bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum Chemical Spin Densities for Radical Cations of Photosynthetic Pigment Models
Authors: Artiukhin Denis G. , Stein Christopher J. , Reiher Markus , Neugebauer Johannes 
Published: May 2017

AbstractThe spin densities of radical cations of magnesium porphyrin, magnesium chlorine and a truncated chlorophyll a model are calculated with density‐functional theory and multiconfigurational quantum chemical methods. The latter serve as a reference for approximate density‐functional theory which yields spin densities that may suffer from the self‐interaction error. We carried out complete active space self‐consistent field calculations with increasing active orbital spaces to systematically converge qualitatively correct spin densities. In particular, for the magnesium chlorine and chlorophyll a model radical cations, this is not easy to achieve because of the lower symmetry compared to magnesium porphyrin. Strategies had to be employed which allowed us to consider very large active orbital spaces. We explored restricted active space self‐consistent field and density‐matrix renormalization group calculations. Based on these reference data, we assessed the accuracy of different density‐functional approximations. We show that in particular, exchange–correlation model potentials with correct asymptotic behavior yield good spin densities, and we find, in agreement with previous studies on different classes of compounds, that hybrid functionals systematically increase spin‐polarization effects with increasing amounts of exact exchange. Our results provide a starting point for investigations of spin densities of more complex systems such as the hinge model for the primary electron donor in photosystem II.
Phytochromes from Agrobacterium fabrum
Authors: Lamparter Tilman , Krauß Norbert , Scheerer Patrick 
Published: May 2017

AbstractAgrobacterium fabrum is a widely used model bacterium for gene transfer from pro‐ to eukaryote, for genetics and metabolism. The phytochrome system of Agrobacterium, encompassing the two phytochromes Agp1 and Agp2, has provided deep insight into phytochrome action in a bacterial organism. This review summarizes recent results on phytochrome evolution, phytochrome regulation of conjugation and plant infection and biochemical studies including the crystal structure of Agp1‐PCM, the photosensory core module of Agp1.
Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers
Authors: Orekhov Philipp , Bothe Arne , Steinhoff Heinz‐Jürgen , Shaitan Konstantin V. , Raunser Stefan , Fotiadis Dimitrios , Schlesinger Ramona , Klare Johann P. , Engelhard Martin 
Published: May 2017

AbstractArchaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two‐component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the “U”‐”V” transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55‐58]. A model of cooperativity at the transmembrane level is discussed.
The Expanded Red/Green Cyanobacteriochrome Lineage: An Evolutionary Hot Spot
Authors: Fushimi Keiji , Ikeuchi Masahiko , Narikawa Rei 
Published: May 2017

AbstractThis article highlights the paper by Rockwell et al. in the current issue of Photochemistry and Photobiology. Rockwell et al. describe the discovery of novel two‐Cys photocycles within the “expanded red/green” (XRG) cyanobacteriochrome (CBCR) lineage. Comprehensive phylogenetic analysis revealed that several XRG CBCRs possess a second Cys residue in the DXCF (Asp‐Xaa‐Cys‐Phe) motif conserved among the DXCF CBCR lineage. Spectral studies identified that these CBCRs showed green/blue or ultraviolet/blue reversible photoconversion abilities. The green/blue reversible photocycle had not been reported previously among the XRG CBCR lineage. Based on these findings, Rockwell et al. replaced three amino acid residues in a red/green reversible CBCR, NpR6012g4, and succeeded in constructing a violet/green reversible photocycle. These findings, together with previous studies, provide a good explanation for the evolutionary flexibility of the XRG CBCRs.
Hierarchical models for white mould in snap bean
Authors: Shah D. A. , Dillard H. R. , Pethybridge S. J. 
Published: May 2017

