Takshan/R1 huggingface dataset:
Improving quality of life through the routine use of the patient concerns inventory for head and neck cancer patients: a cluster preference randomized controlled trial.

BACKGROUND: The consequences of treatment for Head and Neck cancer (HNC) patients has profound detrimental impacts such as impaired QOL, emotional distress, delayed recovery and frequent use of healthcare. The aim of this trial is to determine if the routine use of the Patients Concerns Inventory (PCI) package in review clinics during the first year following treatment can improve overall quality of life, reduce the social-emotional impact of cancer and reduce levels of distress. Furthermore, we aim to describe the economic costs and benefits of using the PCI. METHODS: This will be a cluster preference randomised control trial with consultants either 'using' or 'not using' the PCI package at clinic. It will involve two centres Leeds and Liverpool. 416 eligible patients from at least 10 consultant clusters are required to show a clinically meaningful difference in the primary outcome. The primary outcome is the percentage of participants with less than good overall quality of life at the final one-year clinic as measured by the University of Washington QOL questionnaire version 4 (UWQOLv4). Secondary outcomes at one-year are the mean social-emotional subscale (UWQOLv4) score, Distress Thermometer (DT) score ≥ 4, and key health economic measures (QALY-EQ-5D-5 L; CSRI). DISCUSSION: This trial will provide knowledge on the effectiveness of a consultation intervention package based around the PCI used at routine follow-up clinics following treatment of head and neck cancer with curative intent. If this intervention is (cost) effective for patients, the next step will be to promote wider use of this approach as standard care in clinical practice. TRIAL REGISTRATION: 32,382. Clinical Trials Identifier, NCT03086629 . PROTOCOL: Version 3.0, 1st July 2017.
Protocol based evaluation for feasibility of extubation compared to clinical scoring systems after major oral cancer surgery safely reduces the need for tracheostomy: a retrospective cohort study.

BACKGROUND: Despite risks, complications and negative impact to quality of life, tracheostomy is widely used to bypass upper airway obstruction after major oral cancer surgery (MOCS). Decision to tracheostomy is frequently based on clinical scoring systems which mainly have not been validated by different cohorts. Delayed extubation in the Intensive Care Unit (ICU) may be a suitable alternative in selected cases. We hypothesize that delayed routine ICU extubation after MOCS instead of scoring system based tracheostomy is safe, feasible and leads to lower tracheostomy rates. METHODS: We retrospectively analyzed our clinical protocol which provides routine extubation of patients after MOCS in the ICU. The primary outcome measure was a composite of early reintubation within 24 h or secondary tracheostomy. Secondary outcome measures included airway obstruction related morbidity and mortality. Predictor variables included tumor localisation, surgical procedure and reconstruction method, length of operation and pre-existing morbidity. Furthermore we assessed the ability of four clinical scoring systems to identify patients requiring secondary tracheostomy. Statistical processing includes basic descriptive statistics, Chi-squared test and multivariate logistic regression analysis. RESULTS: Two hundred thirty four cases were enclosed to this retrospective study. Fourteen patients (6%) required secondary tracheostomy, Ten patients (4%) required reintubation within 24 h after extubation. No airway obstruction associated mortality, morbidity and cannot intubate cannot ventilate situation was observed. Seventy five percent of the patients were extubated within 17 h after ICU admission. All evaluated scores showed a poor positive predictive value (0.08 to 0.18) with a sensitivity ranged from 0.13 to 0.63 and specificity ranged from 0.5 to 0.93. CONCLUSIONS: Our data demonstrate that common clinical scoring systems fail to prevent tracheostomy in patients after MOCS. Application of scoring systems may lead to a higher number of unnecessary tracheostomies. Delayed routine extubation in the ICU after MOCS seems an appropriate and safe approach to avoid tracheostomy and the related morbidity.
Findings of the Chronic Obstructive Pulmonary Disease-Sitting and Exacerbations Trial (COPD-SEAT) in Reducing Sedentary Time Using Wearable and Mobile Technologies With Educational Support: Randomized Controlled Feasibility Trial.

