bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic analysis of Saccharum s.l. (Poaceae; Andropogoneae), with emphasis on the circumscription of the South American species
Authors: Welker Cassiano A. D. , Souza‐Chies Tatiana T. , Longhi‐Wagner Hilda M. , Peichoto Myriam Carolina , McKain Michael R. , Kellogg Elizabeth A. 
Published: February 2015

• Premise of the study: Polyploidy and reticulate evolution are often a complication for discovering phylogenetic relationships between genera and species. Despite the huge economic importance of sugarcane (Saccharum officinarum—Poaceae, Andropogoneae), the limits of the genus Saccharum and its species are complex and largely unresolved, involving both polyploidy and reticulate evolution. This study aimed to assess the phylogenetic relationships of Saccharum s.l., including Erianthus and Tripidium, as well as investigate the taxonomic circumscription of the South American species of the genus.• Methods: Molecular cloning and sequencing of five regions of four low‐copy nuclear loci were performed, including Aberrant panicle organization1 (apo1), Dwarf8 (d8), two exons of Erect panicle2 (ep2‐ex7 and ep2‐ex8), and Retarded palea1 (rep1). Concatenated trees were reconstructed using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference analyses.• Key results: The allopolyploid origin of Saccharum was demonstrated using evidence from nuclear genes. The samples of Saccharum s.l. grouped in two distinct clades, with S. arundinaceum and S. ravennae (= Tripidium, or Erianthus sect. Ripidium) apart from all other species analyzed of the genus. Saccharum angustifolium, S. asperum, and S. villosum correspond to distinct clades (different species). The plants with intermediate morphology between S. angustifolium and S. villosum presented a pattern of paralogues consistent with a hybrid origin.• Conclusions: Saccharum s.l. is polyphyletic and Tripidium should be recognized as a distinct genus. However, no strong evidence was found to support the segregation of Erianthus. The taxonomic circumscription of the South American species of the genus was resolved and the occurrence of natural hybrids was documented. Better understanding of the phylogenetic relationships of Saccharum and relatives may be useful for sugarcane breeders to identify potential taxa for interspecific and intergeneric crosses in the genetic improvement of sugarcane.
Non-autonomous consequences of cell death and other perks of being metazoan
Authors: Su Tin Tin 
Published: February 2015

Abstract
Drosophila melanogaster remains a foremost genetic model to study basic cell biological processes in the context of multi-cellular development. In such context, the behavior of one cell can influence another. Non-autonomous signaling among cells occurs throughout metazoan development and disease, and is too vast to be covered by a single review. I will focus here on non-autonomous signaling events that occur in response to cell death in the larval epithelia and affect the life-death decision of surviving cells. I will summarize the use of Drosophila to study cell death-induced proliferation, apoptosis-induced apoptosis, and apoptosis-induced survival signaling. Key insights from Drosophila will be discussed in the context of analogous processes in mammalian development and cancer biology.
Fibroblastic Reticular Cells: Organization and Regulation of the T Lymphocyte Life Cycle
Authors: Brown Flavian D. , Turley Shannon J. 
Published: February 2015

Abstract
The connective tissue of any organ in the body is generally referred to as stroma. This complex network is commonly composed of leukocytes, extracellular matrix components, mesenchymal cells, and a collection of nerves, blood, and lymphoid vessels. Once viewed primarily as a structural entity, stromal cells of mesenchymal origin are now being intensely examined for their ability to directly regulate various components of immune cell function. There is particular interest in the ability of stromal cells to influence the homeostasis, activation, and proliferation of T lymphocytes. One example of this regulation occurs in the lymph node, where fibroblastic reticular cells support the maintenance of naive T cells, induce Ag-specific tolerance, and restrict the expansion of newly activated T cells. In an effort to highlight the varied immunoregulatory properties of fibroblastic reticular cells, we reviewed the most recent advances in this field and provide some insights into potential future directions.
Landing Biomechanics in Participants With Different Static Lower Extremity Alignment Profiles
Authors: Nguyen Anh-Dung , Shultz Sandra J. , Schmitz Randy J. 
Published: February 2015

