Miracle-dz/UniFAR-FTUs huggingface dataset:
Can the Risks of Cerebrospinal Fluid Leak After Vestibular Schwannoma Surgery Be Predicted?

OBJECTIVE Identifying predictive factors of cerebrospinal fluid (CSF) leak after translabyrinthine approach (TLA) for vestibular schwannoma. DESIGN Retrospective study. SETTING Tertiary care center. PATIENTS All patients (n = 275) operated for a vestibular schwannoma by TLA between 2004 and 2013 were included. INTERVENTION Vestibular schwannoma surgery by TLA. MAIN OUTCOMES AND MEASURES The rate of postoperative CSF leak considering the age, sex, body mass index (BMI), tumor staging, and duration of surgical procedure. A logistic regression model was used to identify the predictors and compute a biometric predictive model of CSF leak. RESULTS Thirty-three patients (12.0%) developed a CSF leak after surgery. In a multivariable model, an increased risk of CSF leak was found for younger patients (OR 0.95, 95% CI 0.92-0.98), longer duration of surgery (OR 1.85, 95% CI 1.12-3.05), and the male sex (0 = male; 1 = female; OR 0.22, 95% CI 0.09-0.54), while also adjusting for BMI. The probability of developing a CSF leak after vestibular schwannoma surgery was calculated using a statistical prediction model, with a percentage of false negative of 7.0% and an overall correct prediction of 88.4%. CONCLUSION The predictors of CSF leak after TLA for vestibular schwannoma are young age, male sex, longer duration of surgery, which adjusting for BMI. In this regard, the surgical team should adapt its management during pre- and postoperative period to decrease the likelihood of a leak.
Reversible LSD1 inhibition with HCI-2509 induces the p53 gene expression signature and disrupts the MYCN signature in high-risk neuroblastoma cells

Lysine-Specific Demethylase 1 (LSD1) over-expression correlates with poorly differentiated neuroblastoma and predicts poor outcome despite multimodal therapy. We have studied the efficacy of reversible and specific LSD1 inhibition with HCI-2509 in neuroblastoma cell lines and particularly the effect of HCI-2509 on the transcriptomic profile in MYCN amplified NGP cells. Cell survival assays show that HCI-2509 is cytotoxic to poorly differentiated neuroblastoma cell lines in low micromole or lower doses. Transcriptional profiling of NGP cells treated with HCI-2509 shows a significant effect on p53, cell cycle, MYCN and hypoxia pathway gene sets. HCI-2509 results in increased histone methyl marks and p53 levels along with cell cycle arrest in the G2/M phase and inhibition of colony formation of NGP cells. Our findings indicate that LSD1 inhibition with HCI-2509 has a multi-target effect in neuroblastoma cell lines, mediated in part via p53. MYCN-amplified neuroblastoma cells have a targeted benefit as HCI-2509 downregulates the MYCN upregulated gene set.
Patient safety in community dementia services: what can we learn from the experiences of caregivers and healthcare professionals?

Objectives this study aims to explore how patient safety in community dementia services is understood by caregivers, and healthcare professionals. Methods cross-sectional analysis of guided one-to-one interviews with 10 caregivers, and 10 healthcare professionals. Results caregivers and healthcare professionals identified a range of issues including medication errors, mis-communication between professionals, unclear service pathways and the effects of stress on caregivers' behaviour. Caregivers and professionals differed in their attitudes to balancing safety with patient autonomy and who is responsible for managing safety. Conclusions this article helps to define the nature of safety issues in the context of community care for people with dementia. In contrast to hospital medicine, where the ideal treatment world is safe with all risks managed or minimised, in dementia some risks are actively taken in the interests of promoting autonomy. Caregivers' views differ from those of health professionals but both parties see potential for collaborative working to manage risk in this context, balancing the promotion of autonomy with the minimisation of potential harm.
Differential microRNA expression in cultured palatal fibroblasts from infants with cleft palate and controls

