bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CsoR‐like sulfurtransferase repressor (CstR) is a persulfide sensor in Staphylococcus aureus
Authors: Luebke Justin L. , Shen Jiangchuan , Bruce Kevin E. , Kehl‐Fie Thomas E. , Peng Hui , Skaar Eric P. , Giedroc David P. 
Published: October 2014

SummaryHow cells regulate the bioavailability of utilizable sulfur while mitigating the effects of hydrogen sulfide toxicity is poorly understood. CstR [Copper‐sensing operon repressor (CsoR)‐like sulfurtransferase repressor] represses the expression of the cst operon encoding a putative sulfide oxidation system in Staphylococcus aureus. Here, we show that the cst operon is strongly and transiently induced by cellular sulfide stress in an acute phase and specific response and that cst‐encoded genes are necessary to mitigate the effects of sulfide toxicity. Growth defects are most pronounced when S. aureus is cultured in chemically defined media with thiosulfate (TS) as a sole sulfur source, but are also apparent when cystine is used or in rich media. Under TS growth conditions, cells fail to grow as a result of either unregulated expression of the cst operon in a ΔcstR strain or transformation with a non‐inducible C31A/C60A CstR that blocks cst induction. This suggests that the cst operon contributes to cellular sulfide homeostasis. Tandem high‐resolution mass spectrometry reveals derivatization of CstR by both inorganic tetrasulfide and an organic persulfide, glutathione persulfide, to yield a mixture of Cys31–Cys60′ interprotomer cross‐links, including di‐, tri‐ and tetrasulfide bonds, which allosterically inhibit cst operator DNA binding by CstR.
A worldwide analysis of within‐canopy variations in leaf structural, chemical and physiological traits across plant functional types
Authors: Niinemets Ülo , Keenan Trevor F. , Hallik Lea 
Published: October 2014

SummaryExtensive within‐canopy light gradients importantly affect the photosynthetic productivity of leaves in different canopy positions and lead to light‐dependent increases in foliage photosynthetic capacity per area (AA). However, the controls on AA variations by changes in underlying traits are poorly known. We constructed an unprecedented worldwide database including 831 within‐canopy gradients with standardized light estimates for 304 species belonging to major vascular plant functional types, and analyzed within‐canopy variations in 12 key foliage structural, chemical and physiological traits by quantitative separation of the contributions of different traits to photosynthetic acclimation. Although the light‐dependent increase in AA is surprisingly similar in different plant functional types, they differ fundamentally in the share of the controls on AA by constituent traits. Species with high rates of canopy development and leaf turnover, exhibiting highly dynamic light environments, actively change AA by nitrogen reallocation among and partitioning within leaves. By contrast, species with slow leaf turnover exhibit a passive AA acclimation response, primarily determined by the acclimation of leaf structure to growth light. This review emphasizes that different combinations of traits are responsible for within‐canopy photosynthetic acclimation in different plant functional types, and solves an old enigma of the role of mass‐ vs area‐based traits in vegetation acclimation.

Contents

Summary
973

I.
Introduction
973

II.
Defining the structural, chemical and partitioning controls on foliage photosynthetic potentials
974

III.
Construction of a global database on within‐canopy variation in leaf structural, chemical and photosynthetic characteristics
976

IV.
Methodology for analysis of within‐canopy leaf trait variation: concepts and standardizations
978

V.
Global variation in leaf characteristics through the canopies
981

VI.
Trait scaling with light, plasticity and quantitative limitations
982

VII.
Conclusions: the economics spectrum for the within‐canopy plasticity
989

Acknowledgements
989

References
990
Effects of insect attack to stems on plant survival, growth, reproduction and photosynthesis
Authors: Stephens Andrea E. A. , Westoby Mark 
Published: October 2014

