bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pelvic floor muscle contractility: digital assessment vs transperineal ultrasound
Authors: van Delft K. , Thakar R. , Sultan A. H. 
Published: July 2014

ABSTRACTObjectivesA significant reduction in hiatal area and anteroposterior diameter can be induced by pelvic floor muscle contraction, and this has been demonstrated using three‐dimensional/four‐dimensional (3D/4D) transperineal ultrasound (TPS) in a small group of women. Our objective was to correlate pelvic floor muscle contractility using digital assessment with the change in TPS hiatus measurements during maximum pelvic floor muscle contraction.MethodsNulliparous pregnant women were recruited from the antenatal clinic. Pelvic floor muscle contractility was assessed by digital palpation using the validated Modified Oxford Scale (MOS). Subsequently, women underwent 3D/4D TPS. Measurements of the hiatal area and anteroposterior diameter were taken from the rendered ultrasound images at rest and at maximum contraction, and differences in measurements were expressed as percentages. Spearman's rank (ρ) was used to assess the correlation.ResultsFour hundred and fifty‐nine assessments were performed, of which 268 were from women at around 36 weeks' gestation, and 191 were from women following delivery at 3 months postpartum. The overall correlation between MOS and TPS was found to be ρ = 0.47 for hiatal area (P < 0.001) and ρ = 0.51 for hiatal anteroposterior diameter (P < 0.001).ConclusionsDigital palpation using MOS and TPS can both be used as tools to assess pelvic floor muscle contractility. Although MOS is a simple clinical tool without the need for any equipment, TPS can provide good visual biofeedback when training patients in pelvic floor muscle exercises. As TPS is non‐intrusive, it may be the method of choice for some women. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.
Plasma proteins predict conversion to dementia from prodromal disease
Authors: Hye Abdul , Riddoch‐Contreras Joanna , Baird Alison L. , Ashton Nicholas J. , Bazenet Chantal , Leung Rufina , Westman Eric , Simmons Andrew , Dobson Richard , Sattlecker Martina , Lupton Michelle , Lunnon Katie , Keohane Aoife , Ward Malcolm , Pike Ian , Zucht Hans Dieter , Pepin Danielle , Zheng Wei , Tunnicliffe Alan , Richardson Jill , Gauthier Serge , Soininen Hilkka , Kłoszewska Iwona , Mecocci Patrizia , Tsolaki Magda , Vellas Bruno , Lovestone Simon 
Published: July 2014

AbstractBackgroundThe study aimed to validate previously discovered plasma biomarkers associated with AD, using a design based on imaging measures as surrogate for disease severity and assess their prognostic value in predicting conversion to dementia.MethodsThree multicenter cohorts of cognitively healthy elderly, mild cognitive impairment (MCI), and AD participants with standardized clinical assessments and structural neuroimaging measures were used. Twenty‐six candidate proteins were quantified in 1148 subjects using multiplex (xMAP) assays.ResultsSixteen proteins correlated with disease severity and cognitive decline. Strongest associations were in the MCI group with a panel of 10 proteins predicting progression to AD (accuracy 87%, sensitivity 85%, and specificity 88%).ConclusionsWe have identified 10 plasma proteins strongly associated with disease severity and disease progression. Such markers may be useful for patient selection for clinical trials and assessment of patients with predisease subjective memory complaints.
Protein alterations in women with chronic widespread pain—A proteomic study of the trapezius muscle
Authors: Olausson P. , Ghafouri N. , Sjöström D. , Blixt E. , Gerdle B. , Ghafouri B. 
Published: July 2014

Abstract

Aim
This study aims to investigate the proteome of trapezius muscle biopsies of women with chronic widespread pain (CWP) compared to female pain-free controls using proteomic tools. CWP has a high prevalence (10%) resulting in prominent negative individual and societal consequences. There is no clear consensus concerning the etiology behind CWP although alterations in the central processing of nociception maintained by peripheral nociceptive input has been suggested.

Methods
Two-dimensional gel electrophoresis (2-DE) analysis and nano-liquid chromatography/mass spectrometry (nLC/MS) was used to study the proteome differences of biopsies from the trapezius muscle between 18 female patients diagnosed with CWP and 19 healthy female controls.