Background The role of microRNAs (miRNAs) in animal models of palatogenesis has been shown, but only limited research has been carried out in humans. To date, no miRNA expression study on tissues or cells from cleft palate patients has been published. We compared miRNA expression in palatal fibroblasts from cleft palate patients and age-matched controls. Material and Methods Cultured palatal fibroblasts from 10 non-syndromic cleft lip and palate patients (nsCLP; mean age: 18 ± 2 months), 5 non-syndromic cleft palate only patients (nsCPO; mean age: 17 ± 2 months), and 10 controls (mean age: 24 ± 5 months) were analysed with next-generation small RNA sequencing. All subjects are from Western European descent. Sequence reads were bioinformatically processed and the differentially expressed miRNAs were technically validated using quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Results Using RNA sequencing, three miRNAs (hsa-miR-93-5p, hsa-miR-18a-5p, and hsa-miR-92a-3p) were up-regulated and six (hsa-miR-29c-5p, hsa-miR-549a, hsa-miR-3182, hsa-miR-181a-5p, hsa-miR-451a, and hsa-miR-92b-5p) were down-regulated in nsCPO fibroblasts. One miRNA (hsa-miR-505-3p) was down-regulated in nsCLP fibroblasts. Of these, hsa-miR-505-3p, hsa-miR-92a, hsa-miR-181a, and hsa-miR-451a were also differentially expressed using RT-PCR with a higher fold change than in RNAseq. Limitations The small sample size may limit the value of the data. In addition, interpretation of the data is complicated by the fact that biopsy samples are taken after birth, while the origin of the cleft lies in the embryonic period. This, together with possible effects of the culture medium, implies that only cell-autonomous genetic and epigenetic differences might be detected. Conclusions For the first time, we have shown that several miRNAs appear to be dysregulated in palatal fibroblasts from patients with nsCLP and nsCPO. Furthermore, large-scale genomic and expression studies are needed to validate these findings.
deepTools2: a next generation web server for deep-sequencing data analysis

We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg. de. The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.
Extensive hydrogen supersaturations in the western South Atlantic Ocean suggest substantial underestimation of nitrogen fixation

The nitrogen cycle is fundamental to Earth's biogeochemistry. Yet major uncertainties of quantification remain, particularly regarding the global oceanic nitrogen fixation rate. Hydrogen is produced during nitrogen fixation and will become supersaturated in surface waters if there is net release from diazotrophs. Ocean surveys of hydrogen supersaturation thus have the potential to illustrate the spatial and temporal distribution of nitrogen fixation, and to guide the far more onerous but quantitative methods for measuring it. Here we present the first transect of high resolution measurements of hydrogen supersaturations in surface waters along a meridional 10,000 km cruise track through the Atlantic. We compare measured saturations with published measurements of nitrogen fixation rates and also with model-derived values. If the primary source of excess hydrogen is nitrogen fixation and has a hydrogen release ratio similar to Trichodesmium, our hydrogen measurements would point to similar rates of fixation in the North and South Atlantic, roughly consistent with modelled fixation rates but not with measured rates, which are lower in the south. Possible explanations would include any substantial nitrogen fixation by newly discovered diazotrophs, particularly any having a hydrogen release ratio similar to or exceeding that of Trichodesmium; under-sampling of nitrogen fixation south of the equator related to excessive focus on Trichodesmium; and methodological shortcomings of nitrogen fixation techniques that cause a bias towards colonial diazotrophs relative to unicellular forms. Alternatively our data are affected by an unknown hydrogen source that is greater in the southern half of the cruise track than the northern.
Total Variation Regularized Reweighted Sparse Nonnegative Matrix Factorization for Hyperspectral Unmixing