Studies of insect herbivory have mostly focused on leaf‐feeding even though most woody plant biomass is stem tissue. Attack to stems has the potential to be more detrimental to plant performance than attack to leaves. Here we asked how severe is the impact of insect stem herbivory on plant performance. We quantify the effect of insect stem herbivory via a meta‐analysis of 119 papers in 100 studies (papers by the same authors were treated as the same study). These studies involved 92 plant species and 70 species of insect herbivore (including simulated herbivory).Attack to plant stems reduced plant performance by an average of approximately 22%. Stem herbivory had greatest impacts on plant and branch survival, which was reduced by 63%. Measures of plant reproduction and vegetative biomass were reduced by 33% and 16% respectively, while measurements of photosynthetic rate were not significantly different between plants with and without stem herbivore attack. Stem herbivory led to a decline in leader performance but an increase in performance of laterals, highlighting the importance of plant compensation. Juvenile plants were more severely affected by stem herbivory than adult plants, and studies conducted in greenhouses found more severe effects than studies conducted in the field. Stem herbivory did not have a significant effects on any of the non‐performance responses measured (defence compounds, SLA, root:shoot, phenology and plant carbon and nitrogen).We compare our results with results from various meta‐analyses considering herbivory on other plant parts. The impact of insect herbivory to stems on plant performance appears at least as severe as insect herbivory to roots and leaves, if not more.
Identifying Populations at Risk: Interdisciplinary Environmental Climate Change Tracking
Authors: Anderko Laura , Davies‐Cole John , Strunk Andrew 
Published: October 2014

AbstractBackgroundClimate change, experienced as extreme weather events such as heat waves can lead to poorer air quality and underscores the critical need to consider the consequences of these environmental changes on health. Changes are occurring at a rate that exceeds what the world has experienced over the last 650,000 years, yet little attention has been focused on the potentially catastrophic public health effects of climate change.MethodsThis study instituted a two‐phase approach. In building capacity for an Environmental Public Health Tracking Network, the District of Columbia Department of Health first examined the availability of climate change and health data. These data were then used to assess vulnerabilities and disease burden associated with heat, air quality, and hospitalizations for asthma (N = 5,921) and acute myocardial infarction (AMI) (N = 2,773) during 2007–2010. A Poisson regression analysis was applied to the time series of daily counts for hospitalizations for selected age, race, and gender groups.ResultsAlthough no significant associations were found for PM2.5, PM10, or ozone with asthma‐related or AMI‐related hospitalizations with seasonal changes, surveillance data found disparities in hospitalizations particularly in female, African American residents for both asthma and AMI.ConclusionsTracking Networks are critical for assessing community environmental health vulnerabilities.
Seed dormancy and germination in Jeffersonia dubia (Berberidaceae) as affected by temperature and gibberellic acid
Authors: Rhie Y. H. , Lee S. Y. , Kim K. S. 
Published: October 2014

AbstractThe genus Jeffersonia, which contains only two species, has a trans‐Atlantic disjunct distribution. The aims of this study were to determine the requirements for breaking dormancy and germination of J. dubia seeds and to compare its dormancy characteristics with those of the congener in eastern North America. Ripe seeds of J. dubia contain an underdeveloped embryo and were permeable to water. In nature, seeds were dispersed in May, while embryos began to grow in September, and were fully elongated by late November. Germination started in March of the next year, and seeds emerged as seedlings soon after germination. In laboratory experiments, incubation at high temperatures (25 °C, 25/15 °C) for at least 8 weeks was required to initiate embryo growth, while a transfer to moderate temperatures (20/10 °C, 15/6 °C) was needed for the completion of embryo growth. At least 8 weeks at 5 °C was effective in overcoming physiological dormancy and for germination in seeds after the embryos had fully elongated. Thus, both high and low temperatures were essential to break dormancy. Gibberellic acid (GA3) treatment could substitute for the high temperature requirement, but not for the low temperature requirement. Based on the dormancy‐breaking requirements, it is confirmed that the seeds have deep simple morphophysiological dormancy. This dormancy type is similar to that of seeds of the eastern North American species J. diphylla. Although seeds require 10–11 months from seed dispersal to germination in nature, under controlled conditions they required only 3 months after treatment with 1000 mg·l−1 GA3, followed by incubation at 15/6 °C. This represents practical knowledge for propagation of these plants from seed.
Sources of Law Are not Legal Norms
Authors: Shecaira Fábio Perin 
Published: October 2014

