manuscript "Statistical prediction of the future impairs episodic encoding of the present". Data from four experiments are included. All experiments contained a learning phase, in which participants viewed a series of trial-unique scenes drawn from one of 12 scene categories and were asked to report whether or not the on-screen scene contained a manmade object. Accuracy and response time were measured during this task. Each scene category belonged to one of three conditions: <em>A</em> scenes, which were predictive of <em>B</em> scenes (which were thus predictable), and <em>X</em> scenes which could be preceded or followed by any number of scene categories and thus were neither predictive nor predictable. All experiments also contained a memory phase, in which participants were shown a scene image and were asked to indicate whether or not that particular scene image was presented in the learning phase. All scenes from the learning phase, in addition to a subset of images that were not presented during the learning phase (foils) were presented during the memory phase. After indicating whether an image was old or new, participants then indicated their confidence in their response (Experiments 1a, 1b & 3) or when in time they remember seeing the image (Experiment 2; old responses only). Experiments 1a & 2 additionally contained a category pair test. On each trial, participants were presented with two pairs of images and were asked to indicate which pair felt more familiar to them. Trials consisted either of a true A/B pair and a scrambled A/B pair (for which a trial would be accurate if participants chose the true A/B pair), or two dummy-coded X/X pairs (to which there was no objectively correct answer). </p>
Additional Material: Virtual Humans in AR: Evaluation of Presentation Concepts in an Industrial Assistance Use Case
<p>Additional material to the evaluation on different presentation concepts of a virtual human in HMD-based AR</p>
Challenges in Agile Transformation Journey - A Qualitative Study (Presentation)
<p><em>Context</em>: The agile transformation of an organization is influenced by different factors that can hinder the initiative's success, such as lack of adaptation of agile practices to the organizational context, selection of agile alternatives without using appropriate criteria, and lack of knowledge of the associated challenges. Not all organizations properly recognize these factors. <em>Objective</em>: We aim to identify challenges that can impact the success of agile transformations initiatives. <em>Method</em>: We executed a qualitative study using thematic analysis. We interviewed key persons in charge of the agile journey in four Brazilian organizations. <em>Results</em>: We identified 26 challenges in five dimensions: People, Organizational Culture, Processes, Scalability, and Technology. Among the main challenges are inadequate training, communication difficulties, a culture conflicting with agile values, incompatible organizational structure, and lack of a process to guide the transition. <em>Conclusion</em>: The results suggest urgency in the treatment of agile adoption as a contextualized project for organizational improvements.</p>
Supplementary material 2 from: Bertolino S, Ancillotto L, Bartolommei P, Benassi G, Capizzi D, Gasperini S, Lucchesi M, Mori E, Scillitani L, Sozio G, Falaschi M, Ficetola GF, Cerri J, Genovesi P, Carnevali L, Loy A, Monaco A (2020) A framework for prioritising present and potentially invasive mammal species for a national list. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 31-54. https://doi.org/10.3897/neobiota.62.52934
This is the R-script and the output of the analyses
Supplementary material 1 from: Bertolino S, Ancillotto L, Bartolommei P, Benassi G, Capizzi D, Gasperini S, Lucchesi M, Mori E, Scillitani L, Sozio G, Falaschi M, Ficetola GF, Cerri J, Genovesi P, Carnevali L, Loy A, Monaco A (2020) A framework for prioritising present and potentially invasive mammal species for a national list. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 31-54. https://doi.org/10.3897/neobiota.62.52934
This is the database produced during the research
Supplementary material 3 from: Bertolino S, Ancillotto L, Bartolommei P, Benassi G, Capizzi D, Gasperini S, Lucchesi M, Mori E, Scillitani L, Sozio G, Falaschi M, Ficetola GF, Cerri J, Genovesi P, Carnevali L, Loy A, Monaco A (2020) A framework for prioritising present and potentially invasive mammal species for a national list. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 31-54. https://doi.org/10.3897/neobiota.62.52934
Complete ranking of the species
Video_presentation_session
<p>This is the video presentation session for the activities performed on the antenna front-end.</p>
Data from: The challenges that spatial context present for synthesizing community ecology across scales
Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography. These factors limit the degree to which results from different metacommunity and macro-ecological studies can be compared to draw new inferences, and yet these types of comparisons are widespread in community ecology. Using aquatic community datasets, we demonstrate that spatial context drives analytical results when landscapes are sub-divided. Next, we present a framework for using resampling and neighborhood smoothing to standardize datasets to allow for inferential comparisons. We then provide examples for how addressing these issues enhances our ability to understand the processes shaping ecological communities at landscape scales and allows for informative meta-analytical synthesis. We conclude by calling for greater recognition of issues derived from the modifiable areal unit problem in community ecology, discuss implications of the problem for interpreting the existing literature, and identify tools and approaches for future research.