Limitations on the acceptable proportion (incidence) of pods with white mould may lead to the rejection of entire fields of processing snap bean. The low tolerances (no more than 2% to 6% of pods with white mould) are difficult to estimate with sufficient precision in the field when time is limited. These constraints motivated this study of white mould across three spatial hierarchical levels: pods, plants and quadrats consisting of two adjacent plants within rows. Hierarchical relationships are required when designing formal rules for estimating the incidence of pods with white mould from units higher in the spatial hierarchy. Disease assessments were made on all pods from 38 within‐row transects of 40 plants each of the snap bean cultivar Hystyle. Using probability‐based principles, equations were derived and fitted to data on the incidence of white mould on pods (ipod), plants (ipad) and quadrats (iq(2)), which led to a function directly linking ipod to iq(2). The variance of ipod increased with iq(2), but that may be of little consequence at the lower values of iq(2) likely to be associated with ipod values at processor‐set tolerances. For example, at iq(2) = 0.1 there was a 92% probability that ipod was less than 0.02. Assessing iq(2) may be more efficient than directly estimating ipod because iq(2) was about an order of magnitude higher than ipod. Results suggest it may be feasible to design sampling plans for estimating the proportion of pods with white mould from an assessment of the proportion of diseased quadrats.
Clinical characteristics and survival of systemic sclerosis patients with pulmonary hypertension and elevated wedge pressure: Observations from the PHAROS cohort
Authors: Lammi Matthew R. , Saketkoo Lesley A. , Gordon Jessica K. , Lauto Paula , Fagan Karen , Steen Virginia D. ,   on behalf of the PHAROS Investigators
Published: May 2017

ABSTRACT
Background and objectiveSystemic sclerosis (SSc) is a complex autoimmune disease commonly associated with pulmonary hypertension (PH). When associated with elevated pulmonary artery wedge pressure (PAWP), pulmonary artery pressure (PAP) is either in‐proportion (post‐capillary PH) or higher than expected (combined PH) relative to the increased PAWP.MethodsPatients from the PHAROS registry (a prospective observational cohort of SSc‐PH patients) who had mean PAP ≥ 25 and PAWP > 15 on right heart catheterization were stratified based on diastolic pressure gradient (DPG). Kaplan–Meier analysis was performed to compare survival and PH‐related hospitalization. Baseline factors were compared between patients dying and those who survived using Cox regression analysis.ResultsA total of 59 patients were included, of whom 21 (36%) patients were classified as combined PH and 38 (64%) had post‐capillary PH. No baseline characteristics were significantly different between the two groups. There were no differences in survival or PH‐related hospitalization between the groups. The only baseline factor independently associated with death was lower 6‐min walk distance (6MWD) (hazard ratio (HR): 1.33 per 25 m decrease, 95% CI: 1.11–1.59, P = 0.002). PH‐specific medications were started during follow‐up in significantly more patients in the combined PH group compared with the post‐capillary group (86% vs 50%, P = 0.01).ConclusionOutcomes were similar between SSc patients with post‐capillary PH and combined pre‐ and post‐capillary PH. 6MWD at baseline can predict risk for death in SSc patients with PH and an elevated PAWP. More patients with combined PH were started on PH‐specific medications, and the clinical benefit of treating this subgroup specifically in SSc patients needs further exploration.
Crosstalk Between Enzyme Matrix Metalloproteinases 2 and 9 and Regulatory T Cell Immunity in the Global Burden of Atherosclerosis
Authors: Lekic A. , Brekalo Z. , Kvesic A. , Kovacevic M. , Baricev‐Novakovic Z. , Sutic I. , Bulog A. , Sutic I. , Pavisic V. , Mrakovcic‐Sutic I. 
Published: May 2017