AbstractAnglo‐American authors have paid little attention to a subtle distinction that has important jurisprudential implications. It is the distinction between sources of law (e.g., statutes, precedents, customs) and the legal norms which can be derived from sources by means of interpretation. The distinction might also be rendered as a threefold one, separating sources of law from legal norms and both of these from that which mediates their relation, namely, methods of legal interpretation. This paper intends to state the “source‐norm” distinction clearly and to give examples of jurisprudential insights that are missed, and mistakes that may be made if the distinction is not given its due.
Dietary Protein and Fiber in End Stage Renal Disease
Authors: Sirich Tammy L. 
Published: October 2014

AbstractPrior to the availability of hemodialysis, dietary protein restriction played a large part in the treatment of uremia. This therapy was based on observations that uremic symptoms increased with high protein intake. Early investigators thus presumed that “uremic toxins” were derived from the breakdown of dietary protein; its restriction improved uremic symptoms but caused malnutrition. After the availability of hemodialysis, protein restriction was no longer recommended. Studies in healthy subjects have shown that an intake of 0.6–0.8 g/kg/day is adequate to prevent protein malnutrition. Guidelines for hemodialysis patients, however, currently recommend higher protein intakes of 1.2 g/kg/day. A downside to higher intake may be increased production of protein‐derived uremic solutes that caused the symptoms observed by early investigators. Some of these solutes are produced by colon microbes acting on protein which escapes digestion in the small intestine. Increasing dietary fiber may reduce the production of colon‐derived solutes in hemodialysis patients without adverse effects of protein restriction. Fiber comprises carbohydrates and related substances that are resistant to digestion in the small intestine. Upon delivery to the colon, fiber is broken down to short chain fatty acids, providing energy to both the microbes and the host. With an increased energy supply, the microbes can incorporate dietary protein for growth rather than breaking them down to uremic solutes. Increasing fiber intake in hemodialysis patients has been shown to reduce the plasma levels of selected colon‐derived solutes. Further studies are needed to test whether this provides clinical benefit.
Epidemiology, clinical characteristics, and outcome of invasive aspergillosis in renal transplant patients
Authors: Hoyo I. , Sanclemente G. , de la Bellacasa J. Puig , Cofán F. , Ricart M.J. , Cardona M. , Colmenero J. , Fernández J. , Escorsell A. , Navasa M. , Moreno A. , Cervera C. 
Published: October 2014

AbstractBackgroundInvasive aspergillosis (IA) has been considered an infrequent complication after renal transplantation. We aimed to evaluate the differences in clinical and epidemiologic characteristics of IA between renal and other types of transplantation.MethodsWe reviewed all cases of solid organ transplant (SOT) recipients from Hospital Clinic at Barcelona, who had proven and probable IA, according to the EORTC/MSG criteria, between June 2003 and December 2010.ResultsA total of 1762 transplants were performed. From this cohort, 27 cases of IA were diagnosed (1.5%): in 56% (15/27) liver, 33% (9/27) kidney, and 11% (3/27) combined transplant. The median onset time from renal and non‐renal transplants to IA was 217 and 10 days, respectively (P < 0.001). There were 6 cases (22%) of late IA (>6 months), all in kidney recipients (P < 0.001). Renal transplant patients with IA more frequently had chronic lung disease (44% vs. 6%) and chronic heart failure (33% vs. 6%); they also had none of the classical risk factors for IA defined for liver transplantation (0% vs. 33%, P = 0.001), and therefore they did not receive antifungal prophylaxis (0% vs. 72%, P = 0.001). In 14/24 patients, serum galactomannan antigen was positive, and this related to higher mortality.ConclusionsWhile classical risk factors described for IA in liver recipients are still valid, IA appears later in renal patients and is commonly associated with co‐morbid conditions.
Floral volatile alleles can contribute to pollinator‐mediated reproductive isolation in monkeyflowers (Mimulus)
Authors: Byers Kelsey J. R. P. , Vela James P. , Peng Foen , Riffell Jeffrey A. , Bradshaw Harvey D. 
Published: October 2014