Results
The proteomic analysis revealed 17 proteins to be statistically significantly expressed between the two groups by which 12 were up-regulated and 5 were down-regulated in the CWP group compared to healthy controls. Many of the proteins were important enzymes in metabolic pathways like the glycolysis and gluconeogenesis (Triosephosphate isomerase, Glyceraldehyde-3-phosphate dehydrogenase, Pyruvate kinase isoenzyme M1/M2 and Fructose-bisphosphate aldolase A, all up-regulated in CWP). Other proteins are associated with muscle damage (Ankyrin repeat domain-containing protein 2, down-regulated in CWP), muscle recovery (Alpha-crystallin B chain, up-regulated in CWP) stress and inflammation (carbonic anhydrase 3, up-regulated in CWP). The contractile and structural proteins found have been associated with various types of myopathies (Actin alpha skeletal muscle, up-regulated, Troponin T slow skeletal muscle and Desmin, down-regulated in CWP).

Conclusions
In conclusion, the expression of these proteins belonging to the protein groups, contractile, stress and inflammatory, structural, and metabolic, suggests abnormalities and alterations in the myalgic trapezius muscle.
A revision of the epiphytic species of theLecanora subfuscagroup (Lecanoraceae, Ascomycota) in the Czech Republic
Authors: MALÍČEK Jiří 
Published: July 2014

AbstractDuring a revision of epiphytic species of theLecanora subfuscagroup in the Czech Republic, nine taxa were recorded.Lecanora cinereofusca, although reported for the first time from the country here, is considered to be extinct, as isL. horiza. Lecanora circumborealishas been excluded from the list of Czech lichens.Lecanora rugosellaandL. subrugosarespectively are regarded as extreme morphological forms ofL. chlaroteraandL. argentata, ecologically derived through nutrient enrichment (eutrophication).Lecanora laevisis regarded as a morphotype ofL. horiza. An identification key is provided. The importance of the amphithecium and cortex type as taxonomic characters is discussed in detail. Several new secondary metabolites belonging to the terpenoids, discovered during an investigation of lichen compounds, proved to be taxonomically important. The abundance ofL. allophanaandL. chlaroterahas decreased during the second half of the 20th century, butL. pulicarishas expanded. The main reasons for these changes are air pollution and acidification of substrata;L. pulicaris, for example, formerly a predominant lichen on acid-barked trees, today grows mainly on trees with slightly acidic or subneutral bark.
Acculturative and enculturative stress, depressive symptoms, and maternal warmth: Examining within-person relations among Mexican-origin adolescent mothers
Authors: Zeiders Katharine H. , Umaña-Taylor Adriana J. , Updegraff Kimberly A. , Jahromi Laudan B. 
Published: July 2014

AbstractMexican-origin adolescent mothers face numerous social challenges during dual-cultural adaptation that are theorized to contribute to greater depressive symptoms. Alongside challenges, there are familial resources that may offer protection. As such, the current study examined the trajectories of depressive symptoms among 204 Mexican-origin adolescent mothers (Mage= 16.80,SD= 1.00) across a 4-year period (third trimester of pregnancy, and 10, 24, and 36 months postpartum). Further, we examined the within-person relations of two unique sources of stress experienced during dual-cultural adaptation,acculturativeandenculturative stress, and youths' depressive symptoms; we also tested whether adolescent mothers' perceptions of warmth from their own mothers emerged as protective. Adolescent mothers reported a decline in depressive symptoms after the transition to parenthood. Acculturative and enculturative stress emerged as significant positive within-person predictors of depressive symptoms. Maternal warmth emerged as a protective factor in the relation between enculturative stressors and depressive symptoms; however, for acculturative stressors, the protective effect of maternal warmth only emerged for US-born youth. Findings illustrate the multidimensionality of stress experienced during the cultural adaptation process and a potential mechanism for resilience among Mexican-origin adolescent mothers.
THE KOKURYŪKAI (BLACK DRAGON SOCIETY) AND THE RISE OF NATIONALISM, PAN-ASIANISM, AND MILITARISM IN JAPAN, 1901–1925
Authors: Saaler Sven 
Published: July 2014

In the conduct of prewar Japanese foreign relations, political associations (seiji kessha) – we might also call them pressure groups – exerted considerable political influence, particularly on Japan's relations with China and other Asian nations. One of the best known of these political associations is the Kokuryūkai (the “Amur Society,” also known as the “Black Dragon Society”), which was founded in 1901 and, in 1946, was banned as an ultranationalist association by the American occupation authorities. The Kokuryūkai was also identified as the center of an expansionist conspiracy to steer Japan towards war with the Western powers.In the absence of detailed studies of the Kokuryūkai, this article aims to clarify the organization's political views and activities and to demonstrate its influence on Japanese foreign relations and involvement in East Asia in the early twentieth century. Drawing on primary sources such as the association's publications and its leaders' memoranda and letters, I show that the Kokuryūkai engaged in intensive networking activities and the accumulation of social capital involving not only Japanese but also Chinese and Korean politicians and diplomats. Nevertheless, I conclude that the association's influence on the origins of the Asia-Pacific War should not be overstated, since its activities reached a climax in the late 1910s and effectively ended with the death of founder Uchida Ryōhei in 1937.
The influence of cover crop variety, termination timing and termination method on mulch, weed cover and soil nitrate in reduced-tillage organic systems
Authors: Wayman Sandra , Cogger Craig , Benedict Chris , Burke Ian , Collins Doug , Bary Andy 
Published: July 2014