ContextWhereas static lower extremity alignment (LEA) has been identified as a risk factor for anterior cruciate ligament injury, little is known about its influence on joint motion and moments commonly associated with anterior cruciate ligament injury.ObjectiveTo cluster participants according to combinations of LEA variables and compare these clusters in hip- and knee-joint kinematics and kinetics during the landing phase of a drop-jump task.DesignDescriptive laboratory study.SettingResearch laboratory.Patients or Other ParticipantsA total of 141 participants (50 men: age = 22.2 ± 2.8 years, height = 177.9 ± 9.3 cm, weight = 80.9 ± 13.3 kg; 91 women: age = 21.2 ± 2.6 years, height = 163.9 ± 6.6 cm, weight = 61.1 ± 8.7 kg).Main Outcome Measure(s)Static LEA included pelvic angle, femoral anteversion, quadriceps angle, tibiofemoral angle, genu recurvatum, tibial torsion, and navicular drop. Cluster analysis grouped participants according to their static LEA profiles, and these groups were compared on their hip- and knee-joint kinematics and external moments during the landing phase of a double-legged drop jump.ResultsThree distinct clusters (C1–C3) were identified based on their static LEAs. Participants in clusters characterized with static internally rotated hip and valgus knee posture (C1) and externally rotated knee and valgus knee posture (C3) alignments demonstrated greater knee-valgus motion and smaller hip-flexion moments than the cluster with more neutral static alignment (C2). Participants in C1 also experienced greater hip internal-rotation and knee external-rotation moments than those in C2 and C3.ConclusionsStatic LEA clusters that are positioned anatomically with a more rotated and valgus knee posture experienced greater dynamic valgus along with hip and knee moments during landing. Whereas static LEA contributes to differences in hip and knee rotational moments, sex may influence the differences in frontal-plane knee kinematics and sagittal-plane hip moments.
Reduced Physical Fitness in Patients With Heart Failure as a Possible Risk Factor for Impaired Driving Performance
Authors: Alosco Michael L. , Penn Marc S. , Spitznagel Mary Beth , Cleveland Mary Jo , Ott Brian R. , Gunstad John 
Published: February 2015

AbstractOBJECTIVE. Reduced physical fitness secondary to heart failure (HF) may contribute to poor driving; reduced physical fitness is a known correlate of cognitive impairment and has been associated with decreased independence in driving. No study has examined the associations among physical fitness, cognition, and driving performance in people with HF.METHOD. Eighteen people with HF completed a physical fitness assessment, a cognitive test battery, and a validated driving simulator scenario.RESULTS. Partial correlations showed that poorer physical fitness was correlated with more collisions and stop signs missed and lower scores on a composite score of attention, executive function, and psychomotor speed. Cognitive dysfunction predicted reduced driving simulation performance.CONCLUSION. Reduced physical fitness in participants with HF was associated with worse simulated driving, possibly because of cognitive dysfunction. Larger studies using on-road testing are needed to confirm our findings and identify clinical interventions to maximize safe driving.
Medications Are Associated with Falls in People with Multiple Sclerosis
Authors: Cameron Michelle H. , Karstens Lisa , Hoang Phu , Bourdette Dennis , Lord Stephen 
Published: February 2015

Background: Medication use is associated with falls in many populations, but the relationship between medications and falls in people with multiple sclerosis (MS) is not well understood.
Methods: The number and types of medications used by 248 ambulatory adults with MS in the United States (n = 53) and Australia (n = 195) were assessed. Participants completed fall diaries for 6 months. Associations between number and type of medications reported and falls, adjusting for age, disease severity, comorbidities, sex, and country, were evaluated using multiple logistic regression.
Results: Participants reported taking a median of three medications and two supplements. A total of 143 participants (58%) fell at least once in the 6 months, and 110 (44%) experienced one or more injurious falls. The adjusted relative odds of a fall or an injurious fall increased by 13% (P = .048) and 11% (P = .049), respectively, for each medication and by 43% (P = .015) and 55% (P = .001) for each neurologically active medication. Reported use of MS disease-modifying therapy was associated with 48% decreased odds of falling (P = .035) but not significantly decreased odds of injurious falls.
Conclusions: Reporting use of more medications and more neurologically active medications is associated with falls and injurious falls in people with MS. Close evaluation of the need for each medication, with associated minimization of neurologically active medications in patients with MS, may help prevent falls. Use of MS disease-modifying therapies may be associated with fewer falls. This relationship needs further evaluation.
Relationship of Admissions Variables and College of Osteopathic Medicine Variables to Performance on COMLEX-USA Level 3
Authors: Baker Helen H. , Shuman Victoria L. , Ridpath Lance C. , Pence Lorenzo L. , Fisk Robert M. , Boisvert Craig S. 
Published: February 2015