SummaryPollinator‐mediated reproductive isolation is a major factor in driving the diversification of flowering plants. Studies of floral traits involved in reproductive isolation have focused nearly exclusively on visual signals, such as flower color. The role of less obvious signals, such as floral scent, has been studied only recently. In particular, the genetics of floral volatiles involved in mediating differential pollinator visitation remains unknown. The bumblebee‐pollinated Mimulus lewisii and hummingbird‐pollinated Mimulus cardinalis are a model system for studying reproductive isolation via pollinator preference. We have shown that these two species differ in three floral terpenoid volatiles – d‐limonene, β‐myrcene, and E‐β‐ocimene – that are attractive to bumblebee pollinators. By genetic mapping and in vitro analysis of enzyme activity we demonstrate that these interspecific differences are consistent with allelic variation at two loci, LIMONENE‐MYRCENE SYNTHASE (LMS) and OCIMENE SYNTHASE (OS). Mimulus lewisii LMS (MlLMS) and OS (MlOS) are expressed most strongly in floral tissue in the last stages of floral development. Mimulus cardinalis LMS (McLMS) is weakly expressed and has a nonsense mutation in exon 3. Mimulus cardinalis OS (McOS) is expressed similarly to MlOS, but the encoded McOS enzyme produces no E‐β‐ocimene. Recapitulating the M. cardinalis phenotype by reducing the expression of MlLMS by RNA interference in transgenic M. lewisii produces no behavioral difference in pollinating bumblebees; however, reducing MlOS expression produces a 6% decrease in visitation. Allelic variation at the OCIMENE SYNTHASE locus is likely to contribute to differential pollinator visitation, and thus promote reproductive isolation between M. lewisii and M. cardinalis. OCIMENE SYNTHASE joins a growing list of ‘speciation genes’ (‘barrier genes’) in flowering plants.
La conjecture de Tate entière pour les cubiques de dimension quatre
Authors: Charles François , Pirutka Alena 
Published: October 2014

AbstractWe prove the integral Tate conjecture for cycles of codimension$2$on smooth cubic fourfolds over an algebraic closure of a field finitely generated over its prime subfield and of characteristic different from$2$or$3$. The proof relies on the Tate conjecture with rational coefficients, proved in that setting by the first author, and on an argument of Voisin coming from complex geometry.
Electro Hydraulic Gas Exchange Valve Actuation of 4-Stroke Large Bore Diesel Engine
Authors: Herranen Mika , Huhtala Kalevi 
Published: October 2014

After several years of study, a large bore diesel engine Electro-Hydraulic Valve Actuation (EHVA) system has reached a development point where the system has been successfully used for years in laboratory test engine environment too. During the evolution of the EHVA, insight of the hydraulic and control systems features has been cleared. This paper concludes main findings and results of EHVA research in Tampere University of Technology / IHA.
The hydraulic circuit effect to the power consumption of EHVA is clear. 3-way controlled actuator has advantages compared to 4-way controlled system. Direction control valve defines controllability of the system, and has source of the largest single component power loss. Hydraulic actuator design has also a fair effect to the overall power consumption when pressure force vs. required flow changes heavily, due to load forces. Mechanically, return spring design of the gas exchange valve has great effect to power consumption too.
Controller design is dependent on what kind of performance is required. The controller compensates lack of control valve bandwidth, and reacts to changing environmental variables. In this state, the Iterative Learning Controller (ILC) has proved the best choice. If gas exchange valve exact lift motion during the lift event is not important but variation between the strokes is kept in narrow range, a Model-Based Controller (MBC) is a strong option.
Technical Cleanliness of Assembled Fluid Power Components
Authors: Elo Lauri , Pekkonen Juuso , Rinkinen Jari 
Published: October 2014