BACKGROUND: Targeting sedentary time post exacerbation may be more relevant than targeting structured exercise for individuals with chronic obstructive pulmonary disease. Focusing interventions on sitting less and moving more after an exacerbation may act as a stepping stone to increase uptake to pulmonary rehabilitation. OBJECTIVE: The aim of this paper was to conduct a randomized trial examining trial feasibility and the acceptability of an education and self-monitoring intervention using wearable technology to reduce sedentary behavior for individuals with chronic obstructive pulmonary disease admitted to hospital for an acute exacerbation. METHODS: Participants were recruited and randomized in hospital into 3 groups, with the intervention lasting 2 weeks post discharge. The Education group received verbal and written information about reducing their time in sedentary behavior, sitting face-to-face with a study researcher. The Education+Feedback group received the same education component along with real-time feedback on their sitting time, stand-ups, and steps at home through a waist-worn inclinometer linked to an app. Patients were shown how to use the technology by the same study researcher. The inclinometer also provided vibration prompts to encourage movement at patient-defined intervals of time. Patients and health care professionals involved in chronic obstructive pulmonary disease exacerbation care were interviewed to investigate trial feasibility and acceptability of trial design and methods. Main quantitative outcomes of trial feasibility were eligibility, uptake, and retention, and for acceptability, were behavioral responses to the vibration prompts. RESULTS: In total, 111 patients were approached with 33 patients recruited (11 Control, 10 Education, and 12 Education+Feedback). Retention at 2-week follow-up was 52% (17/33; n=6 for Control, n=3 for Education, and n=8 for Education+Feedback). No study-related adverse events occurred. Collectively, patients responded to 106 out of 325 vibration prompts from the waist-worn inclinometer (32.62%). Within 5 min of the prompt, 41% of responses occurred, with patients standing for a mean 1.4 (SD 0.8) min and walking for 0.4 (SD 0.3) min (21, SD 11, steps). Interviews indicated that being unwell and overwhelmed after an exacerbation was the main reason for not engaging with the intervention. Health care staff considered reducing sedentary behavior potentially attractive for patients but suggested starting the intervention as an inpatient. CONCLUSIONS: Although the data support that it was feasible to conduct the trial, modifications are needed to improve participant retention. The intervention was acceptable to most patients and health care professionals. TRIAL REGISTRATION: International Standard Randomized Controlled Trial Number (ISRCTN) 13790881; http://www.isrctn.com/ISRCTN13790881 (Archived by WebCite at http://www.webcitation.org/6xmnRGjFf).
A Deep Learning Algorithm for Prediction of Age-Related Eye Disease Study Severity Scale for Age-Related Macular Degeneration from Color Fundus Photography.

PURPOSE: Age-related macular degeneration (AMD) is a common threat to vision. While classification of disease stages is critical to understanding disease risk and progression, several systems based on color fundus photographs are known. Most of these require in-depth and time-consuming analysis of fundus images. Herein, we present an automated computer-based classification algorithm. DESIGN: Algorithm development for AMD classification based on a large collection of color fundus images. Validation is performed on a cross-sectional, population-based study. PARTICIPANTS: We included 120 656 manually graded color fundus images from 3654 Age-Related Eye Disease Study (AREDS) participants. AREDS participants were >55 years of age, and non-AMD sight-threatening diseases were excluded at recruitment. In addition, performance of our algorithm was evaluated in 5555 fundus images from the population-based Kooperative Gesundheitsforschung in der Region Augsburg (KORA; Cooperative Health Research in the Region of Augsburg) study. METHODS: We defined 13 classes (9 AREDS steps, 3 late AMD stages, and 1 for ungradable images) and trained several convolution deep learning architectures. An ensemble of network architectures improved prediction accuracy. An independent dataset was used to evaluate the performance of our algorithm in a population-based study. MAIN OUTCOME MEASURES: κ Statistics and accuracy to evaluate the concordance between predicted and expert human grader classification. RESULTS: A network ensemble of 6 different neural net architectures predicted the 13 classes in the AREDS test set with a quadratic weighted κ of 92% (95% confidence interval, 89%-92%) and an overall accuracy of 63.3%. In the independent KORA dataset, images wrongly classified as AMD were mainly the result of a macular reflex observed in young individuals. By restricting the KORA analysis to individuals >55 years of age and prior exclusion of other retinopathies, the weighted and unweighted κ increased to 50% and 63%, respectively. Importantly, the algorithm detected 84.2% of all fundus images with definite signs of early or late AMD. Overall, 94.3% of healthy fundus images were classified correctly. CONCLUSIONS: Our deep learning algoritm revealed a weighted κ outperforming human graders in the AREDS study and is suitable to classify AMD fundus images in other datasets using individuals >55 years of age.
Combined influence of epoch length, cut-point and bout duration on accelerometry-derived physical activity.

