Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding associations of hemodialysis practices with clinical and patient-reported outcomes: examples from the DOPPS

Due to the scarcity of randomized clinical trials (RCTs) in nephrology [1], particularly in dialysis, there has been uncertainty about optimal practices. Using standardized data collection, the Dialysis Outcomes and Practice Patterns Study (DOPPS) has shown very large betweenand within-country differences in hemodialysis (HD) practices and patient outcomes. These observational data are especially useful in areas where results from clinical trials are not yet available or where a randomized design may not be feasible, e.g. for ethical reasons or high cost. Observational studies have influenced medical treatments for many decades, but can result in biased and misleading findings if appropriate statistical methodology is not applied, since treatments are often confounded by clinical indication. For example, we observe that HD patients treated with erythropoietin have lower—not higher—post-treatment hemoglobin levels than patients not treated with this agent because the indication for therapy is a low hemoglobin level [2]. In the DOPPS, a vast amount of information on potential confounders, as well as application of sophisticated statistical techniques, contributes to improve comparability among treatment groups with the intent to yield more robust results. In the following sections, we review selected studies from the DOPPS that have clinical implications for practice at the dialysis facility, and we provide some comments about the reasons for the analytical approaches used.
ATR in Scottish Gaelic Tense Sonorants: A Preliminary Report

In the modern Goidelic languages, there are two classes of sonorants, called “tense” and “lax”. One way the two classes are distinguished is by the quality of the preceding vowel: before the so-called “tense” sonorants, vowels are either lengthened or diphthongized, depending on the vowel and on the dialect. It is not always clear, however, that there is a difference to be found in the sonorants themselves. The phenomenon of vowel diphthongization/lengthening in modern Goidelic languages dates back to their ancestor language, Old Irish. In Old Irish, the coronal sonorants [l], [n] and [r] came in two versions, which correspond to the present day tense/lax contrast. (Historical records are such that the nature of the Old Irish contrast is unknown, though the Scottish Gaelic orthography suggests a geminate/singleton distinction, see Figure 2.) Modern Irish and Scottish Gaelic are closely related branches of Goidelic languages. In both languages, vowel diphthongization is observed; in Scottish Gaelic there is also vowel lengthening before [r]. Examples (Ó Sé 1995) in Table 1 are taken from dialects of Modern Irish, showing the contrast between diphthongization and the lack thereof in vowels in each of the phonological environments. Capital letters are used to transcribe tense sonorants. In Scottish Gaelic, tense and lax sonorants contrast in codas, so for this study we focused on codas; onset distribution is less clear. We also focused only ∗This work was made possible in part by James S. McDonnell Foundation grant #220020045 BBNB to Diana Archangeli. We are also grateful for support from the College of Social and Behavioral Sciences at the University of Arizona, and to Colin Gorrie, Jessamyn Schertz, and Jae Hyun Sung for helpful discussion.
Toroviruses: replication, evolution and comparison with other members of the coronavirus-like superfamily.

General introduction. Based on their morphological and physicochemical characteristics, the Toroviridae were initially proposed to constitute a new family of enveloped RNA viruses (Horzinek & Weiss, 1984; Horzinek et al., 1987). However, recent analysis of the genetic information and replication strategy of the prototype Berne virus (BEV) (Snijder et al., 1988, 1990a, c) has revealed that toroviruses are not unique: they are clearly related to the Coronaviridae and, more distantly, to the arteriviruses (den Boon et al., 1991b). This information has led to the reclassification of the toroviruses as a new genus in the coronavirus family (Pringle, 1992) and to the introduction of the unofficial term ‘coronavirus-like superfamily’ to indicate the evolutionary ties between the three virus groups mentioned above. The history of torovirus research not only illustrates the taxonomic consequences present-day molecular analysis may have; the BEV genome has also turned out to be a showcase for the two driving forces in RNA virus evolution: divergence from a common ancestor and RNA recombination (Snijder et al., 1991a).
Adoption of Electronic Personal Health Records in Canada: Perceptions of Stakeholders.

