bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal association of neuropsychological test performance using unsupervised learning reveals a distinct signature of Alzheimer's disease status
Authors: Joshi Prajakta S. , Heydari Megan , Kannan Shruti , Alvin Ang Ting Fang , Qin Qiuyuan , Liu Xue , Mez Jesse , Devine Sherral , Au Rhoda , Kolachalama Vijaya B. 
Published: December 2019

AbstractIntroductionSubtle cognitive alterations that precede clinical evidence of cognitive impairment may help predict the progression to Alzheimer's disease (AD). Neuropsychological (NP) testing is an attractive modality for screening early evidence of AD.MethodsLongitudinal NP and demographic data from the Framingham Heart Study (FHS; N = 1696) and the National Alzheimer's Coordinating Center (NACC; N = 689) were analyzed using an unsupervised machine learning framework. Features, including age, logical memory‐immediate and delayed recall, visual reproduction‐immediate and delayed recall, the Boston naming tests, and Trails B, were identified using feature selection, and processed further to predict the risk of development of AD.ResultsOur model yielded 83.07 ± 3.52% accuracy in FHS and 87.57 ± 1.19% accuracy in NACC, 80.52 ± 3.93%, 86.74 ± 1.63% sensitivity in FHS and NACC respectively, and 85.63 ± 4.71%, 88.41 ± 1.38% specificity in FHS and NACC, respectively.DiscussionOur results suggest that a subset of NP tests, when analyzed using unsupervised machine learning, may help distinguish between high‐ and low‐risk individuals in the context of subsequent development of AD within 5 years. This approach could be a viable option for early AD screening in clinical practice and clinical trials.
Projected Changes to Extreme Precipitation Along North American West Coast From the CESM Large Ensemble
Authors: Ma Weiming , Norris Jesse , Chen Gang 
Published: December 2019

AbstractPrecipitation events along the North American (NA) west coast are strongly modulated by atmospheric rivers, yet the mechanisms of their influences on the probability distributions of precipitation events are not well studied. Simulations from the Community Earth System Model (CESM) large ensemble under global warming are investigated using a moisture budget conditioned onto precipitation events for the recurrence intervals ranging from 0.1 to 50 years. In the midlatitudes, the increases in precipitation intensity and accumulation for all events over the NA west coast are predominantly controlled by moisture increases. In contrast, changes in the subtropical precipitation distributions in southwestern NA are associated with moisture increases and duration decreases for all events, with additional dynamical amplification for the heaviest precipitation events. These interpretations from the conditional moisture budget are more consistent with future projection of atmospheric rivers than the conventional mean and transient decomposition of the moisture budget.
Multiharmonic Toroidal Standing Alfvén Waves in the Midnight Sector Observed During a Geomagnetically Quiet Period
Authors: Takahashi Kazue , Vellante Massimo , Del Corpo Alfredo , Claudepierre Seth G. , Kletzing Craig , Wygant John , Koga Kiyokazu 
Published: December 2019

AbstractExcitation of toroidal mode standing Alfvén waves in the midnight sector of the inner magnetosphere in association with substorms is well documented, but studies are sparse on dayside sources for the waves. This paper reports observation of midnight toroidal waves by the Van Allen Probe B spacecraft during a geomagnetically quiet period on 12–13 May 2013. The spacecraft detected toroidal waves excited at odd harmonics below 30 mHz as it moved within the plasmasphere from
2100 magnetic local time to
0030 magnetic local time through midnight in the dipole
range 4.2–6.1. The frequencies and the relationship between the electric and magnetic field components of the waves are consistent with theoretical toroidal waves for a reflecting ionosphere. At the time of the nightside toroidal waves, compressional waves were observed by geostationary satellites located on the dayside, and the amplitudes of both types of waves varied with the cone angle of the interplanetary magnetic field. The nightside toroidal waves were likely driven by fast mode waves that resulted from transmission of upstream ultralow frequency waves into the magnetosphere. Ground magnetometers located near the footprint of the spacecraft did not detect toroidal waves.
Deformation of Granular Aggregates: Static and Dynamic Bulk Moduli
Authors: Muqtadir Arqam , Al‐Dughaimi Saud , Dvorkin Jack 
Published: December 2019