AbstractChanges in immune and inflammatory responses may play a crucial role in the development and progression of atherosclerosis, as an autoimmune, chronic and progressive inflammatory disease. Immunological activity and vascular inflammation during atherosclerosis can be modulated by autoimmune responses against self‐antigens, according to changeable risk factors (cholesterol, oxidized low‐density lipoprotein (ox‐LDL) in the vascular wall, fatty acids, etc.), and accompanied by accumulation of leucocytes and proinflammatory cytokines, which stimulate the transcription of matrix metalloproteinases (MMPs), whose concentration are increased in foam cell‐rich regions. Regulatory T cells (Tregs) represent a unique subpopulation of T cells specialized in the regulation of immune response and in the suppression of proatherogenic T cells. The aim of our study was to examine the interactions between the concentration of enzyme matrix metalloproteinases 2 and 9 (MMP‐2 and 9) in urine and the percentage of Tregs in peripheral blood of two groups of patients: with carotid artery stenosis (CAS), undergoing surgery and with mild atherosclerosis (A) from general practice. The method of enzyme immunoassay (ELISA) was used to determine enzyme MMP expression, and Tregs was examined by flow cytometric analysis. Our data have showed a large increase in the enzyme MMP‐2 and 9 in the urine of CAS and A patients in comparison with healthy controls and indicated this method as an easy marker for the monitoring of the development of atherosclerosis. Simultaneously, the diminished number of Tregs in the same patients pointed the importance of these regulatory mechanisms in the etiopathogenesis of atherosclerosis and possible Tregs‐mediated therapy.
Interrelationships and diversification of ArgynnisFabricius and SpeyeriaScudder butterflies
Authors: DE MOYA ROBERT S. , SAVAGE WESLEY K. , TENNEY CHRIS , BAO XIAOSHAN , WAHLBERG NIKLAS , HILL RYAN I. 
Published: May 2017

AbstractDiverse radiations of insects are often associated with adaptations to host plants, and well‐resolved phylogenetic relationships are required to fully understand them. Palearctic Argynnis and related subgenera, together with North American Speyeria butterflies make up a radiation whose species hypotheses are confounded by shared wing colour patterns between sympatric populations of closely related recognized species. Previous studies of this group indicate that Speyeria is a lineage within Argynnis, but sampling in these studies has either involved too few Speyeria species or incomplete sampling of Argynnis species. Thus, no comprehensive phylogenetic analysis exists for all members that answers the question of monophyly of Speyeria, or other subgeneric taxa, and their relationship to Argynnis species. We completed a phylogenetic analysis of all North American Speyeria species and all but one species within Argynnis, using one mitochondrial (cytochrome c oxidase I, COI) and four nuclear genes [elongation factor 1 alpha (EF1α), wingless (WG), glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH), and ribosomal protein S5 (RPS5)]. The results indicate three major lineages within Argynnis s.l.: two Palearctic and one containing both Palearctic and Nearctic species. In summary, the phylogenetic analyses suggest the need for reorganization into three natural groups: Argynnis, Fabriciana and Speyeria. Within each of these genera the phylogenetic hypothesis indicates an evolutionary history marked by rapid diversification and potential extinction, followed by ongoing lineage sorting. The position of North American Speyeria is nested within the Palearctic lineages, which indicates that the radiation began in Asia and was fuelled by existing Viola diversity in North America. Dating analyses of Viola and Speyeria corroborate this hypothesis. The current North American Speyeria species are mixed on the tree, indicating a recent and ongoing radiation. These results provide needed clarity on the evolution of this group, which contains species of conservation concern.
Blood transfusion in the surgical treatment of adolescent idiopathic scoliosis—a single‐center experience of patient blood management in 210 cases
Authors: Ohrt‐Nissen Søren , Bukhari Naeem , Dragsted Casper , Gehrchen Martin , Johansson Pär I. , Dirks Jesper , Stensballe Jakob , Dahl Benny 
Published: May 2017

BACKGROUNDThe surgical treatment of adolescent idiopathic scoliosis can be associated with substantial blood loss, requiring allogeneic red blood cell (RBC) transfusion. This study describes the use of RBC and the effect of a standardized perioperative patient blood management program.STUDY DESIGN AND METHODSPatients treated with posterior instrumented fusion were consecutively enrolled over a 6‐year period. Patient blood management strategies were implemented in 2011, including prophylactic tranexamic acid, intraoperative permissive hypotension, restrictive fluid therapy (including avoidance of synthetic colloids), restrictive RBC trigger according to institutional standardized protocol, the use of cell savage, and goal‐directed therapy according to thrombelastography.RESULTSIn total, 210 patients were included. 64 patients (31%) received RBC transfusions. A decline in the intraoperative rate of RBC transfusion was observed, from 77% in 2011 to 13% in 2016 (p < 0.001). Patients in the transfusion group had a significantly larger major curve, lower preoperative hemoglobin, higher estimated blood loss, and an increased use of crystalloid volume resuscitation. Multiple logistic regression showed that significant predictors for RBC transfusion were preoperative hemoglobin level (odds ratio [OR], 0.40; 95% confidence interval [CI], 0.27‐0.57), estimated blood loss (OR, 1.26; 95% CI, 1.15‐1.42), and year of surgery (indicating the effect of patient blood management) (OR per year, 0.76; 95% CI, 0.58‐0.99).CONCLUSIONA perioperative patient blood management program substantially reduced the need for RBC transfusion. A preoperative evaluation of anemia is essential to further minimize transfusion rates.
Comparison of transfusion thresholds during neonatal extracorporeal membrane oxygenation
Authors: Sawyer Alexandra A. , Wise Linda , Ghosh Santu , Bhatia Jatinder , Stansfield Brian K. 
Published: May 2017