BACKGROUND Healthcare stakeholders have a great interest in the adoption and use of electronic personal health records (ePHRs) because of the potential benefits associated with them. Little is known, however, about the level of adoption of ePHRs in Canada and there is limited evidence concerning their benefits and implications for the healthcare system. This study aimed to describe the current situation of ePHRs in Canada and explore stakeholder perceptions regarding barriers and facilitators to their adoption. METHODS Using a qualitative descriptive study design, we conducted semi-structured phone interviews between October 2013 and February 2014 with 35 individuals from seven Canadian provinces. The participants represented six stakeholder groups (patients, ePHR administrators, healthcare professionals, organizations interested in health technology development, government agencies, and researchers). A detailed summary of each interview was created and thematic analysis was conducted. RESULTS We observed that there was no consensual definition of ePHR in Canada. Factors that could influence ePHR adoption were related to knowledge (confusion with other electronic medical records [EMRs] and lack of awareness), system design (usability and relevance), user capacities and attitudes (patient health literacy, education and interest, support for professionals), environmental factors (government commitment, targeted populations) and legal and ethical issues (information control and custody, confidentiality, privacy and security). CONCLUSION ePHRs are slowly entering the Canadian healthcare landscape but provinces do not seem well-prepared for the implementation of this type of record. Guidance is needed on critical issues regarding ePHRs, such as ePHR definition, data ownership, access to information and interoperability with other electronic health records (EHRs). Better guidance on these issues would provide a greater awareness of ePHRs and inform stakeholders including clinicians, decision-makers, patients and the public. In turn, it may facilitate their adoption in the country.
Peripheral Endocannabinoids Associated With Energy Expenditure in Native Americans of Southwestern Heritage

Context The endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), as well as the related acylethanolamide oleoylethanolamide (OEA), have been implicated in energy expenditure (EE) regulation and metabolic diseases. Muscle (fat-free mass) and fat (fat mass) are metabolically active compartments and main determinants of EE. Objective To assess whether human muscle, adipose, and plasma endocannabinoids correlate with EE. Design Muscle, adipose, and plasma AEA, 2-AG, and OEA concentrations were measured via liquid chromatography-mass spectrometry. EE was assessed by indirect whole-room calorimetry. Setting Clinical trial. Participants Obese/overweight Native Americans of full (n = 35) and at least half (n = 21) Southwestern heritage. Main Outcome Measures Twenty-four-hour EE, sleeping EE (SLEEP), resting EE (REE), respiratory quotient (RQ), and macronutrient oxidation. Results In full Natives, muscle AEA concentration correlated with SLEEP (r = -0.65, P = 0.004) and REE (r = -0.53, P = 0.02). Muscle 2-AG was associated with SLEEP (r = -0.75, P = 0.0003). Adipose OEA concentration correlated with RQ (r = -0.47, P = 0.04) and lipid oxidation (r = 0.51, P = 0.03). Plasma OEA concentration was associated with SLEEP (r = -0.52, P = 0.04). After adjustment for major determinants, these lipids explained nearly 20% of the additional variance of the respective measure. Similarly, in Native Americans of at least half Southwestern heritage, investigated lipids correlated with EE measures. Conclusion Endocannabinoids in metabolically relevant peripheral tissues explained a large part of EE variation and may be involved in regulating EE. Dysregulation of peripheral endocannabinoids may predispose people to metabolic diseases via an effect on EE and lipid oxidation.
Microstructural Modeling of Hot Spot and Failure Mechanisms in RDX Energetic Aggregates.

Abstract : Hot spot formation and failure mechanisms, such as dynamic fracture and shear strain localization, for RDX (cyclotrimethylene trinitramine)-polymer binder aggregates were investigated for dynamic thermo-mechanical loading conditions. A formulation based on a dislocation-density based crystalline plasticity and a finite viscoelasticity framework was coupled to a microstructurally-based dynamic fracture nucleation and propagation method, and it was used to investigate interrelated high strain-rate failure modes in RDX-polymer binder energetic aggregates. The effects of grain boundary (GB) misorientations, porosity, grain morphologies, dislocation densities, and crystal-binder interactions were coupled with adiabatic plasticity heating, thermal decomposition, thermal conduction, and dissipated heat to predict and understand hot spot formation for a PCTFE (Polychlorotrifluoroethylene) polymer binder. The validated predictions indicate that hot spots were induced by inelastic deformation modes, which resulted in unbounded temperatures due to localized plasticity and thermal decomposition at the peripheries of the voids. Viscous dissipation, due to the estane polymer binder, where the operating temperatures were above the glass transition temperature, resulted in RDX crystal interactions due to hydrostatic compression of the polymer binder. This hydrostatic compression constrained the polymer binder interfaces, which enhanced RDX inelastic deformation modes and resulted in and accelerated hot spot formation at the RDX crystal peripheries in the interfacial regions between the estane binder and the RDX crystals. The effects of dynamic crack nucleation and propagation were also investigated in energetic aggregates subjected to high strain rate loading conditions.
Factorized local appearance models

We propose a novel local appearance modeling method for object detection and recognition in cluttered scenes. The approach is based on the joint distribution of local feature vectors at multiple salient points and factorization with Independent Component Analysis (ICA). The resulting non-parametric densities are simple multiplicative histograms. This leads to computationally tractable joint probability densities which can model high-order dependencies. Testing and evaluation shows that the factorized density model with spatial encoding improves modeling accuracy and outperforms global appearance models in image/object retrieval. Furthermore, experiments in detection of substantially occluded objects in cluttered scenes have demonstrated promising results.
A New Spectrum Sensing Method Using Output Analysis of the PFD

