Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Outcome After Intracranial Pressure Monitoring for Children With Severe Traumatic Brain Injury

Importance Intracranial pressure (ICP) monitoring is a mainstay of therapy for children with traumatic brain injury (TBI), but its overall association with patient outcome is unclear. Objective To test the hypothesis that ICP monitoring is associated with improved functional survival of children with severe TBI. Design, Setting, and Participants A propensity-weighted effectiveness analysis was conducted using 2 linked national databases with data from 30 US children’s hospitals from January 1, 2007, to December 31, 2012, on 3084 children with severe TBI. Clinical events including neurosurgical procedures were identified using validated computable phenotypes. Data analysis was conducted from September 1, 2016, to March 1, 2017. Exposure Placement of an ICP monitor. Main Outcomes and Measures A composite of hospital mortality, discharge to hospice, or survival with placement of new tracheostomy and gastrostomy tubes. Results Of the 3084 children in the study (1128 girls and 1956 boys; mean [SD] age, 7.03 [5.44] years), 1002 (32.4%) underwent ICP monitoring, with substantial hospital variation (6% to 50% by hospital). Overall, 484 children (15.7%) experienced the primary composite outcome. A propensity approach using matching weights generated good covariate balance between those who did and those who did not undergo ICP monitoring. Using a propensity-weighted logistic regression model clustered by hospital, no statistically significant difference was found in functional survival between monitored and unmonitored patients (odds ratio of poor outcome among those who underwent ICP monitoring, 1.31; 95% CI, 0.99-1.74). In a prespecified secondary analysis, no difference in mortality was found (odds ratio, 1.16; 95% CI, 0.89-1.50). Prespecified subgroup analyses of children younger and older than 2 years of age and among those with unintentional and inflicted (intentional) injuries also showed no difference in outcome with ICP monitoring. Conclusions and Relevance With the use of linked national data and validated computable phenotypes, no evidence was found of a benefit from ICP monitoring on functional survival of children with severe TBI. Intracranial pressure monitoring is a widely but inconsistently used technology with incompletely demonstrated effectiveness. A large prospective cohort study or randomized trial is needed.
Examining the Association of Economic Development with Intercity Multimodal Transport Demand in China: A Focus on Spatial Autoregressive Analysis

Transportation is generally perceived as a catalyst for economic development. This has been highlighted in previous studies. However, less attention has been paid to examine the relationship between economy and transport demand by exploring spatially cross-sectional data, especially for countries with significant regional economic imbalance, like China. In this article, we assess the economic influence of intercity multimodal transport demand at the prefecture level in China. Spatial autoregressive regression models are used to examine the impact of transport demand on economy by deep analysis of transport modes (land, air, and water) and regions (eastern, central, and western). Through contrasting results from spatial lag model and spatial error model with those from the ordinary least square, this study finds that the estimation results can become more accurate by controlling for spatial autocorrelation, especially at the national level. Through rigorous analysis it is identified that except for water passenger traffic, all other intercity transport demand significantly contribute to a city’s economic development level in gross domestic product. In particular, air transport demands distribute more evenly and are estimated with the highest beta coefficients at both national and regional levels. In addition, the beta coefficients for land, air and water transportation are estimated with different magnitudes and significances at the national and regional levels. This study contributes to the ongoing discussion on the relationship between intercity multimodal transport demand and economic development level. Findings from this paper provide planning makers with valid and efficient strategies to better develop the economy by leveraging the special “⊣” cluster pattern of economic development and the benefits of air transportation.
Muscle Mechanography: A Novel Method to Measure Muscle Function in Older Adults.

Muscle function decline is a commonly observed process that occurs with aging. Low muscle function, an essential component of sarcopenia, is associated with negative outcomes, including falls, fractures, and dependency. Although many tools have been developed and are used to assess muscle function in older adults, most have important limitations. Muscle mechanography is a novel method that can quantitatively assess muscle function by performing movements such as heel raises, chair rises, or jumps on a ground reaction force plate. It can also assess balance by measuring sway of the center of pressure. Muscle mechanography promises to have advantages over currently used tools, appears to have better reproducibility, and can assess a broader range of physical function-from master athletes to frail individuals. Older adults can safely perform muscle mechanography measurements. Further research is needed to determine whether muscle mechanography can predict outcomes such as falls, fractures, and mortality. [Res Gerontol Nurs. 2017; 10(1):17-24. ].
Breast cytology. Statistical analysis and cytohistologic correlations.