Abstract

Context: New accreditation standards require that all US colleges of osteopathic medicine (COMs) publically report the first-time pass rates of graduates on the Comprehensive Osteopathic Medical Licensing Examination-USA (COMLEX-USA) Level 3. Little is known about the extent to which admissions variables or COM performance measures relate to Level 3 performance.

Objective: To examine the relationship of admissions variables and COM performance to scores on Level 3 and to assess whether a relationship existed between Level 3 scores and sex, curriculum track, year of graduation, and residency specialty in the first postgraduate year.

Methods: Data were analyzed from 4 graduating classes (2008-2011) of the West Virginia School of Osteopathic Medicine in Lewisburg. Relationships were examined between first-attempt scores on COMLEX-USA Level 3 and Medical College Admission Test (MCAT) scores; undergraduate grade point averages (GPAs); GPAs in COM year 1, year 2, and clinical rotation years (years 3 and 4); and first-attempt scores on COMLEX-USA Level 1, Level 2-Cognitive Evaluation, and Level 2-Performance Evaluation.

Results: Of the 556 graduates during this 4-year period, COMLEX-USA Level 3 scores were available for 552 graduates (99.3%). No statistically significant differences were found in Level 3 scores based on sex, curriculum track, graduating class, or residency specialty. The strongest relationship between Level 3 scores and any admissions variable was with total MCAT score, which accounted for 4.2% of the variation in Level 3 scores. The strongest relationship between Level 3 scores and COM year performance measures was with year 2 GPA, which accounted for 35.4% of the variation in Level 3 scores. Level 1 scores accounted for 38.5% of the variation in Level 3 scores, and Level 2-Cognitive Evaluation scores accounted for the greatest percentage of variation (45.7%). The correlation of Level 3 scores with passing the Level 2-Performance Evaluation on the first attempt was not statistically significant.

Conclusion: A weak relationship was found between admissions variables and performance on COMLEX-USA Level 3, suggesting that graduates with lower MCAT scores and undergraduate GPAs may have overcome their early disadvantage. Strong relationships were found between Level 3 scores and year 2 GPAs, as well as scores on COMLEX-USA Level 1 and Level 2-Cognitive Evaluation.
Sensitivity of liquid clouds to homogenous freezing parameterizations
Authors: Herbert Ross J. , Murray Benjamin J. , Dobbie Steven J. , Koop Thomas 
Published: February 2015

AbstractWater droplets in some clouds can supercool to temperatures where homogeneous ice nucleation becomes the dominant freezing mechanism. In many cloud resolving and mesoscale models, it is assumed that homogeneous ice nucleation in water droplets only occurs below some threshold temperature typically set at −40°C. However, laboratory measurements show that there is a finite rate of nucleation at warmer temperatures. In this study we use a parcel model with detailed microphysics to show that cloud properties can be sensitive to homogeneous ice nucleation as warm as −30°C. Thus, homogeneous ice nucleation may be more important for cloud development, precipitation rates, and key cloud radiative parameters than is often assumed. Furthermore, we show that cloud development is particularly sensitive to the temperature dependence of the nucleation rate. In order to better constrain the parameterization of homogeneous ice nucleation laboratory measurements are needed at both high (>−35°C) and low (<−38°C) temperatures.
Substorm onset: Current sheet avalanche and stop layer
Authors: Haerendel Gerhard 
Published: February 2015