In this brief, a new blind spectrum sensing method is proposed based on frequency comparison using a phase frequency detector (PFD). The PFD output patterns are utilized in a way to sense the spectrum with no knowledge of incoming signals, noise, or channel parameters. The detection and false alarm error probabilities are analytically calculated for additive white Gaussian noise and sine-wave input and are simulated for different inputs. It is shown that the required detection and false alarm probabilities can be achieved by changing the system parameters. The results show that the proposed method has lower complexity and outperforms the previous single-antenna blind method over flat fading channel.
Spatial‐temporal active wave computing using infrared proximity array

In this paper, it is shown that the spatial‐temporal dynamics of the perceived 3D surface using an infrared proximity array gives well‐characterized spatial‐temporal dynamics at the output of the cellular nonlinear network (CNN) wave computer. For practical reasons, the continuous input is a series of consecutive infrared images, which are the consecutive states of the input stream. The spatial‐temporal dynamics of the output can be well characterized by quantitative and qualitative (specific morphology and oscillation frequency) spatial and temporal features. By processing a changing image flow as an input of the CNN wave computer, specific attributes of the input can be identified, which are unidentifiable while processing the still input images individually. Theoretical considerations were experimentally analyzed through template tuning and the depth modality of the measurement setup. Computations are performed on a CNN software simulator interfaced to an infrared proximity array. Copyright © 2012 John Wiley & Sons, Ltd.
Trimethoprim/sulfamethoxazole versus vancomycin in the treatment of healthcare/ventilator-associated MRSA pneumonia: a case–control study

Objectives: Therapeutic options available to treat MRSA pneumonia are limited. Trimethoprim/sulfamethoxazole is an attractive treatment because of its bactericidal anti-MRSA activity, oral and parenteral formulations and good penetration to the lung tissue. We aimed to compare the efficacy and safety of trimethoprim/sulfamethoxazole with vancomycin in the treatment of healthcare/ventilator-associated MRSA pneumonia. Methods: We carried out a retrospective case–control study of all consecutive hospitalized adult patients diagnosed with MRSA pneumonia at Beilinson Hospital during 2010–15 and treated with either vancomycin or trimethoprim/sulfamethoxazole. The primary outcomes were all-cause mortality at 30 days and clinical failure at the end of treatment. In order to reduce bias affecting the decision to use a specific antibiotic and as a sensitivity analysis, a propensity-score model for choosing between vancomycin and trimethoprim/sulfamethoxazole was used. Results: We identified 42 patients with MRSA pneumonia treated with trimethoprim/sulfamethoxazole and 39 treated with vancomycin. There were no significant differences in the baseline characteristics between the groups. Vancomycin-treated patients showed significantly higher 30 day mortality on both multivariate analysis (HR = 5.28; 95% CI = 1.50–18.60; P < 0.05) and sensitivity analysis with propensity score [vancomycin 13/24 (54.1%) versus trimethoprim/sulfamethoxazole 4/24 (16.7%); P < 0.05], and higher clinical failure rates [vancomycin 23/39 (59%) versus trimethoprim/sulfamethoxazole 15/42 (35.7%); P < 0.05], also in the sensitivity analysis with propensity score [vancomycin 14/24 (58.3%) versus trimethoprim/sulfamethoxazole 6/24 (25%); P < 0.05]. The rates of side effects in both arms were comparable. Conclusions: Trimethoprim/sulfamethoxazole appears to be superior to vancomycin in the treatment of MRSA pneumonia. A large-scale randomized controlled trial is needed to evaluate these findings.
The Dutch Pancreas Biobank Within the Parelsnoer Institute: A Nationwide Biobank of Pancreatic and Periampullary Diseases

Objectives Large biobanks with uniform collection of biomaterials and associated clinical data are essential for translational research. The Netherlands has traditionally been well organized in multicenter clinical research on pancreatic diseases, including the nationwide multidisciplinary Dutch Pancreatic Cancer Group and Dutch Pancreatitis Study Group. To enable high-quality translational research on pancreatic and periampullary diseases, these groups established the Dutch Pancreas Biobank. Methods The Dutch Pancreas Biobank is part of the Parelsnoer Institute and involves all 8 Dutch university medical centers and 5 nonacademic hospitals. Adult patients undergoing pancreatic surgery (all indications) are eligible for inclusion. Preoperative blood samples, tumor tissue from resected specimens, pancreatic cyst fluid, and follow-up blood samples are collected. Clinical parameters are collected in conjunction with the mandatory Dutch Pancreatic Cancer Audit. Results Between January 2015 and May 2017, 488 patients were included in the first 5 participating centers: 4 university medical centers and 1 nonacademic hospital. Over 2500 samples were collected: 1308 preoperative blood samples, 864 tissue samples, and 366 follow-up blood samples. Conclusions Prospective collection of biomaterials and associated clinical data has started in the Dutch Pancreas Biobank. Subsequent translational research will aim to improve treatment decisions based on disease characteristics.
Minimally Invasive Transforaminal Lumbar Interbody Fusion: Meta-analysis of the Fusion Rates. What is the Optimal Graft Material?