BACKGROUNDThe objective of this study was to assess complications and patient outcomes associated with a lower reflexive red blood cell (RBC) transfusion threshold for neonates undergoing extracorporeal membrane oxygenation (ECMO) for hypoxic respiratory failure.STUDY DESIGN AND METHODSA retrospective cohort study was conducted at a single tertiary neonatal intensive care unit of neonates undergoing ECMO support for refractory hypoxic respiratory failure for more than 24 hours between December 2009 and December 2014. Seventy‐two neonates received ECMO support for hypoxic respiratory failure for longer than 24 hours during the study period. Patient cohorts were determined based on transfusion threshold of hematocrit (Hct) level of less than 40% (December 2009‐October 2012) and Hct level of less than 35% (November 2012‐December 2014).RESULTSPatients who had a lower threshold for transfusion (Hct < 35) had a lower mean Hct (38.3% vs. 41.4%, p < 0.0001) and received less total RBC transfusion volume (10.4 mL/kg/day vs. 13.3 mL/kg/day, p = 0.002) while undergoing ECMO support. Survival off ECMO, survival to discharge, and complication rates were similar between the cohorts.CONCLUSIONSA lower Hct threshold of 35% is associated with a reduction in RBC transfusion volume and does not appear to alter complication rates or patient outcomes for neonates receiving ECMO support for respiratory failure.
Altered timing of riboflavin and ultraviolet light pathogen inactivation improves platelet in vitro quality
Authors: Schubert Peter , Culibrk Brankica , Karwal Simrath , Serrano Katherine , Levin Elena , Yi QiLong , Thiele Thomas , Greinacher Andreas , Marschner Susanne , Devine Dana V. 
Published: May 2017

BACKGROUNDThe platelet (PLT) storage lesion is in part caused by the collection and/or production process. Pathogen inactivation (PI) further accelerates its development leading to a reduced in vitro PLT functionality and hence quality. Although the treatment of PLT concentrates (PCs) with riboflavin and ultraviolet light PI should occur within 22 hours of collection, in this study the impact of treatment timing on in vitro PLT quality was investigated.STUDY DESIGN AND METHODSApheresis PCs were PI treated on the day of production or on Days 1, 3, or 4 of storage or left untreated as control. A panel of in vitro variables was used to monitor quality throughout 7‐day storage, including metabolism, PLT activation, and release of microparticles. Changes in phosphorylation profiles of proteins in the lysate and levels of PLT factor 4, thrombospondin, and epidermal growth factor (EGF) in the releasate were analyzed by immunoblots or enzyme‐linked immunosorbent assay.RESULTSBy Day 7 of storage, units illuminated on Day 4 showed a smaller impact of the PI process than units treated on the day of production or one day after on PLT quality such as PLT activation; metabolic activity; microvesicle and EGF release; and phosphorylation of p38, ERK, and HSP27. PCs treated on Day 3 of storage displayed an intermediate effect.CONCLUSIONThe timing of PI treatment of PCs influences in vitro PLT quality. Based on these results, timing recommendations should be reconsidered. If PI is applied, inventory management in blood banks might improve with a more flexible collection and treatment regime.
Selected Probiotic Lactobacilli Have the Capacity To Hydrolyze Gluten Peptides during Simulated Gastrointestinal Digestion
Authors: Francavilla Ruggiero , De Angelis Maria , Rizzello Carlo Giuseppe , Cavallo Noemi , Dal Bello Fabio , Gobbetti Marco 
Published: May 2017