Data from: The influence of the fetal leg position on the outcome in vaginally intended deliveries out of breech presentation at term – a FRABAT prospective cohort study
<p>Introduction: Vaginal delivery out of a breech presentation in pregnancies at term are being re-implemented into clinical practice. Still, recommendations regarding exclusion criteria leading to caesarean sections are based on expert opinions, not on evidence based guidelines. The difference in perinatal outcome and course of delivery in births with babies in frank breech position and babies in incomplete or complete breech presentation never has been investigated in a large patient cohort.</p> <p>Objective: To compare perinatal outcome of vaginally intended breech deliveries between births out of frank breech position and incomplete/complete breech<br> presentation. Design: Prospective cohort study Sample: 884 women at term with a singleton in frank breech presentation (FB) and 284 women with incomplete or complete breech presentation (CB) intending vaginal birth between January 2004 and December 2018</p> <p>Methods: Maternal and fetal outcome was compared between groups using Pearson's Chi Square test. Birth duration parameters were analysed using logistic regression. Results: There were no differences in cesarean section rates (FB: 25.1%, CB 22.2%, p=0.317). Short-term fetal morbidity did not differ between groups (FB: 2.5%, CB: 2.8%, p=0.761). In vaginal deliveries the necessity to perform manual assistance was significantly more frequent in deliveries of infants in CB (FB: 39.9%, CB: 51.6%, p= 0.0013). Cord loops (FB: 10.1%, CB: 18.0%, p=0.0004) and cesarean sections necessary because of cord prolapses (FB: 1.4%, CB 8.1%, p=0.005) were significantly more often in deliveries with babies in CB.</p> <p>Conclusion: This study provides evidence, that perinatal morbidity is not associated with the fetal leg posture in vaginally intended breech deliveries. The higher risk for the need of manual assistance during vaginal birth in deliveries of babies out of complete or incomplete breech presentation suggests that obstetrical departments reimplementing the vaginal breech in their repertoire might start with births of babies out of frank breech presentation.</p>
Data from: Is high-sensitivity troponin, alone or in combination with copeptin, sensitive enough for ruling out NSTEMI in very early presenters at admission? A post-hoc analysis performed in emergency departments
Objectives: Copeptin and high-sensitivity cardiac troponin (HS-cTn) assays improve the early detection of NSTEMI. Their sensitivities may however be reduced in very early presenters. Setting: We performed a post-hoc analysis of three prospective studies that included patients who presented to the Emergency Department for chest pain onset (CPO) of less than 6 hours. Participants: 449 patients were included, in whom 12% had NSTEMI. CPO occurred <2h from ED presentation in 160, between 2-4h in 143, and >4h in 146 patients. The prevalence of NSTEMI was similar in all groups (9%, 13% and 12%, respectively, p=0.281). Measures: Diagnostic performances of HS-cTn and copeptin at presentation were examined according to CPO. The discharge diagnosis was adjudicated by 2 experts, including cTnI. HS-cTn and copeptin were blindly measured. Results: Diagnostic accuracies of cTnI, cTnI+copeptin and HS-cTnT (but not HS-cTnT+copeptin) lower through CPO categories. For patients with CPO<2h, the choice of a threshold value of 14 ng/L for HS-cTnT resulted in 3 false negative (Sensitivity 80% [95%CI: 51-95]; specificity 85% [78-90]; 79% of correctly ruled-out patients) and that of 5 ng/L in 2 false negative ( Sensitivity 87% [59-98]; specificity 58% [50-66]; 52% of correctly ruled-out patients). The addition of copeptin to HS-cTnT induced a decrease of misclassified patients to 1 in patients with CPO<2h (Sensitivity 93% [66-100]; specificity 41% [33-50]). Conclusion: A single measurement of HS-cTn, alone or in combination with copeptin at admission, seems not safe enough for ruling out NSTEMI in very early presenters (with CPO<2h). Trial registrations: French Health Ministry (no. DC-2009-1052), French Local Ethic comity « Comité de Protection des Personnes Ile-de-France » III (Hôpital Cochin) et VI (CHU Pitié-Salpétrière).