OBJECTIVE To analyze the sensitivity, specificity, positive and negative predictive values and the efficacy of fine needle aspiration (FNA) in our material, to investigate the influence of the histologic type and stage of carcinoma on the quality of the aspirates and on the detection rates of mammary carcinoma, and to investigate the rate of inadequate samples and the accuracy of cytologic diagnoses, with an emphasis on the rate of false positive diagnoses in benign mammary lesions. STUDY DESIGN The results of 1,472 FNAs of the breast obtained over three years were subjected to a retrospective analysis. RESULTS The cytologic diagnoses were benign in 1,003 cases (68.1%), suspicious in 49 (3.3%) and malignant in 181 (12.3%); 239 (16.2%) of the aspirates were inadequate. In 393 (26.6%) of the cases and in 85% of cytologically malignant smears, the aspirate was compared with histologic examination. The rate of false negative FNAs was 9.0%. The proportion of inadequate cases was clearly related to stage (pT): it was 9.5% in pT1, 5.0% in pT2 and 0% in pT3. Among invasive carcinomas the sensitivity was 89.9%, specificity 99.3% and overall accuracy 88.5%. Among the cases diagnosed cytologically as benign, 182 were compared with biopsies. Of these, 79.9% were true negative, 0.5% (1 case) was false positive, and 15.4% had insufficient cells for evaluation. CONCLUSION FNA cytology has improved decision making and the selection of patients for biopsy of mammary lesions and has contributed to saving time in the clinical management of breast lumps. In no case did FNA lead to inadequate clinical measures or other disadvantages to patients. Thus, FNA cytology is an indispensible diagnostic tool in the management of breast lesions.
Robust lysosomal calcium signaling through channel TRPML1 is impaired by lysosomal lipid accumulation

The transient receptor potential cation channel mucolipin 1 (TRPML1) channel is a conduit for lysosomal calcium efflux, and channel activity may be affected by lysosomal contents. The lysosomes of retinal pigmented epithelial (RPE) cells are particularly susceptible to build‐up of lysosomal waste products because they must degrade the outer segments phagocytosed daily from adjacent photoreceptors; incomplete degradation leads to accumulation of lipid waste in lysosomes. This study asks whether stimulation of TRPML1 can release lysosomal calcium in RPE cells and whether such release is affected by lysosomal accumulations. The TRPML agonist ML‐SA1 raised cytoplasmic calcium levels in mouse RPE cells, hesRPE cells, and ARPE‐19 cells; this increase was rapid, robust, reversible, and reproducible. The increase was not altered by extracellular calcium removal or by thapsigargin but was eliminated by lysosomal rupture with glycyl‐l‐phenylalanine‐β‐naphthylamide. Treatment with desipramine to inhibit acid sphingomyelinase or YM201636 to inhibit PIKfyve also reduced the cytoplasmic calcium increase triggered by ML‐SA1, whereas RPE cells from TRPML1−/− mice showed no response to ML‐SA1. Cotreatment with chloroquine and U18666A induced formation of neutral, autofluorescent lipid in RPE lysosomes and decreased lysosomal Ca2+ release. Lysosomal Ca2+ release was also impaired in RPE cells from the ATP‐binding cassette, subfamily A, member 4−/− mouse model of Stargardt's retinal dystrophy. Neither TRPML1 mRNA nor total lysosomal calcium levels were altered in these models, suggesting a more direct effect on the channel. In summary, stimulation of TRPML1 elevates cytoplasmic calcium levels in RPE cells, but this response is reduced by lysosomal accumulation. —Gómez, N. M. , Lu, W. Lim, J. C. , Kiselyov, K. , Campagno, K. E. , Grishchuk, Y. , Slaugenhaupt, S. A. , Pfeffer, B. , Fliesler, S. J., Mitchell, C. H. Robust lysosomal calcium signaling through channel TRPML1 is impaired by lysosomal lipid accumulation. FASEB J. 32, 782–794 (2018). www.fasebj. org
Effect of polymorphic phase transformations within an alumina layer on the ignition of aluminum particles