ABSTRACT
The aim of this study was to demonstrate the capacity of probiotic lactobacilli to hydrolyze immunogenic gluten peptides. Eighteen commercial strains of probiotic lactobacilli with highly variable peptidase activity (i.e., aminopeptidase N, iminopeptidase, prolyl endopeptidyl peptidase, tripeptidase, prolidase, prolinase, and dipeptidase), including toward Pro-rich peptides, were tested in this study. Ten probiotic strains were selected on the basis of their specific enzyme activity. When pooled, these 10 strains provided the peptidase portfolio that is required to completely degrade the immunogenic gluten peptides involved in celiac disease (CD). The selected probiotic mixture was able to completely hydrolyze well-known immunogenic epitopes, including the gliadin 33-mer peptide, the peptide spanning residues 57 to 68 of the α9-gliadin (α9-gliadin peptide 57-68), A-gliadin peptide 62-75, and γ-gliadin peptide 62-75. During digestion under simulated gastrointestinal conditions, the pool of 10 selected probiotic lactobacilli strongly hydrolyzed the wheat bread gluten (ca. 18,000 ppm) to less than 10 ppm after 360 min of treatment. As determined by multidimensional chromatography (MDLC) coupled to nanoelectrospray ionization (nano-ESI)-tandem mass spectrometry (MS/MS), no known immunogenic peptides were detected in wheat bread that was digested in the presence of the probiotics. Accordingly, the level of cytokines (interleukin 2 [IL-2], IL-10, and interferon gamma [IFN-γ]) produced by duodenal biopsy specimens from CD patients who consumed wheat bread digested by probiotics was similar to the baseline value (negative control). Probiotics that specifically hydrolyze gluten polypeptides could also be used to hydrolyze immunogenic peptides that contaminate gluten-free products. This could provide a new and safe adjunctive therapy alternative to the gluten-free diet (GFD).

IMPORTANCE
This study confirmed that probiotic
Lactobacillus
strains have different enzymatic abilities for hydrolyzing polypeptides, including the Pro-rich epitopes involved in the pathology of CD. Ten lactobacilli with complementary peptidase activities that hydrolyze gluten peptides during simulated gastrointestinal digestion were selected and tested. The results collected showed the potential of probiotic formulas as novel dietary treatments for CD patients.
Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples
Authors: Kasturi Kuppuswamy N. , Drgon Tomas 
Published: May 2017

ABSTRACT

The methods currently used for detecting
Salmonella
in environmental samples require 2 days to produce results and have limited sensitivity. Here, we describe the development and validation of a real-time PCR
Salmonella
screening method that produces results in 18 to 24 h. Primers and probes specific to the gene
invA
, group D, and
Salmonella enterica
serovar Enteritidis organisms were designed and evaluated for inclusivity and exclusivity using a panel of 329
Salmonella
isolates representing 126 serovars and 22 non-
Salmonella
organisms. The
invA
- and group D-specific sets identified all the isolates accurately. The PCR method had 100% inclusivity and detected 1 to 2 copies of
Salmonella
DNA per reaction. Primers specific for
Salmonella
-differentiating fragment 1 (Sdf-1) in conjunction with the group D set had 100% inclusivity for 32
S
. Enteritidis isolates and 100% exclusivity for the 297 non-Enteritidis
Salmonella
isolates. Single-laboratory validation performed on 1,741 environmental samples demonstrated that the PCR method detected 55% more positives than the
V
itek
i
mmuno
d
iagnostic
a
ssay
s
ystem (VIDAS) method. The PCR results correlated well with the culture results, and the method did not report any false-negative results. The receiver operating characteristic (ROC) analysis documented excellent agreement between the results from the culture and PCR methods (area under the curve, 0.90; 95% confidence interval of 0.76 to 1.0) confirming the validity of the PCR method.

IMPORTANCE
This validated PCR method detects 55% more positives for
Salmonella
in half the time required for the reference method, VIDAS. The validated PCR method will help to strengthen public health efforts through rapid screening of
Salmonella
spp. in environmental samples.