AbstractSand and glass bead samples were monotonically loaded from 0 to 50 MPa and then monotonically unloaded, all under hydrostatic stress conditions. Sand deformed irreversibly and its porosity loss was permanent. In contrast, the glass bead deformation was almost fully reversible with the initial porosity recovered. During loading, the static bulk modulus in all sand samples increased from 0 to about 0.5 GPa between 0‐ and 15‐MPa stress and remained constant for the remainder of the loading. Such behavior, somewhat unexpected in a granular system, means that sand deforms as a linear elastic body during loading from 15 to 50 MPa. The unloading behavior was very different—the static bulk modulus almost linearly decreased from about 4 GPa at 50 MPa to zero as the stress was reduced. Once again, this behavior was very different from that observed in glass beads, where the static bulk modulus during loading was essentially the same as during unloading and appeared to be a unique function of stress, independent of the direction of its variation. Moreover, the static and dynamic bulk moduli in glass beads, the latter computed from Vp, Vs, and density measured during the loading/unloading cycle, were very close to each other. In contrast, the dynamic bulk modulus in dry sand exceeded the static modulus during unloading by a factor of 1.5 to 2.0. We used a quantitative theory based on contact mechanics and the concept of stress heterogeneity in particulates to analytically match the observed results.
Larval Fish Habitats and Deoxygenation in the Northern Limit of the Oxygen Minimum Zone off Mexico
Authors: Sánchez‐Velasco Laura , Godínez Víctor M. , Ruvalcaba‐Aroche Erick D. , Márquez‐Artavia Amaru , Beier Emilio , Barton Eric D. , Jiménez‐Rosenberg S. Patricia A. 
Published: December 2019

AbstractThe present state of deoxygenation in the northern limits of the shallow oxygen minimum zone off Mexico is examined in order to detect its effects on larval fish habitats and consider the sensitivity of fish larvae to decreased dissolved oxygen. A series of cruises between 2000 and 2017 indicated a significant vertical expansion of low oxygen waters. The upper limit of suboxic conditions (<4.4 μmol/kg) has risen ~100 m at 19.5°N off Cabo Corrientes and ~50 m at 25°N in the mouth of the Gulf of California. The larval habitat distribution was related to the geographic variability of dissolved oxygen and water masses between these two latitudes. One recurrent larval habitat, with Bregmaceros bathymaster larvae as the indicator species, extended throughout the water column off Cabo Corrientes from Subtropical Subsurface Water (suboxic conditions) to the surface (220 μmol/kg). The second recurrent habitat was located between the oxycline (>44 μmol/kg) and the surface in association with the Gulf of California Water, with Benthosema panamense as the indicator species. During the warm El Niño event of 2015–2016, a tropical larval fish habitat (Auxis spp.) associated with Tropical Surface Water appeared to change the larval habitat distributions. These results indicate that some species are resilient to changes of dissolved oxygen and temperature generated by El Niño events and by continuing deoxygenation, although other species with more limited environmental windows could be affected by deoxygenation, probably leading to a change of the pelagic ecosystem over time.
Wave Period and Grain Size Controls on Short‐Wave Suspended Sediment Transport Under Shoaling and Breaking Waves
Authors: Christensen Drude F. , Hughes Michael G. , Aagaard Troels 
Published: December 2019

AbstractBeach recovery is key to the continued existence of sandy beaches and is typically driven by the onshore‐directed transport of sediment by short waves during low‐moderate energy conditions. The physical processes governing beach recovery are not well understood, but the theoretically developed dimensionless fall velocity, Ω = H/wsT, was suggested to be important for separating onshore/offshore sediment motion (Dean, 1973). In this paper, the effect of wave period and sediment grain size on short‐wave suspended sediment flux was investigated based on field measurements obtained beneath shoaling and breaking waves at Durras and Vejers beaches. The efficiency of the breaking waves in transporting suspended sediment onshore was roughly the same for the two beaches, despite the wave periods being larger and the mean sediment grain size coarser at Durras beach. The flux efficiencies were, however, shown to be degraded by wave‐current interactions and long/short‐wave interactions at Durras beach, especially. Excluding time series of strong undertow velocities (< −0.1 m/s) and infragravity wave‐energy (>5 m2/s3) resulted in significantly larger flux efficiencies beneath breaking waves at Durras beach compared to Vejers beach. These results indicate that wave‐current interactions and long/short‐wave interactions should be taken into consideration along with the wave period and mean grain size when estimating short‐wave suspended sediment fluxes. The results also showed that plunging breakers were more efficient in suspending sediment and transporting it onshore compared to spilling breakers/surf bores. This finding suggests that wave breaker type also is an important parameter to incorporate when modeling beach recovery.
Two Improvements to Gardner's Method of Measuring the Hydraulic Conductivity of Non‐saturated Media: Accounting for Impedance Effects and Non‐constant Imposed Suction Increment
Authors: Stanić Filip , Delage Pierre , Cui Yu‐Jun , De Laure Emmanuel , Versini Pierre‐Antoine , Schertzer Daniel , Tchiguirinskaia Ioulia 
Published: December 2019