Blind hyperspectral unmixing (HU), which includes the estimation of endmembers and their corresponding fractional abundances, is an important task for hyperspectral analysis. Recently, nonnegative matrix factorization (NMF) and its extensions have been widely used in HU. Unfortunately, most of the NMF-based methods can easily lead to an unsuitable solution, due to the nonconvexity of the NMF model and the influence of noise. To overcome this limitation, we make the best use of the structure of the abundance maps, and propose a new blind HU method named total variation regularized reweighted sparse NMF (TV-RSNMF). First, the abundance matrix is assumed to be sparse, and a weighted sparse regularizer is incorporated into the NMF model. The weights of the weighted sparse regularizer are adaptively updated related to the abundance matrix. Second, the abundance map corresponding to a single fixed endmember should be piecewise smooth. Therefore, the TV regularizer is adopted to capture the piecewise smooth structure of each abundance map. In our multiplicative iterative solution to the proposed TV-RSNMF model, the TV regularizer can be regarded as an abundance map denoising procedure, which improves the robustness of TV-RSNMF to noise. A number of experiments were conducted in both simulated and real-data conditions to illustrate the advantage of the proposed TV-RSNMF method for blind HU.
An Improved Super-Resolution Source Reconstruction Method

The source reconstruction method (SRM) is a technique developed for antenna diagnostics and for carrying out near-field (NF) to far-field (FF) transformation. The SRM is based on the application of the electromagnetic equivalence principle, in which one establishes an equivalent current distribution that radiates the same fields as the actual currents induced in the antenna under test (AUT). The knowledge of the equivalent currents allows the determination of the antenna radiating elements, as well as the prediction of the AUT-radiated fields outside the equivalent currents domain. The unique feature of the novel methodology presented in this paper is that it can resolve equivalent currents that are smaller than half a wavelength in size, thus providing super-resolution. Furthermore, the measurement field samples can be taken at field spacings greater than half a wavelength, thus going beyond the classical sampling criteria. These two distinctive features are possible due to the choice of a model-based parameter estimation methodology where the unknowns are approximated by a continuous basis and, secondly, through the use of the analytic Green's function. The latter condition also guarantees the invertibility of the electric field operator and provides a stable solution for the currents even when evanescent waves are present in the measurements. In addition, the use of the singular value decomposition in the solution of the matrix equations provides the user with a quantitative tool to assess the quality and the quantity of the measured data. Alternatively, the use of the iterative conjugate gradient (CG) method in solving the ill-conditioned matrix equations can also be implemented. Two examples of an antenna diagnostics method are presented to illustrate the applicability and accuracy of the proposed methodology.
Patient experience of primary care and advance care planning: a multicentre cross-sectional study in Japan

Background Advance care planning (ACP) is becoming increasingly important in the primary care setting because of its positive impact on the end-of-life care. Objective We aimed to investigate the relationship between patient experience of primary care and ACP. Methods This cross-sectional study was conducted in 28 primary care clinics in Japan. We assessed patient experience of primary care using a Japanese version of Primary Care Assessment Tool (JPCAT), which comprises six domains: first contact, longitudinality, coordination, comprehensiveness (services available), comprehensiveness (services provided) and community orientation. The primary outcome measures were ACP discussion between patients and primary care providers and completion of advance directives (AD). We used a generalized linear mixed model to adjust clustering within clinics and individual covariates. Results Data were analysed for 535 primary care patients. After adjustment for patients' sociodemographic and health characteristics, the JPCAT total score was found to be significantly associated with ACP discussion [odds ratio (OR) per 1 SD increase = 4.33; 95% confidence interval (CI), 2.53-7.47] but not with completion of AD (OR per 1 SD increase = 1.42; 95% CI, 0.94-2.12). All domains of JPCAT, which represent attributes of primary care, had positive associations with ACP discussion. First contact and comprehensiveness (services provided) domain scores were significantly associated with completion of AD. Conclusions We found that better patient experience of primary care was strongly associated with ACP discussion. Our findings reinforce the significance of patient experience in primary care as part of quality end-of-life care.
Asymmetry in the clockwise and counterclockwise rotation of the bacterial flagellar motor