The demands on the cleanliness of fluid power systems increase continuously. The KompuNW project, which was launched in 2011, aimed to find out the technical cleanliness of fluid power components in Finland, and the technical cleanliness was measured with commercial cleanliness cabinets. These cabinets apply well for hydraulic components where a rinsing pen should reach the test component surfaces that need to be controlled. In some cases the flow rate or the pressure produced by the cleanliness cabinets is insufficient for detaching particles from the surfaces of hollow components e.g. hydraulic cylinders or oil reservoirs. For this reason the functional test bench, designed and constructed in IHA, uses low viscosity hydraulic oil to extract contaminants from the assembled fluid power components. The extracted particles can then be analysed in the test bench with a microscope or an inline particle counter.
This paper has several aims. First the backgrounds of fluid power components are described. Then this paper will present the differences in the definitions and codes of oil cleanliness (ISO 4406:1999, SAE AS4059E:2005) and component cleanliness (ISO 16232:2007). In addition, the differences between the test bench and the commercial cleanliness cabinets are presented. Standards ISO 16232:2007-5 and ISO 18413:2002 were applied in the design of the test bench. The main points of these standards are introduced in this paper, too.
Finally the extraction procedures of a hydraulic cylinder and oil reservoir are shown with examples of the extraction curves of these components.
Part 1: Targeting cancer pathways: Tumor resistance
Authors: Yaffe Michael B. , Engelman Jeffrey , Deininger Michael W. 
Published: October 2014

This webinar is the first in a series focusing on the pathways that allow for cancer development and progression, the emerging research in identifying and targeting these pathways, and the innovations in the development of cancer treatment options. Recent advances in our understanding of cancer have revealed that the disease cannot be understood through simple analysis of genetic mutations within cancerous cells. Instead, tumors should be considered complex tissues in which the cancer cells evolve and communicate with the surrounding cellular microenvironment to promote their own survival and dissemination. Although therapies against specific signaling proteins or pathways have been remarkably successful at treating certain cancers, the tumors frequently develop resistance, leading to even more aggressive forms of the disease.
This webinar will focus on how rewiring of signaling pathways in response to drug treatment contributes to resistance and how this knowledge can be leveraged to develop more effective treatment strategies.
Compensatory Substitutions in the HIV-1 Capsid Reduce the Fitness Cost Associated with Resistance to a Capsid-Targeting Small-Molecule Inhibitor
Authors: Shi Jiong , Zhou Jing , Halambage Upul D. , Shah Vaibhav B. , Burse Mallori J. , Wu Hua , Blair Wade S. , Butler Scott L. , Aiken Christopher 
Published: October 2014

ABSTRACT

The HIV-1 capsid plays multiple roles in infection and is an emerging therapeutic target. The small-molecule HIV-1 inhibitor PF-3450074 (PF74) blocks HIV-1 at an early postentry stage by binding the viral capsid and interfering with its function. Selection for resistance resulted in accumulation of five amino acid changes in the viral CA protein, which collectively reduced binding of the compound to HIV-1 particles. In the present study, we dissected the individual and combinatorial contributions of each of the five substitutions Q67H, K70R, H87P, T107N, and L111I to PF74 resistance, PF74 binding, and HIV-1 infectivity. Q67H, K70R, and T107N each conferred low-level resistance to PF74 and collectively conferred strong resistance. The substitutions K70R and L111I impaired HIV-1 infectivity, which was partially restored by the other substitutions at positions 67 and 107. PF74 binding to HIV-1 particles was reduced by the Q67H, K70R, and T107N substitutions, consistent with the location of these positions in the inhibitor-binding pocket. Replication of the 5Mut virus was markedly impaired in cultured macrophages, reminiscent of the previously reported N74D CA mutant. 5Mut substitutions also reduced the binding of the host protein CPSF6 to assembled CA complexes
in vitro
and permitted infection of cells expressing the inhibitory protein CPSF6-358. Our results demonstrate that strong resistance to PF74 requires accumulation of multiple substitutions in CA to inhibit PF74 binding and compensate for fitness impairments associated with some of the sequence changes.

IMPORTANCE
The HIV-1 capsid is an emerging drug target, and several small-molecule compounds have been reported to inhibit HIV-1 infection by targeting the capsid. Here we show that resistance to the capsid-targeting inhibitor PF74 requires multiple amino acid substitutions in the binding pocket of the CA protein. Three changes in CA were necessary to inhibit binding of PF74 while maintaining viral infectivity. Replication of the PF74-resistant HIV-1 mutant was impaired in macrophages, likely owing to altered interactions with host cell factors. Our results suggest that HIV-1 resistance to capsid-targeting inhibitors will be limited by functional constraints on the viral capsid protein. Therefore, this work enhances the attractiveness of the HIV-1 capsid as a therapeutic target.