EFFECT OF POLYMORPHIC PHASE TRANSFORMATIONS WITHIN AN ALUMINA LAYER ON THE IGNITION OF ALUMINUM PARTICLES by Mikhail Aleksiyovych Trunov Experimental measurements of aluminum ignition temperature and models used to describe aluminum ignition are reviewed. It is shown that the current models cannot describe ignition of aluminum powders of different sizes and ignited under various experimental conditions. The properties of and phase changes occurring in the alumina scale existing on the surface of aluminum particles at different temperatures are systematically studied. The mechanism of aluminum oxidation is quantified and a new simplified ignition model is developed. Thermogravimetry was used to study the oxidation of aluminum powders of various particle sizes and surface morphologies in oxygen at temperatures up to 1500 °C. Partially oxidized samples were recovered from selected intermediate temperatures and the oxide phases present were analyzed by x-ray diffraction. Both micronand nanosized aluminum powders were observed to exhibit characteristic stagewise oxidation in the temperature range from 300 to 1500 °C. Kinetic parameters for both direct oxidative growth of alumina scale and phase transformations between different alumina polymorphs were determined from the thermal analysis data for a selected micron-sized powder. The observed oxidation trends for other micronand nano-sized powders were well interpreted considering the established kinetics. Melting of aluminum nanopowders was studied by differential scanning calorimetry in argon environment. No correlation was found between the melting and oxidation. The developed aluminum ignition model describes ignition of a particle inserted in a hot oxygenated gas environment — scenario similar to the particle ignition in a reflected shock in a shock tube experiment. The model treats heterogeneous oxidation as an exothermic process leading to ignition. The ignition is assumed to occur when the particle's temperature exceeds the alumina melting point. The model analyzes processes of simultaneous growth and phase transformations in the oxide scale. Additional assumptions about oxidation rates are made to account for discontinuities produced in the oxide scale as a result of increase in its density caused by the polymorphic phase changes. The model predicts that particles of different sizes ignite at different environment temperatures. Generally, finer particles ignite at lower temperatures. The model consistently interprets a wide range of the previously published experimental data describing aluminum ignition. EFFECT OF POLYMORPHIC PHASE TRANSFORMATIONS WITHIN AN ALUMINA LAYER ON THE IGNITION OF ALUMINUM PARTICLES by Mikhail Aleksiyovych Trunov A Dissertation Submitted to the Faculty of New Jersey Institute of Technology in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Mechanical Engineering Department of Mechanical Engineering
Diapycnal Velocity in the Double-Diffusive Thermocline

A series of large-scale numerical simulations is presented, which incorporate parameterizations of vertical mixing of temperature and salinity by double-diffusion and by small-scale turbulence. These simulations reveal the tendency of double-diffusion to constrain diapycnal volume transport, both upward and downward. For comparable values of mixing coefficients, the average diapycnal velocity in the double-diffusive thermocline is much less than in the corresponding turbulent regime. The insulating effect of double-diffusion is rationalized using two theoretical models. The first argument is based on the assumed vertical advective-diffusive balance. The second theory uses the Rhines and Young technique to evaluate the net diapycnal transport across regions bounded by closed streamlines at a given density surface. The numerical simulations and associated analytical arguments in this study underscore fundamental differences between double-diffusive mixing and mechanically generated small-scale turbulence. When both double-diffusion and turbulence are taken into account, we find that the constraints on diapycnal velocity loosen (tighten) with the increase (decrease) of the fraction of the overall mixing attributed to turbulence. The range of diapycnal velocities that could be realized in doubly-diffusive fluids is determined by the variation in the heat/salt flux ratio. We hypothesize that the unique ability of double-diffusive mixing to actively control diapycnal volume transport may have significant ramifications for the structure and dynamics of thermohaline circulation in the ocean.
Industrial Kiln Drying and its Effect on Microstructure, Impregnation and Properties of Scots Pine Timber Impregnated for Above Ground Use. Part 2. Effect of Drying on Microstructure and Some Mechanical Properties of Scots Pine Wood