BACKGROUND: It is difficult to compare accelerometer-derived estimates of moderate-to-vigorous physical activity (MVPA) between studies due to differences in data processing procedures. We aimed to evaluate the effects of accelerometer processing options on total and bout-accumulated time spent in MVPA in adults. METHODS: 267 participants from the ProActive Trial provided 1236 days of valid physical activity (PA) data, collected using a 5-s epoch with ActiGraph GT1M accelerometers. We integrated data over 5-s to 60-s epoch lengths (EL) and applied two-level mixed effects regression models to MVPA time, defined using 1500 to 2500 counts/minute (cpm) cut-points (CP) and bout durations (BD) from 1 to 15 min. RESULTS: Total MVPA time was lower on longer EL and higher CP (47 vs 26 min/day and 26 vs 5 min/day on 1500 vs 2500 cpm on 5-s and 60-s epoch, respectively); this could be approximated as MVPA=exp[2.197+0.279*log(CP)+6.120*log(EL) - 0.869*log(CP)*log(EL)] with an 800 min/day wear-time. In contrast, EL was positively associated with time spent in bout-accumulated MVPA; the approximating equation being MVPA=exp[54.679 - 6.268*log(CP)+6.387*log(EL) - 10.000*log(BD) - 0.162*log(EL)*log(BD) - 0.626*log(CP)*log(EL)+1.033*log(CP)*log(BD)]. BD and CP were inversely associated with MVPA, with higher values attenuating the influence of EL. CONCLUSIONS: EL, CP and BD interact to influence estimates of accelerometer-determined MVPA. In general, higher CP and longer BD result in lower MVPA but the direction of association for EL depends on BD. Reporting scaling coefficients for these key parameters across their frequently used ranges would facilitate comparisons of population-level accelerometry estimates of MVPA.
Systems Biology-Derived Biomarkers to Predict Progression of Renal Function Decline in Type 2 Diabetes.

OBJECTIVE: Chronic kidney disease (CKD) in diabetes has a complex molecular and likely multifaceted pathophysiology. We aimed to validate a panel of biomarkers identified using a systems biology approach to predict the individual decline of estimated glomerular filtration rate (eGFR) in a large group of patients with type 2 diabetes and CKD at various stages. RESEARCH DESIGN AND METHODS: We used publicly available "omics" data to develop a molecular process model of CKD in diabetes and identified a representative parsimonious set of nine molecular biomarkers: chitinase 3-like protein 1, growth hormone 1, hepatocyte growth factor, matrix metalloproteinase (MMP) 2, MMP7, MMP8, MMP13, tyrosine kinase, and tumor necrosis factor receptor-1. These biomarkers were measured in baseline serum samples from 1,765 patients recruited into two large clinical trials. eGFR decline was predicted based on molecular markers, clinical risk factors (including baseline eGFR and albuminuria), and both combined, and these predictions were evaluated using mixed linear regression models for longitudinal data. RESULTS: The variability of annual eGFR loss explained by the biomarkers, indicated by the adjusted R(2) value, was 15% and 34% for patients with eGFR ≥60 and <60 mL/min/1.73 m(2), respectively; variability explained by clinical predictors was 20% and 31%, respectively. A combination of molecular and clinical predictors increased the adjusted R(2) to 35% and 64%, respectively. Calibration analysis of marker models showed significant (all P < 0.0001) but largely irrelevant deviations from optimal calibration (calibration-in-the-large: -1.125 and 0.95; calibration slopes: 1.07 and 1.13 in the two groups, respectively). CONCLUSIONS: A small set of serum protein biomarkers identified using a systems biology approach, combined with clinical variables, enhances the prediction of renal function loss over a wide range of baseline eGFR values in patients with type 2 diabetes and CKD.
Blood compatibility of magnesium and its alloys.