AbstractA new scenario is presented for the onset of a substorm and the nature of the breakup arc. There are two main components, current sheet avalanche and stop layer. The first refers to an earthward flow of plasma and magnetic flux from the central current sheet of the tail, triggered spontaneously or by some unknown interaction with an auroral streamer or a suddenly appearing eastward flow at the end of the growth phase. The second offers a mechanism to stop the flow abruptly at the interface between magnetosphere and tail and extract momentum and energy to be partially processed locally and partially transmitted as Poynting flux toward the ionosphere. The stop layer has a width of the order of the ion inertial length. The different dynamics of the ions entering freely and the magnetized electrons create an electric polarization field which stops the ion flow and drives a Hall current by which flow momentum is transferred to the magnetic field. A simple formalism is used to describe the operation of the process and to enable quantitative conclusions. An important conclusion is that by necessity the stop layer is also highly structured in longitude. This offers a natural explanation for the coarse ray structure of the breakup arc as manifestation of elementary paths of energy and momentum transport. The currents aligned with the rays are balanced between upward and downward directions. While the avalanche is invoked for explaining the spontaneous substorm onset at the inner edge of the tail, the expansion of the breakup arc for many minutes is taken as evidence for a continued formation of new stop layers by arrival of flow bursts from the near‐Earth neutral line. This is in line with earlier conclusions about the nature of the breakup arc. Small‐scale structure, propagation speed, and energy flux are quantitatively consistent with observations. However, the balanced small‐scale currents cannot constitute the substorm current wedge. The source of the latter must be located just earthward of the stop layer in the near‐dipolar magnetosphere and be powered by the internal energy of the flow bursts. The stop layer mechanism is in some way the inverse of reconnection, as it converts flow into electromagnetic energy, and may have wide applicability in astrophysical plasmas.
Experimental study on plunging breaking waves in deep water
Authors: Lim Ho‐Joon , Chang Kuang‐An , Huang Zhi‐Cheng , Na Byoungjoon 
Published: February 2015

AbstractThis study presents a unique data set that combines measurements of velocities and void fraction under an unsteady deep water plunging breaker in a laboratory. Flow properties in the aerated crest region of the breaking wave were measured using modified particle image velocimetry (PIV) and bubble image velocimetry (BIV). Results show that the maximum velocity in the plunging breaker reached 1.68C at the first impingement of the overturning water jet with C being the phase speed of the primary breaking wave, while the maximum velocity reached 2.14C at the beginning of the first splash‐up. A similarity profile of void fraction was found in the successive impinging and splash‐up rollers. In the highly foamy splashing roller, the increase of turbulent level and vorticity level were strongly correlated with the increase of void fraction when the range of void fraction was between 0 and 0.4 (from the trough level to approximately the center of the roller). The levels became constant when void fraction was greater than 0.5. The mass flux, momentum flux, kinetic energy, potential energy, and total energy were computed and compared with and without the void fraction being accounted for. The results show that all the mean and turbulence properties related to the air‐water mixture are considerably overestimated unless void fraction is considered. When including the density variation due to the air bubbles, the wave energy dissipated exponentially a short distance after breaking; about 54% and 85% of the total energy dissipated within one and two wavelengths beyond the breaking wave impingement point, respectively.
Glider observations and modeling of sediment transport in Hurricane Sandy
Authors: Miles Travis , Seroka Greg , Kohut Josh , Schofield Oscar , Glenn Scott 
Published: February 2015

AbstractRegional sediment resuspension and transport are examined as Hurricane Sandy made landfall on the Mid‐Atlantic Bight (MAB) in October 2012. A Teledyne‐Webb Slocum glider, equipped with a Nortek Aquadopp current profiler, was deployed on the continental shelf ahead of the storm, and is used to validate sediment transport routines coupled to the Regional Ocean Modeling System (ROMS). The glider was deployed on 25 October, 5 days before Sandy made landfall in southern New Jersey (NJ) and flew along the 40 m isobath south of the Hudson Shelf Valley. We used optical and acoustic backscatter to compare with two modeled size classes along the glider track, 0.1 and 0.4 mm sand, respectively. Observations and modeling revealed full water column resuspension for both size classes for over 24 h during peak waves and currents, with transport oriented along‐shelf toward the southwest. Regional model predictions showed over 3 cm of sediment eroded on the northern portion of the NJ shelf where waves and currents were the highest. As the storm passed and winds reversed from onshore to offshore on the southern portion of the domain waves and subsequently orbital velocities necessary for resuspension were reduced leading to over 3 cm of deposition across the entire shelf, just north of Delaware Bay. This study highlights the utility of gliders as a new asset in support of the development and verification of regional sediment resuspension and transport models, particularly during large tropical and extratropical cyclones when in situ data sets are not readily available.
Cross‐shelf exchange in the shelf of the East China Sea
Authors: Zhou Feng , Xue Huijie , Huang Daji , Xuan Jiliang , Ni Xiaobo , Xiu Peng , Hao Qiang 
Published: February 2015