Data from: Proportion of women presenters at medical grand rounds at major academic centres in Canada: a retrospective observational study
Objective: To assess the proportion of women who presented research or medical grand rounds at five major academic hospitals in Canada. Design: A cross sectional study. Setting: Five major university–affiliated hospitals in Toronto and Calgary. Results: Overall, at all sites and types of academic rounds, there were an average of 17% fewer women presenting than men (p < 0.001). There were an average of 32% and 21% more men presenting at the city wide grand rounds in City A and B respectively (p < 0.001, p = 0.002). There were more male speakers at 4 out of 5 types of rounds. The proportion of women presenting on average was proportional to the Canadian workforce, but on average, below the proportion of female residents and medical students (median ratio 1.1, 0.7 and 0.8 respectively). Conclusion: Our study demonstrated a lower proportion of females in an important outlet for academic recognition and role modeling. This provides a possible contributing factor to the under representation of women in academic medicine, and an area that can be systematically targeted to promote equity.
Data from: Missed opportunities for earlier diagnosis of HIV in patients that presented with advanced HIV disease: a retrospective cohort study
OBJECTIVE: To quantify and characterize missed opportunities for earlier HIV diagnosis in patients diagnosed with advanced HIV. DESIGN: A retrospective observational cohort study. SETTING: A central tertiary medical center in Israel. MEASURES: The proportion of patients with advanced HIV, the proportion of missed opportunities to diagnose them earlier, and the rate of clinical indicator diseases (CIDs) in those patients RESULTS: Between 2010-2015, 356 patients were diagnosed with HIV, 118 (33.4 %) were diagnosed late, 57 (16%) with advanced HIV disease. Old age (OR=1.45 [95% CI 1.16-1.74]) and being heterosexual (OR=2.65 [95% CI 1.21-5.78]) were significant risk factors for being diagnosed late. All patients with advanced disease had at least one CID that did not lead to an HIV test in the 5 years prior to AIDS diagnosis. The median time between CID and AIDS diagnosis was 24 month (IQR 10-30). 60% of CIDs were missed by a general practitioner and 40% by a specialist. CONCLUSIONS: Missed opportunities to early diagnosis of HIV occur both in primary and secondary care. Lack of national guidelines, lack of knowledge regarding CIDs and communication barriers with patients may contribute to HIV late diagnosis. 'Strengths and limitations of this study' This study shows for the first time rate and reasons for missed opportunities to diagnose HIV in a low prevalence country like Israel. This study may shed light on the reasons why primary care physicians or specialists are missing to diagnose HIV earlier. Nonexistence of clear national guidelines for HIV testing and ignoring HIV clinically indicator diseases are major reasons for missed diagnosis of HIV. This study was carried out in one center and may not reflect the picture in the all country; Also, the total number of patients is low and this may limit generability of the study
Data from: TAPBPR alters MHC class I peptide presentation by functioning as a peptide exchange catalyst
Our understanding of the antigen presentation pathway has recently been enhanced with the identification that the tapasin-related protein TAPBPR is a second MHC I-specific chaperone. We sought to determine whether, like tapasin, TAPBPR can also influence MHC I peptide selection by functioning as a peptide exchange catalyst. We show that TAPBPR can catalyse the dissociation of peptides from peptide-MHC I complexes, enhance the loading of peptide-receptive MHC I molecules, and discriminate between peptides based on affinity in vitro. In cells, the depletion of TAPBPR increased the diversity of peptides presented on MHC I molecules, suggesting that TAPBPR is involved in restricting peptide presentation. Our results suggest TAPBPR binds to MHC I in a peptide-receptive state and, like tapasin, works to enhance peptide optimisation. It is now clear there are two MHC class I specific peptide editors, tapasin and TAPBPR, intimately involved in controlling peptide presentation to the immune system.
Data from: Past and present resource availability affect mating rate but not choice in Drosophila melanogaster
The choices of when, where, and with whom to mate represent some of the most important decisions an individual can make to increase their fitness. Several studies have shown that the resources available to an individual during development can dramatically alter their mating rate later in life, and even the choice of mate. However, an individual's surroundings and available resources can change rapidly, and it is not clear how quickly the redistribution of resources towards reproduction can change. To address this important question, we measured mating rate and mate choice among Drosophila melanogaster males that were manipulated in terms of both past resources (control vs. starvation) and the resources available during mate choice (food vs. no food). We found that males given access to ample resources prior to mate choice showed higher mating rates than those that were starved, in agreement with previous studies. However, we also found that this effect can be reversed quickly, as starved males given the opportunity to mate in a high-quality environment mated at frequencies equivalent to their fed counterparts. While past and present resources affected mating rate, they did not affect mate choice, as males mated with high quality females at high frequencies regardless of their condition and environment. Our results show that both current condition as well as the promise of future resources can dramatically influence individuals' investment into reproduction, and that such mating decisions are extremely plastic and reliant on environmental cues.