RATIONALE: Blood compatibility analysis in the field of biomaterials is a highly controversial topic. Especially for degradable materials like magnesium and its alloys no established test methods are available. OBJECTIVE: The purpose of this study was to apply advanced test methodology for the analysis of degrading materials to get a mechanistic insight into the corrosion process in contact with human blood and plasma. METHODS AND RESULTS: Pure magnesium and two magnesium alloys were analysed in a modified Chandler-Loop setup. Standard clinical parameters were determined, and a thorough analysis of the resulting implant surface chemistry was performed. The contact of the materials to blood evoked an accelerated inflammatory and cell-induced osteoconductive reaction. Corrosion products formed indicate a more realistic, in vivo like situation. CONCLUSIONS: The active regulation of corrosion mechanisms of magnesium alloys by different cell types should be more in the focus of research to bridge the gap between in vitro and in vivo observations and to understand the mechanism of action. This in turn could lead to a better acceptance of these materials for implant applications. STATEMENT OF SIGNIFICANCE: The presented study deals with the first mechanistic insights during whole human blood contact and its influence on a degrading magnesium-based biomaterial. The combination of clinical parameters and corrosion layer analysis has been performed for the first time. It could be of interest due to the intended use of magnesium-based stents and for orthopaedic applications for clinical applications. An interest for the readers of Acta Biomaterialia may be given, as one of the first clinically approved magnesium-based devices is a wound-closure device, which is in direct contact with blood. Moreover, for orthopaedic applications also blood contact is of high interest. Although this is not the focus of the manuscript, it could help to rise awareness for potential future applications.
Stenting the Eustachian tube to treat chronic otitis media - a feasibility study in sheep.

BACKGROUND: Untreated chronic otitis media severely impairs quality of life in affected individuals. Local destruction of the middle ear and subsequent loss of hearing are common sequelae, and currently available treatments provide limited relief. Therefore, the objectives of this study were to evaluate the feasibility of the insertion of a coronary stent from the nasopharynx into the Eustachian tube in-vivo in sheep and to make an initial assessment of its positional stability, tolerance by the animal, and possible tissue reactions. METHODS: Bilateral implantation of bare metal cobalt-chrome coronary stents of two sizes was performed endoscopically in three healthy blackface sheep using a nasopharyngeal approach. The postoperative observation period was three months. RESULTS: Stent implantation into the Eustachian tube was feasible with no intra- or post-operative complications. Health status of the sheep was unaffected. All stents preserved their cylindrical shape. All shorter stents remained in position and ventilated the middle ear even when partially filled with secretion or tissue. One of the long stents became dislocated toward the nasopharynx. Both of the others remained fixed at the isthmus but appeared to be blocked by tissue or secretion. Tissue overgrowth on top of the struts of all stents resulted in closure of the tissue-lumen interface. CONCLUSION: Stenting of the Eustachian tube was successfully transferred from cadaver studies to an in-vivo application without complications. The stent was well tolerated, the middle ears were ventilated, and clearance of the auditory tube appeared possible. For fixation, it seems to be sufficient to place it only in the cartilaginous part of the Eustachian tube.
H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum.