AbstractA high‐resolution, 3‐dimensional primitive equation model is used to investigate the cross‐shelf exchange in the East China Sea (ECS). Favorable comparisons between field data and model simulations from both climatological run and hindcast run for 2006 indicate that the model has essential skills in capturing the key physics of the ECS. Temporal and spatial variations of the cross‐shelf exchanges are further analyzed. It was demonstrated from both observations and simulations that in 2006 high saline water could be delivered to the north of the Changjiang River mouth (near 32°N) as a result of stronger than typical cross‐shelf exchanges at the shelf break and flows through the Taiwan Strait with an annual mean rate of 2.59 and 1.83 Sv, respectively. A few new places at the shelf break were also identified where persistent and vigorous onshore or offshore exchanges occur throughout the year. Cross‐shelf exchange is largely determined by the along‐shelf geostrophic balance with weak seasonality, which is modulated in upper layers by northeasterly monsoon from early‐fall to late‐spring and at seabed by bottom friction during December–January, May, and August–September. Nonlinear effect, with strong spatial variations and intraseasonal variability, is a secondary but persistent contributor to the net seaward transport, except for northeast of Taiwan where the nonlinear effect becomes significant but more varied.
Multidecadal variations of the surface Kuroshio between 1950s and 2000s and its impacts on surrounding waters
Authors: Hsin Yi‐Chia 
Published: February 2015

AbstractBased on the analyses of 59 year (1950–2008) surface geostrophic velocities, the multidecadal changes of Kuroshio from the eastern Luzon to the southern Japan are investigated. Result shows that the upstream Kuroshio from the east of Luzon to southern East China Sea suffers much more obvious multidecadal changes. Except for the decade of 1980, the Kuroshio east of Luzon possesses a multidecadal tendency opposite to that east of Taiwan. Besides 1980s, the multidecadal change of Kuroshio bordering Taiwan is mainly governed by the eddy activity off the eastern Taiwan, while the wind stress curl plays a major role in the Kuroshio in the east of Luzon and in the Luzon Strait. The wind‐stress‐induced Ekman transport plays a secondary role in regulating the Kuroshio east of Luzon. In addition, the multidecadal fluctuation of Kuroshio east of Luzon also modulates the westward intrusion in the Luzon Strait. Instead, the Ekman transport dominated the whole upstream Kuroshio area from the eastern Luzon to the vicinity of Taiwan during the exceptional decade of 1980. Associated changes of water properties in the northern South China Sea and southern East China Sea are also ascribed to the multidecadal changes of surface Kuroshio in the upstream area.
Turbulence in theEastChinaSea:The summertime stratification
Authors: Lozovatsky Iossif , Lee Jae‐Hak , Fernando H. J. S. , Kang Sok Kuh , Jinadasa S. U. P. 
Published: February 2015

AbstractA series of 134 microstructure profiles were taken in the central East China Sea from a drifting ship, covering more than 12 miles over the sloping bottom. The water depthzvaried in the range 52–62 m; the tidal elevation of semidiurnal component was ±1 m. Prior to the onset of 25 h drift, a hydrographic section consisting of 9 stations, 15 miles apart, was taken in the area. A shallow mixed surface layer (SL) underlain by a diurnal pycnocline (z < 13 m), a sharp thermohalocline (13 < z < 30 m), and about 20 m tall bottom boundary layer (BBL) were the main features of summertime stratification. The splitting of upper pycnocline by a warmer, saltier intrusion led to the generation of turbulent patches at the lower, but not at the upper, density interface of this water body, suggesting asymmetry of mixing across the intrusion. In a limited range of the normalized squared buoyancy frequency,, the turbulent kinetic energy dissipation ratedecreased sharply as, whereW/kg ands−1. Measurements in the sharp pycnocline and in lesser‐stratified transitional layers between the pycnocline and the SL and BBL show that the cumulative distribution functionscan be modeled either by the generalized extreme value (GEV) distribution or the lognormal distribution.