Summary Scots pine (Pinus sylvestris L.) planks were dried in industrial progressive, conventional batch and high temperature kilns. The timber was further impregnated in an industrial autoclave with three preservatives used for above ground use. Samples dried by the three test methods and control samples were thereafter processed for scanning electron microscopy observations. Small clear specimens were sawn for determination of impact bending strength, modulus of elasticity and rupture (MOE and MOR) and hardness. The high temperature dried wood (at 115 °C) was characterised by partially damaged apertures in some bordered pits and nano- (10–20 nm) and micro checks (1–2 μm) in the warty and S3 layers of the cell walls. It is probable that certain modifications in the structure of the wood polymer complex also occurred due to hemicellulose thermal degradation. The above-mentioned structural changes facilitated the penetration of the preservative during impregnation and its evacuation during the final stage of vacuum. The industrial progressive and conventional batch kiln drying had no visible effect on the microstructure of Scots pine wood. There was no critical reduction of the impact bending strength, hardness and MOE of the dried untreated wood regardless of the drying method. MOR was significantly decreased after the conventional kiln drying, but not following high temperature drying. Impregnation with Tanalith E and conventional batch kiln drying aggravated the MOE and MOR of the high temperature dried wood, but both MOE and MOR did not differ significantly from those of progressive and conventional batch kiln dried samples.
Abstract Profiles of Structural Stability Point to Universal Tendencies, Family-Specific Factors, and Ancient Connections between Languages

Language is the best example of a cultural evolutionary system, able to retain a phylogenetic signal over many thousands of years. The temporal stability (conservatism) of basic vocabulary is relatively well understood, but the stability of the structural properties of language (phonology, morphology, syntax) is still unclear. Here we report an extensive Bayesian phylogenetic investigation of the structural stability of numerous features across many language families and we introduce a novel method for analyzing the relationships between the “stability profiles” of language families. We found that there is a strong universal component across language families, suggesting the existence of universal linguistic, cognitive and genetic constraints. Against this background, however, each language family has a distinct stability profile, and these profiles cluster by geographic area and likely deep genealogical relationships. These stability profiles seem to show, for example, the ancient historical relationships between the Siberian and American language families, presumed to be separated by at least 12,000 years, and possible connections between the Eurasian families. We also found preliminary support for the punctuated evolution of structural features of language across families, types of features and geographic areas. Thus, such higher-level properties of language seen as an evolutionary system might allow the investigation of ancient connections between languages and shed light on the peopling of the world.
Fine Needle Aspiration of Chromophobe Renal Cell Carcinoma

OBJECTIVE To describe the cytomorphologic findings of chromophobe renal cell carcinoma (CRCC) in order to preoperatively distinguish this rare neoplasm from other primary or secondary tumors arising from the kidney or presenting as retroperitoneal masses. STUDY DESIGN Clinical data, fine needle aspiration (FNA) and follow-up surgical specimens from 4 patients with CRCC (3 primaries and 1 metastatic to the liver) were reviewed. Electron microscopy was available for 2 histologic specimens. RESULTS Two tumors (1 primary and 1 metastatic case) were readily identified as CRCC on FNA. The 2 remaining cases were diagnosed as renal cell carcinoma (RCC) consistent with CRCC. All tumors showed aspirates with moderate to high cellularity, with the cells arranged in small clusters and single cells. Neoplastic cells had abundant heterogeneous cytoplasm, a thickened cell membrane, nuclear hyperchromasia, nuclear outline irregularity, significant nuclear size variation, intranuclear inclusions and frequent binucleation. Histology of the 4 renal tumors was characteristic of CRCC, with positivity for Hale's colloidal iron in all cases. Ultrastructurally, characteristic cytoplasmic microvesicles were observed in the 2 cases that we studied. CONCLUSION In the adequate clinicoradiologic setting, CRCC has distinctive cytologic features that may allow an accurate preoperative FNA diagnosis.
Epistasis Underlying a Fitness Trait Within a Natural Population of the Pitcher-Plant Mosquito, Wyeomyia smithii