Cells of Escherichia coli are able to swim up gradients of chemical attractants by modulating the direction of rotation of their flagellar motors, which spin alternately clockwise (CW) and counterclockwise (CCW). Rotation in either direction has been thought to be symmetric and exhibit the same torques and speeds. The relationship between torque and speed is one of the most important measurable characteristics of the motor, used to distinguish specific mechanisms of motor rotation. Previous measurements of the torque–speed relationship have been made with cells lacking the response regulator CheY that spin their motors exclusively CCW. In this case, the torque declines slightly up to an intermediate speed called the “knee speed” after which it falls rapidly to zero. This result is consistent with a “power-stroke” mechanism for torque generation. Here, we measure the torque–speed relationship for cells that express large amounts of CheY and only spin their motors CW. We find that the torque decreases linearly with speed, a result remarkably different from that for CCW rotation. We obtain similar results for wild-type cells by reexamining data collected in previous work. We speculate that CCW rotation might be optimized for runs, with higher speeds increasing the ability of cells to sense spatial gradients, whereas CW rotation might be optimized for tumbles, where the object is to change cell trajectories. But why a linear torque–speed relationship might be optimum for the latter purpose we do not know.
Sensation Seeking and Adaptation in Parabonauts

Evidence from extreme environments suggests that there are relationships between difficulties of adaptation and psychological factors such as personality. In the framework of microgravity research on humans, the aim of this exploratory study was to investigate inter-individual differences of parabonauts on the basis of quality of adaptation to the physical demands of parabolic flights. The personality characteristics of two groups of parabonauts with a different quality of adaptation (an Adaptive group, N = 7, and a Maladaptive group, N = 15) were assessed using the Sensation Seeking Scale, Brief COPE, and MSSQ-Short. Compared to the Maladaptive group, the individuals of the Adaptive group scored higher on Boredom Susceptibility (i.e., a subscale of the Sensation Seeking Scale), lower on scales of susceptibility to motion sickness (MSSQ-Short) and tended to score lower on Instrumental Support Seeking (i.e., a subscale of the Brief COPE). These results suggest that individuals of the Adaptive group are more intolerant to monotony, present an aversion to repetitive and routine activities, are less susceptible to motion sickness and less dependent on problem-focused strategies. These characteristics may have contributed to developing a certain degree of flexibility in these subjects when faced with the parabolic flight situation and thus, may have favored them. The identification of differences of personality characteristics between individuals who have expressed difficulties of adaptation from those who have adapted successfully could help to prevent the risk of maladaptation and improve the well-being of (future) commercial or occupational aerospace passengers. More generally, these results could be extended to extreme environments and professional and/or sports domains likely to involve risk taking and unusual situations.
Estimating One-Year Risk of Incident Chronic Kidney Disease: Retrospective Development and Validation Study Using Electronic Medical Record Data From the State of Maine

Background Chronic kidney disease (CKD) is a major public health concern in the United States with high prevalence, growing incidence, and serious adverse outcomes. Objective We aimed to develop and validate a model to identify patients at risk of receiving a new diagnosis of CKD (incident CKD) during the next 1 year in a general population. Methods The study population consisted of patients who had visited any care facility in the Maine Health Information Exchange network any time between January 1, 2013, and December 31, 2015, and had no history of CKD diagnosis. Two retrospective cohorts of electronic medical records (EMRs) were constructed for model derivation (N=1,310,363) and validation (N=1,430,772). The model was derived using a gradient tree-based boost algorithm to assign a score to each individual that measured the probability of receiving a new diagnosis of CKD from January 1, 2014, to December 31, 2014, based on the preceding 1-year clinical profile. A feature selection process was conducted to reduce the dimension of the data from 14,680 EMR features to 146 as predictors in the final model. Relative risk was calculated by the model to gauge the risk ratio of the individual to population mean of receiving a CKD diagnosis in next 1 year. The model was tested on the validation cohort to predict risk of CKD diagnosis in the period from January 1, 2015, to December 31, 2015, using the preceding 1-year clinical profile. Results The final model had a c-statistic of 0.871 in the validation cohort. It stratified patients into low-risk (score 0-0.005), intermediate-risk (score 0.005-0.05), and high-risk (score ≥ 0.05) levels. The incidence of CKD in the high-risk patient group was 7.94%, 13.7 times higher than the incidence in the overall cohort (0.58%). Survival analysis showed that patients in the 3 risk categories had significantly different CKD outcomes as a function of time (P<.001), indicating an effective classification of patients by the model. Conclusions We developed and validated a model that is able to identify patients at high risk of having CKD in the next 1 year by statistically learning from the EMR-based clinical history in the preceding 1 year. Identification of these patients indicates care opportunities such as monitoring and adopting intervention plans that may benefit the quality of care and outcomes in the long term.
Medication nebulizer performance. Effects of diluent volume, nebulizer flow, and nebulizer brand.