Background: The global demand for affordable carbon has never been stronger, and there is an imperative in many industrial processes to use waste streams to make products. Gas-fermenting acetogens offer a potential solution and several commercial gas fermentation plants are currently under construction. As energy limits acetogen metabolism, supply of H2 should diminish substrate loss to CO2 and facilitate production of reduced and energy-intensive products. However, the effects of H2 supply on CO-grown acetogens have yet to be experimentally quantified under controlled growth conditions. Results: Here, we quantify the effects of H2 supplementation by comparing growth on CO, syngas, and a high-H2 CO gas mix using chemostat cultures of Clostridium autoethanogenum. Cultures were characterised at the molecular level using metabolomics, proteomics, gas analysis, and a genome-scale metabolic model. CO-limited chemostats operated at two steady-state biomass concentrations facilitated co-utilisation of CO and H2. We show that H2 supply strongly impacts carbon distribution with a fourfold reduction in substrate loss as CO2 (61% vs. 17%) and a proportional increase of flux to ethanol (15% vs. 61%). Notably, H2 supplementation lowers the molar acetate/ethanol ratio by fivefold. At the molecular level, quantitative proteome analysis showed no obvious changes leading to these metabolic rearrangements suggesting the involvement of post-translational regulation. Metabolic modelling showed that H2 availability provided reducing power via H2 oxidation and saved redox as cells reduced all the CO2 to formate directly using H2 in the Wood-Ljungdahl pathway. Modelling further indicated that the methylene-THF reductase reaction was ferredoxin reducing under all conditions. In combination with proteomics, modelling also showed that ethanol was synthesised through the acetaldehyde:ferredoxin oxidoreductase (AOR) activity. Conclusions: Our quantitative molecular analysis revealed that H2 drives rearrangements at several layers of metabolism and provides novel links between carbon, energy, and redox metabolism advancing our understanding of energy conservation in acetogens. We conclude that H2 supply can substantially increase the efficiency of gas fermentation and thus the feed gas composition can be considered an important factor in developing gas fermentation-based bioprocesses.
Development of a personalized therapeutic strategy for ERBB-gene-mutated cancers.

Background: The application of genomic technologies to patient tumor samples identified groups of signaling pathways which acquire activating mutations. Some cancers are dependent on these mutations and the aberrant proteins resulting from these mutations can be targeted by novel drugs which can eradicate the cancer. Methods: We used www.cbioportal.org to determine the frequency of ERBB mutations in solid tumors. We then determined the sensitivity of a panel of cell lines to clinically available PI3K inhibitors. Using proliferation and apoptosis assays as well as functional interrogation with reverse phase protein arrays we demonstrated the impact of targeting ERBB-mutant cancers with the combination of a PI3K inhibitor and the pan-HER family inhibitor afatinib. Results: In over 14,000 patients we found that 12% of their tumors have an ERBB family gene mutation (EGFR, ERBB2, ERBB3 and ERBB4). In cancers not commonly associated with HER family protein overexpression, such as ovarian, endometrial, melanoma and head and neck cancers (n = 2116), we found that ERBB family mutations are enriched, occurring at rates from 14% to 34% and commonly co-occur with PIK3CA mutations. Importantly, we demonstrate that ERBB family mutant cancers are sensitive to treatment with PI3K inhibitors. Finally we show that the combination of afatinib and copanlisib represents a novel therapeutic strategy for patients whose cancers harbor both ERBB family and PIK3CA mutation. Conclusions: We demonstrate that ERBB family mutations are common in cancers not associated with overexpression or amplification of HER family proteins. These ERBB family mutant cancers are sensitive to treatment with PI3K inhibitors, and when combined with pan-HER inhibitors have synergistic antiproliferative effects.
Medullary unidentified bright objects in Neurofibromatosis type 1: a case series.

BACKGROUND: In Neurofibromatosis type 1, cerebral Unidentified Bright Objects are a well-known benign entity that has been extensively reported in the literature. In our case series, we wish to focus on a further possible location of such lesions, the spinal cord, which we have defined as medullary Unidentified Bright Objects. These have been, to our knowledge, scarcely described in previous works. CASE PRESENTATION: We report the cases of 7 patients with medullary Unidentified Bright Objects in Neurofibromatosis type 1 that we have followed for up to 9 years in our Regional Referral Center for Neurofibromatosis. In all of our patients, these lesions were completely asymptomatic and reported on Magnetic Resonance exams the patients underwent for other clinical indications. CONCLUSIONS: The aim of our work is to increase awareness of the possibility of medullary Unidentified Bright Objects in Neurofibromatosis type 1 patients, which can simulate neoplastic lesions, suggesting a more conservative approach in these cases.