AbstractOverwintered cover crops mechanically terminated into mulch can be a weed management tool for reduced-tillage organic agriculture. However, the impacts of management options for cover cropping are not well understood, including cover crop variety, termination timing and termination method. In a field experiment, conducted in 2012 and 2013 in Western Washington, we examined three grains, four vetches and one barley–vetch mix terminated with two mechanical methods and at two different times. We determined the influence of cover crop variety and termination time on cover crop biomass production and tissue nitrogen (N), effectiveness of cover crop termination, soil nitrate–N and percent weed cover. We also determined the influence of termination method on percent weed cover. Cover crop biomass ranged between 3 and 9 Mg ha−1and was not influenced by termination time; the greatest production was from three varieties of grain. Rye varieties were more effectively terminated with a roller–crimper than barley. Mean soil nitrate–N levels ranged from 1.9 to 18 mg kg−1and were the greatest with vetches. Post-termination weed cover was greater in 2013 than in 2012 and the cover crop variety influenced weed cover at the Late termination time only. Neither plant N concentration in the cover crop mulch nor soil nitrate influenced weed cover. The results of this study indicate that cover crop biomass and termination timing are important factors influencing weed cover and termination effectiveness in cover crop mulch.
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
Authors: Gibson Molly K , Forsberg Kevin J , Dantas Gautam 
Published: July 2014

Abstract
Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.
Tipping elements in the human intestinal ecosystem
Authors: Lahti Leo , Salojärvi Jarkko , Salonen Anne , Scheffer Marten , de Vos Willem M. 
Published: July 2014

AbstractThe microbial communities living in the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify groups of bacteria that exhibit robust bistable abundance distributions. These bacteria are either abundant or nearly absent in most individuals, and exhibit decreased temporal stability at the intermediate abundance range. The abundances of these bimodally distributed bacteria vary independently, and their abundance distributions are not affected by short-term dietary interventions. However, their contrasting alternative states are associated with host factors such as ageing and overweight. We propose that the bistable groups reflect tipping elements of the intestinal microbiota, whose critical transitions may have profound health implications and diagnostic potential.
Electronic Structure, Dielectric Response and Surface Charge Distribution of RGD (1FUV) Peptide
Authors: Adhikari Puja , Wen Amy M. , French Roger H. , Parsegian V. Adrian , Steinmetz Nicole F. , Podgornik Rudolf , Ching Wai-Yim 
Published: July 2014

AbstractLong and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report aunified methodologyfor theab initioquantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). Thisab initio unified methodologyyields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.
Environmental impact of geometric earthwork construction in pre-Columbian Amazonia
Authors: Carson John Francis , Whitney Bronwen S. , Mayle Francis E. , Iriarte José , Prümers Heiko , Soto J. Daniel , Watling Jennifer 
Published: July 2014

SignificanceThe discovery of extensive geometric earthworks beneath apparently pristine rainforest across southern Amazonia has fueled debate over the scale of environmental impact caused by ancient human societies. Whereas some claim that these sites are evidence of vast deforestation by populous pre-Columbian (pre-A.D. 1492) societies, others propose a model of small-scale, localized clearance. We tested these contrasting hypotheses by reconstructing environmental change in a region of geometric earthworks in northeast Bolivia over the last 6,000 y. Our unexpected findings reveal a surprising third scenario, in which earthwork builders took advantage of a naturally open savanna landscape, which existed under drier-than-present climatic conditions before ∼2,000 y ago. This finding suggests lower environmental impact, less labor, and possibly a smaller population than previously assumed.
Crystal structure of mammalian selenocysteine-dependent iodothyronine deiodinase suggests a peroxiredoxin-like catalytic mechanism
Authors: Schweizer Ulrich , Schlicker Christine , Braun Doreen , Köhrle Josef , Steegborn Clemens 
Published: July 2014