BACKGROUND Medication nebulizers are commonly used to delivery aerosolized medications to patients with respiratory disease. We evaluated output and respirable aerosol available to the patient (inhaled mass) for 17 medication nebulizers using a spontaneous breathing lung model. METHODS Three nebulizer fill volumes (3, 4, and 5 mL containing 2.5 mg of albuterol) and 3 oxygen flows (6, 8, and 10 L/min) were evaluated using the 17 nebulizers. A cotton plug at the nebulizer mouthpiece was used to trap aerosol during simulated spontaneous breathing. Following each trial, the amount of albuterol remaining in the nebulizer and the amount deposited in the cotton plug were determined spectrophotometrically. Aerosol particle size was determined using an 11-stage cascade impactor. RESULTS Increasing fill volume decreased the amount of albuterol trapped in the dead volume (p < 0.001) and increased the amount delivered to the patient (p < 0.001). Increasing flow increased the mass output of particles in the respirable range of 1 to 5 microns (p = 0.004), but the respirable mass delivered to the patient was affected to a greater extent by nebulizer brand (p < 0.001) than flow. Although 2.5 mg of albuterol was placed into the nebulizers, less than 0.5 mg in the respirable range of 1 to 5 microns was delivered to the mouthpiece. CONCLUSIONS The performance of medication nebulizers is affected by fill volume, flow, and nebulizer brand. When they are used for research applications, the nebulizer characteristics must be evaluated and reported for the conditions used in the investigation.
A boundedness criterion for general maximal operators

We consider maximal operators MB with respect to a basis B. In the case when MB satisfies a reversed weak type inequality, we obtain a boundedness criterion for MB on an arbitrary quasiBanach function space X. Being applied to specific B and X this criterion yields new and short proofs of a number of well-known results. Our principal application is related to an open problem on the boundedness of the two-dimensional one-sided maximal function M + on L p.
Seeking Web-Based Information About Attention Deficit Hyperactivity Disorder: Where, What, and When

Background Attention Deficit Hyperactivity Disorder (ADHD) is a common neurodevelopmental disorder, prevalent among 2-10% of the population. Objective The objective of this study was to describe where, what, and when people search online for topics related to ADHD. Methods Data were collected from Microsoft’s Bing search engine and from the community question and answer site, Yahoo Answers. The questions were analyzed based on keywords and using further statistical methods. Results Our results revealed that the Internet indeed constitutes a source of information for people searching the topic of ADHD, and that they search for information mostly about ADHD symptoms. Furthermore, individuals personally affected by the disorder made 2.0 more questions about ADHD compared with others. Questions begin when children reach 2 years of age, with an average age of 5.1 years. Most of the websites searched were not specifically related to ADHD and the timing of searches as well as the query content were different among those prediagnosis compared with postdiagnosis. Conclusions The study results shed light on the features of ADHD-related searches. Thus, they may help improve the Internet as a source of reliable information, and promote improved awareness and knowledge about ADHD as well as quality of life for populations dealing with the complex phenomena of ADHD.