AbstractGardner's (1956, https://doi.org/10.2136/sssaj1956.03615995002000030006x) transient method of measuring the hydraulic conductivity function of unsaturated media has been largely used, together with the improved graphical method proposed by Kunze and Kirkham (1962, https://doi.org/10.2136/sssaj1962.03615995002600050006x) to account for the impedance effect resulting from using a low hydraulic conductivity ceramic disk in porous plate testing. These methods are nowadays seldom used, since they have been replaced by numerical back analysis and methods for parameter optimization. Based on tests carried out on a specific device allowing to determine the water retention and transport properties of water in a coarse granular media at low suctions (up to 50 kPa), it was found necessary to account (i) for impedance effects and (ii) for the effects of nonconstant suction increments, as is often the case when using the hanging column technique. A new method is proposed to account for impedance effects, based on an analytical solution of the equations governing water transfer. The validity of this method is tested by considering experimental data from three distinct materials: a coarse green roof volcanic substrate, poorly graded sand, and undisturbed silty clay. Compared to the graphical method Kunze and Kirkham's method, it is less operator‐dependent and hence more objective. It is also simpler than numerical back analysis methods, since it does not require any use of numerical code or parameter optimization algorithm, providing a more direct and reliable access to the hydraulic conductivity. An analytical solution is also proposed to solve the problem resulting from the application of a nonconstant suction increment.
Gender Surgery Beyond Chest and Genitals: Current Insurance Landscape
Authors: Ngaage Ledibabari M , McGlone Katie L , Xue Shan , Knighton Brooks J , Benzel Caroline A , Rada Erin M , Coon Devin , Berli Jens , Rasko Yvonne M 
Published: December 2019

Abstract

Background
Plastic surgery plays an essential role in the treatment of gender dysphoria. International standards of care currently consider genital and chest surgeries to be medically necessary. Ancillary procedures such as facial surgery, chondrolaryngoplasty, hair restoration/removal, and body contouring are considered cosmetic surgeries except in individual circumstances.

Objective
The authors sought to assess the frequency of coverage provision for ancillary transition-related surgeries through a cross-sectional analysis of US insurance policies.

Methods
The authors selected insurance companies based on state enrollment data and market share. Policies were identified through web-based search and telephone interviews. A list of eligible procedures was compiled and grouped into 5 categories: body masculinization, body feminization, facial procedures, hair restoration/removal, and chondrolaryngoplasty. Medical necessity criteria from publicly accessible policies were then abstracted.

Results
Sixty-one insurance companies held an established policy. One-third of these policies offered favorable coverage for at least 1 ancillary procedure. Chondrolaryngoplasty was the most covered category (26%, n = 16), whereas body masculinization was the least covered (8%, n = 5). Almost two-thirds of the companies with favorable policies listed coverage criteria. We identified 4 recurring requirements: age, hormone therapy, continuous living in a congruent gender role, and referral from a mental health professional.

Conclusions
There is a low prevalence of US insurance coverage for ancillary gender surgeries and wide variability in coverage criteria. Reevaluation of ancillary transition-related procedures from cosmetic to medically necessary based on clinical judgement or establishment of defined coverage criteria may augment coverage and better address the needs of transgender patients.
Bringing data from curated pathway resources to Cytoscape with OmniPath
Authors: Ceccarelli Francesco , Turei Denes , Gabor Attila , Saez-Rodriguez Julio 
Published: December 2019

Abstract

Summary
Multiple databases provide valuable information about curated pathways and other resources that can be used to build and analyze networks. OmniPath combines 61 (and continuously growing) network resources into a comprehensive collection, with over 120 000 interactions. We present here the OmniPath App, a Cytoscape plugin to flexibly import data from OmniPath via a simple and intuitive interface. Thus, it makes possible to directly access the large body of high-quality knowledge provided by OmniPath within Cytoscape for inspection and further use with other tools.