We selected on divergent photoperiodic response in three separate lines from a natural population of the pitcher-plant mosquito, Wyeomyia smithii. Line crosses reveal that there exists within a population, diverse epistatic variation for a fitness trait that could contribute to adaptive potential following founder events or rapid climate change.
Overlapping community detection at scale: a nonnegative matrix factorization approach

Network communities represent basic structures for understanding the organization of real-world networks. A community (also referred to as a module or a cluster) is typically thought of as a group of nodes with more connections amongst its members than between its members and the remainder of the network. Communities in networks also overlap as nodes belong to multiple clusters at once. Due to the difficulties in evaluating the detected communities and the lack of scalable algorithms, the task of overlapping community detection in large networks largely remains an open problem. In this paper we present BIGCLAM (Cluster Affiliation Model for Big Networks), an overlapping community detection method that scales to large networks of millions of nodes and edges. We build on a novel observation that overlaps between communities are densely connected. This is in sharp contrast with present community detection methods which implicitly assume that overlaps between communities are sparsely connected and thus cannot properly extract overlapping communities in networks. In this paper, we develop a model-based community detection algorithm that can detect densely overlapping, hierarchically nested as well as non-overlapping communities in massive networks. We evaluate our algorithm on 6 large social, collaboration and information networks with ground-truth community information. Experiments show state of the art performance both in terms of the quality of detected communities as well as in speed and scalability of our algorithm.
Structural Basis of Biological NO Generation by Octaheme Oxidoreductases*

Background: Multiheme proteins have crucial roles in diverse nitrogen cycle processes. Results: The kustc1061 octaheme protein from anaerobic ammonium-oxidizing (anammox) bacteria specifically oxidizes hydroxylamine to NO. Conclusion: Enzyme specificity derives from subtle amino acid changes near the P460 catalytic heme. Significance: The presence of kustc1061 homologs in anammox and other bacteria enables the detoxification of hydroxylamine, thereby generating NO for respiratory purposes. Nitric oxide is an important molecule in all domains of life with significant biological functions in both pro- and eukaryotes. Anaerobic ammonium-oxidizing (anammox) bacteria that contribute substantially to the release of fixed nitrogen into the atmosphere use the oxidizing power of NO to activate inert ammonium into hydrazine (N2H4). Here, we describe an enzyme from the anammox bacterium Kuenenia stuttgartiensis that uses a novel pathway to make NO from hydroxylamine. This new enzyme is related to octaheme hydroxylamine oxidoreductase, a key protein in aerobic ammonium-oxidizing bacteria. By a multiphasic approach including the determination of the crystal structure of the K. stuttgartiensis enzyme at 1.8 Å resolution and refinement and reassessment of the hydroxylamine oxidoreductase structure from Nitrosomonas europaea, both in the presence and absence of their substrates, we propose a model for NO formation by the K. stuttgartiensis enzyme. Our results expand the understanding of the functions that the widespread family of octaheme proteins have.
Loneliness and depressive symptoms: the moderating role of the transition into retirement

ABSTRACT Objectives: The transition to retirement implies significant changes in daily routine and in the social environment. More specifically, it requires more self-directed efforts in order to stay socially engaged. Hence, for those who suffer from loneliness, the transition to retirement could result in increased depressive symptoms due to the lack of structured daily routine. Methods: We used two waves of the Health and Retirement Study, and tested whether the transition to retirement between the two waves moderates the effects of loneliness on depressive symptoms. Results: The transition to retirement moderated the effect of loneliness in wave 1 on depressive symptoms in wave 2, such that for those who retired, the effect was stronger in comparison to those who stayed employed. Conclusions: Although many manage to easily transition into retirement, lonely older workers are at increased risk for maladjustment and the experience of depressive symptoms following retirement. This group could perhaps benefit from interventions aimed at increasing daily social interactions and establishing a socially satisfying routine.