Data from: Patients with primary biliary cholangitis and fatigue present with depressive symptoms and selected cognitive deficits, but with normal attention performance and brain structure
Background: In primary biliary cholangitis (PBC) fatigue is a major clinical challenge of unknown etiology. By demonstrating that fatigue in PBC is associated with an impaired cognitive performance, previous studies have pointed out the possibility of brain abnormalities underlying fatigue in PBC. Whether structural brain changes are present in PBC patients with fatigue, however, is unclear. To evaluate the role of structural brain abnormalities in PBC patients severely affected from fatigue we, therefore, performed a case-control cerebral magnetic resonance imaging (cMRI) study and correlated changes of white and grey brain matter with the cognitive and attention performance. Methods: 20 female patients with PBC and 20 female age-matched controls were examined in this study. The assessment of fatigue, psychological symptoms, cognitive and attention performance included clinical questionnaires, established cognition tests and a computerized test battery of attention performance. T1-weighted cMRI and diffusion tensor imaging (DTI) scans were acquired with a 3 Tesla scanner. Structural brain alterations were investigated with voxel-based morphometry (VBM) and DTI analyses. Results were correlated to the cognitive and attention performance. Results: Compared to healthy controls, PBC patients had significantly higher levels of fatigue and associated psychological symptoms. Except for an impairment of verbal fluency, no cognitive or attention deficits were found in the PBC cohort. The VBM and DTI analyses revealed neither major structural brain abnormalities in the PBC cohort nor correlations with the cognitive and attention performance. Conclusions: Despite the high burden of fatigue and selected cognitive deficits, the attention performance of PBC patients appears to be comparable to healthy people. As structural brain alterations do not seem to be present in PBC patients with fatigue, fatigue in PBC must be regarded as purely functional. Future studies should evaluate, whether functional brain changes underlie fatigue in PBC.
Data from: TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway
Recently we revealed that TAPBPR is a peptide exchange catalyst important for optimal peptide selection by MHC class I molecules. Here we asked if any other co-factors associate with TAPBPR which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex, dependent on a conserved cysteine at position 94 in TAPBPR, in which TAPBPR promotes the association of UGT1 with peptide-receptive class I molecules. We reveal that the interaction between TAPBPR and UGT1 facilities the reglucosylation of the glycan on class I, promoting their recognition by calreticulin. Our results suggest that in addition to being a peptide-editor, TAPBPR improves peptide optimisation by promoting peptide-receptive MHC class I molecules to associate with the peptide-loading complex.
Data from: Management of behavioural change in patients presenting with a diagnosis of dementia: a video vignette study with Australian general practitioners
Objective: To test the impact of feedback on the proposed management of standardised patients presenting with behavioural change with a diagnosis of dementia in Australian primary care. Materials and methods: A video vignette study was performed with Australian general practitioners (GPs) in 2013. Participants viewed six pairs of matched videos depicting people presenting changed behaviour in the context of a dementia diagnosis in two phases. In both phases GPs indicated their diagnosis and management. After phase 1, GPs were offered feedback on management strategies for the patients depicted. Analyses focused on identification of change in management between the two phases of the study. Factors impacting on the intention to coordinate care for such patients were tested in a questionnaire based on the Theory of Planned Behaviour. Results: Forty-five GPs completed the study. There was significant improvement in the proposed management of three of the six scenarios after the intervention. Older GPs were more likely to refer appropriately (OR=1.11 (1.01 to 1.23), p=0.04.). Overall referral to support agencies was more likely after the intervention (OR=2.52 (1.53 to 4.14), p<0.001). Older GPs were less likely to intend to coordinate care for such patients (OR=0.89 (0.81 to 0.98) p=0.02). Participants who felt confident about their ability to coordinate care were more likely to do so (OR=3.79 (1.08 to 13.32) p=0.04). Conclusions: The intervention described in this study promoted multidisciplinary management of patients with behavioural problems with a diagnosis of dementia. Increasing practitioner confidence in their ability to coordinate care may increase the proportion of GPs who will respond to patients and carers in this context. Older GPs may benefit in particular.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.