Availability and implementation
The OmniPath App has been developed for Cytoscape 3 in the Java programing language. The latest source code and the plugin can be found at: https://github.com/saezlab/Omnipath_Cytoscape and http://apps.cytoscape.org/apps/omnipath, respectively.

Supplementary information
Supplementary data are available at Bioinformatics online.
Histological Markers of Clinical Relapse in Endoscopically Quiescent Ulcerative Colitis
Authors: Kevans David , Kirsch Richard , Dargavel Callum , Kabakchiev Boyko , Riddell Robert , Silverberg Mark S 
Published: December 2019

Abstract

Background
In ulcerative colitis (UC) patients who have achieved mucosal healing, active microscopic colonic mucosal inflammation is commonly observed. We aimed to assess the association between histological activity and disease relapse in endoscopically quiescent UC.

Methods
Ulcerative colitis patients with endoscopically quiescent disease and ≥12 months of follow-up were included. Biopsies were reviewed for the presence of basal plasmacytosis (BPC) and active histological inflammation, defined as a Geboes score (GS) ≥3.2. Primary outcome measures were disease relapse at 18 months and time to first relapse after index colonoscopy.

Results
Seventy-six UC patients (51% male; mean age, 38.6 years; median follow-up [range], 75.2 [2–118] months) were included. Sixty-two percent had an endoscopic Mayo score of 0 at index colonoscopy. Basal plasmacytosis was present in 46% and active histological inflammation in 30% of subjects. Presence of BPC was associated with a significantly shorter time to disease relapse (P = 0.01). Active histological inflammation was significantly associated with clinical relapse at 18 months (P = 0.0005) and shorter time to clinical relapse (P = 0.0006). Multivariate analysis demonstrated active histological inflammation to be independently associated with clinical relapse at 18 months and time to clinical relapse.

Conclusions
In endoscopically quiescent UC, active histological inflammation and the presence of BPC are adjunctive histological markers associated with increased likelihood of disease relapse. Although prospective studies are required, the presence of these histological markers should be a factor considered when making therapeutic decisions in UC.
Variation in Tick Load Among Bird Body Parts: Implications for Studying the Role of Birds in the Ecology and Epidemiology of Tick-Borne Diseases
Authors: Roselli Megan A , Cady Samantha M , Lao Sirena , Noden Bruce H , Loss Scott R 
Published: December 2019

Abstract
Wild birds play important roles in the maintenance and dispersal of tick populations and tick-borne pathogens, yet in field studies of tick-borne disease ecology and epidemiology there is limited standardization of how birds are searched for ticks. We conducted a qualitative literature review of 100 field studies where birds were searched for ticks to characterize which parts of a bird’s anatomy are typically sampled. To increase understanding of potential biases associated with different sampling approaches, we described variation in tick loads among bird body parts using field-collected data from 459 wild-caught birds that were searched across the entire body. The literature review illustrated a lack of clarity and consistency in tick-searching protocols: 57% of studies did not explicitly report whether entire birds or only particular body parts were searched, 34% reported concentrating searches on certain body parts (most frequently the head only), and only 9% explicitly reported searching the entire bird. Based on field-collected data, only 22% of ticks were found on the head, indicating that studies focusing on the head likely miss a large proportion of ticks. We provide tentative evidence that feeding locations may vary among tick species; 89% of Amblyomma americanum, 73% of Ambloyomma maculatum, and 56% of Haemaphysalis leporispalustris were on body parts other than the head. Our findings indicate a need for clear reporting and increased standardization of tick searching methodologies, including sampling the entire bird body, to provide an unbiased understanding of the role of birds in the maintenance and emergence of tick-borne pathogens.
Supporting National Forest System Planning with Forest Inventory and Analysis Data
Authors: Wurtzebach Zachary , DeRose R Justin , Bush Renate R , Goeking Sara A , Healey Sean , Menlove Jim , Pelz Kristen A , Schultz Courtney , Shaw John D , Witt Chris 
Published: December 2019