BACKGROUND Minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF) is an increasingly popular procedure with several potential advantages over traditional open TLIF. OBJECTIVE The current study aimed to compare fusion rates of different graft materials used in MIS-TLIF, via meta-analysis of the published literature. METHODS A Medline search was performed and a database was created including patient's type of graft, clinical outcome, fusion rate, fusion assessment modality, and duration of follow-up. Meta-analysis of the fusion rate was performed using StatsDirect software (StatsDirect Ltd, Cheshire, United Kingdom). RESULTS A total of 1533 patients from 40 series were included. Fusion rates were high, ranging from 91.8% to 99%. The imaging modalities used to assess fusion were computed tomography scans (30%) and X-rays (70%). Comparison of all recombinant human bone morphogenetic protein (rhBMP) series with all non-rhBMP series showed fusion rates of 96.6% and 92.5%, respectively. The lowest fusion rate was seen with isolated use of autologous local bone (91.8%). The highest fusion rate was observed with combination of autologous local bone with bone extender and rhBMP (99.1%). The highest fusion rate without the use of BMP was seen with autologous local bone + bone extender (93.1%). The reported complication rate ranged from 0% to 35.71%. Clinical improvement was observed in all studies. CONCLUSION Fusion rates are generally high with MIS-TLIF regardless of the graft material used. Given the potential complications of iliac bone harvesting and rhBMP, use of other bone graft options for MIS-TLIF is reasonable. The highest fusion rate without the use of rhBMP was seen with autologous local bone plus bone extender (93.1%).
A Selective Glial Barrier at Motor Axon Exit Points Prevents Oligodendrocyte Migration from the Spinal Cord

Nerve roots have specialized transition zones that permit axon extension but limit cell movement between the CNS and PNS. Boundary cap cells prevent motor neuron soma from following their axons into the periphery, thereby contributing to a selective barrier. Transition zones also restrict movement of glial cells. Consequently, axons that cross the CNS–PNS interface are insulated by central and peripheral myelin. The mechanisms that prevent the migratory progenitors of oligodendrocytes and Schwann cells, the myelinating cells of the CNS and PNS, respectively, from crossing transition zones are not known. Here, we show that interactions between myelinating glial cells prevent their movements across the interface. Using in vivo time-lapse imaging in zebrafish we found that, in the absence of Schwann cells, oligodendrocyte progenitors cross ventral root transition zones and myelinate motor axons. These studies reveal that distinct mechanisms regulate the movement of axons, neurons, and glial cells across the CNS–PNS interface.
Contributions of Neuroimaging to Understanding Language Deficits in Acute Stroke

Abstract Advances in structural and functional imaging techniques have provided new insights into our understanding of brain and language relationships. In this article, we review the various structural and functional imaging methods currently used to study language deficits in acute stroke. We also discuss the advantages and the limitations of each imaging modality and the applications of each modality in the clinical and research settings in the study of language deficits.
Adverse Childhood Experiences and Higher-Level Functional Limitations Among Older Japanese People: Results From the JAGES Study

Background A life-course perspective is essential in understanding the determinants of higher-level functional limitations. We examine the impact of adverse childhood experiences (ACEs) on higher-level functional limitations in older people. Methods Data were from the Japan Gerontological Evaluation Study 2013, a population-based cohort of independent people aged 65 years or older across Japan (n = 19,220). ACEs before the age of 18 were assessed in terms of seven adversities: parental death, parental divorce, parental mental illness, family violence, physical abuse, psychological neglect, and psychological abuse. Associations between the cumulative number of ACEs and higher-level functional limitations were investigated by multivariate Poisson regression with robust error variances, adjusted for age, gender, childhood disadvantage, adult sociodemographics, adult health behaviors, and health status. Results Of the older people, 36.3% reported at least one ACE. Older people who had experienced two or more ACEs showed significantly greater higher-level functional limitations than those with no ACE in a crude model (prevalence ratio, PR = 1.61, 95% confidence interval, CI = 1.51-1.71). After adjusting the covariates, this association remained (PR = 1.19, 95% CI = 1.12-1.27). Conclusions ACEs showed robust independent effects on higher-level functional limitations among older Japanese without disabilities, even after adjusting for potential covariates in childhood and adulthood. The current findings may help in understanding the impact of the latent effects of ACEs on functional limitations in older people.