Significance
Deiodinases activate and inactivate thyroid hormones through a unique biochemical reaction. Enzymes expand their catalytic capabilities through special heteroatoms in cofactors or in the rare but essential amino acid selenocysteine, and deiodinases use an active-site selenocysteine for the reductive elimination of iodide from the aromatic iodothyronine rings. The mechanism of deiodinases has remained elusive despite many mutational and enzymatic studies. We solved the crystal structure of the deiodinase catalytic domain and find that it resembles a family of peroxiredoxin(s) (Prx). Structure and biochemical data suggest a deiodinase catalytic mechanism with Prx-like elements and enable us to assign unexpected functions to residues previously reported to contribute to deiodinase catalysis. Our findings indicate how deiodinases may have evolved from a common reductase ancestor.
Intratumor heterogeneity alters most effective drugs in designed combinations
Authors: Zhao Boyang , Hemann Michael T. , Lauffenburger Douglas A. 
Published: July 2014

Significance
Tumors within each cancer patient have been found to be extensively heterogeneous both spatially across distinct regions and temporally in response to treatment. This poses challenges for prognostic/diagnostic biomarker identification and rational design of optimal drug combinations to minimize reoccurrence. Here we present a computational approach incorporating drug efficacy and drug side effects to derive effective drug combinations and study how tumor heterogeneity affects drug selection. We find that considering subpopulations beyond just the predominant subpopulation in a heterogeneous tumor may result in nonintuitive drug combinations. Additional analyses reveal general properties of effective drugs. This study highlights the importance of optimizing drug combinations in the context of intratumor heterogeneity and offers a principled approach toward their rational design.
Herbarium specimens show contrasting phenological responses to Himalayan climate
Authors: Hart Robbie , Salick Jan , Ranjitkar Sailesh , Xu Jianchu 
Published: July 2014

SignificanceNatural events in temperate ecosystems are triggered by seasonal temperature changes. Climate change may shift the timing of these events. We use a century of herbarium collections of Himalayan rhododendrons to investigate climate-driven change in flowering time. Although increased annual temperatures are associated with earlier flowering, increased fall temperatures are associated with delayed flowering. Annual warming may advance flowering through positive effects on overwintering bud formation, whereas fall warming may delay flowering through an impact on chilling requirements. These contrasting effects have resulted in opposing changes in flowering time, even as temperatures have warmed rapidly in the past 45 y. This study demonstrates the value of natural history collections to inform ecological questions, especially regarding climate change.
Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals
Authors: Ye Kaixiong , Lu Jian , Ma Fei , Keinan Alon , Gu Zhenglong 
Published: July 2014

SignificanceThere are hundreds to thousands of copies of mitochondrial DNA (mtDNA) in each human cell in contrast to only two copies of nuclear DNA. High-frequency pathogenic mtDNA mutations have been found in patients with classic mitochondrial diseases, premature aging, cancers, and neurodegenerative diseases. In this study we investigated the distribution of heteroplasmic mutations, their pathogenic potential, and their underlying evolutionary forces using genome sequence data from the 1000 Genomes Project. Our results demonstrated the prevalence of low-frequency high-pathogenic-potential mtDNA mutations in healthy human individuals. These deleterious mtDNA mutations, when reaching high frequency, could provide a likely source of mitochondrial dysfunction. Managing the expansion of deleterious mtDNA mutations could be a promising means of preventing disease progression.
Suppression of tunneling two-level systems in ultrastable glasses of indomethacin
Authors: Pérez-Castañeda Tomás , Rodríguez-Tinoco Cristian , Rodríguez-Viejo Javier , Ramos Miguel A. 
Published: July 2014

Significance
Glasses are disordered solids usually obtained by supercooling a liquid bypassing crystallization. A remarkable feature of glasses is that, independently of their nature and composition, they exhibit universal properties in the low-temperature range. Of interest here, the specific heat is characterized by a linear term below 1 K, ascribed to quantum tunneling between two states of similar energy. We have investigated if this ubiquitous behavior also applies to so-called “ultrastable glasses,” directly synthesized from the vapor phase into low-energy positions of the potential-energy landscape. Interestingly, we find a full suppression of the linear term in the specific heat, which questions the current view of the popular tunneling model and sheds light on the microscopic origin of two-level systems in glasses.
Simple chained guide trees give high-quality protein multiple sequence alignments
Authors: Boyce Kieran , Sievers Fabian , Higgins Desmond G. 
Published: July 2014

Significance
To make sense of protein sequences, they need to be compared with each other. It is common to make a multiple sequence alignment where gaps are inserted to line up homologous residues in columns. Automatic methods such as Clustal, Muscle, or Mafft have been widely used since the 1980s but have difficulty in making alignments of much more than a few thousand sequences. This is mainly due to the time required to calculate what is called the guide tree, a clustering of the sequences that is used to guide the multiple alignment. We have discovered that if you use simple chained guide trees, you can increase the accuracy of alignments and, in principle, make alignments of any size.