AbstractIn 2012, the US Forest Service promulgated new regulations for land-management planning that emphasize the importance of scientifically credible assessment and monitoring strategies for adaptive forest planning and the maintenance or restoration of ecological integrity. However, in an era of declining budgets, the implementation of robust assessment and monitoring strategies represents a significant challenge for fulfilling the intent of the new planning rule. In this article, we explore opportunities for using data and products produced by the USDA Forest Service’s Forest Inventory and Analysis (FIA) Program to support the implementation of the 2012 Planning Rule. FIA maintains a nationally consistent statistical sample of field plots that covers most national forests with hundreds of plots. We suggest that leveraging FIA data and products can generate efficiencies for assessment, planning, and monitoring requirements detailed in the 2012 Planning Rule, and help fulfill the adaptive intent of the new planning rule. However, strong national leadership and investment in regional-level analytical capacity, FIA liaisons, and decision-support tools are essential for systematically realizing the benefits of FIA data for forest planning across the National Forest System.
Promoting Sustainability in Public Natural-Resource Agencies: Insights from the USDA Forest Service
Authors: Ma Zhao , Steele Diana , Cutler Aurora , Newcomb Katie 
Published: December 2019

AbstractHow employees think about and act upon sustainability is important for public natural-resource agencies. We analyzed survey data from 8,875 USDA Forest Service employees to assess their knowledge, attitudes, behaviors, and perceived opportunities and constraints for promoting broadly defined sustainability. Most survey respondents considered promoting sustainability important to Forest Service’s work, particularly to on-the-ground natural-resource management and planning. They recognized the interconnectedness between promoting sustainability and addressing climate change, and viewed it important to incorporate sustainability into what they were doing rather than developing new initiatives. These results highlight an opportunity for promoting sustainability as a unifying framework for Forest Service’s diverse work. To do so requires the cultivation of an agency-wide shared vision of the interconnectedness between sustainability, climate change, and the management and conservation of natural resources. This further requires efforts to enhance leadership commitment, sustainability-oriented social norms, and mechanisms for peer-to-peer exchange, learning, and support.
Efficacy evaluation of 2D, 3D U-Net semantic segmentation and atlas-based segmentation of normal lungs excluding the trachea and main bronchi
Authors: Nemoto Takafumi , Futakami Natsumi , Yagi Masamichi , Kumabe Atsuhiro , Takeda Atsuya , Kunieda Etsuo , Shigematsu Naoyuki 
Published: December 2019

ABSTRACT
This study aimed to examine the efficacy of semantic segmentation implemented by deep learning and to confirm whether this method is more effective than a commercially dominant auto-segmentation tool with regards to delineating normal lung excluding the trachea and main bronchi. A total of 232 non-small-cell lung cancer cases were examined. The computed tomography (CT) images of these cases were converted from Digital Imaging and Communications in Medicine (DICOM) Radiation Therapy (RT) formats to arrays of 32 × 128 × 128 voxels and input into both 2D and 3D U-Net, which are deep learning networks for semantic segmentation. The number of training, validation and test sets were 160, 40 and 32, respectively. Dice similarity coefficients (DSCs) of the test set were evaluated employing Smart SegmentationⓇ Knowledge Based Contouring (Smart segmentation is an atlas-based segmentation tool), as well as the 2D and 3D U-Net. The mean DSCs of the test set were 0.964 [95% confidence interval (CI), 0.960–0.968], 0.990 (95% CI, 0.989–0.992) and 0.990 (95% CI, 0.989–0.991) with Smart segmentation, 2D and 3D U-Net, respectively. Compared with Smart segmentation, both U-Nets presented significantly higher DSCs by the Wilcoxon signed-rank test (P &lt; 0.01). There was no difference in mean DSC between the 2D and 3D U-Net systems. The newly-devised 2D and 3D U-Net approaches were found to be more effective than a commercial auto-segmentation tool. Even the relatively shallow 2D U-Net which does not require high-performance computational resources was effective enough for the lung segmentation. Semantic segmentation using deep learning was useful in radiation treatment planning for lung cancers.