bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amyloid fibril polymorphism: a challenge for molecular imaging and therapy
Authors: Fändrich M. , Nyström S. , Nilsson K. P. R. , Böckmann A. , LeVine H. , Hammarström P. 
Published: January 2018

AbstractThe accumulation of misfolded proteins (MPs), both unique and common, for different diseases is central for many chronic degenerative diseases. In certain patients, MP accumulation is systemic (e.g. TTR amyloid), and in others, this is localized to a specific cell type (e.g. Alzheimer's disease). In neurodegenerative diseases, NDs, it is noticeable that the accumulation of MP progressively spreads throughout the nervous system. Our main hypothesis of this article is that MPs are not only markers but also active carriers of pathogenicity. Here, we discuss studies from comprehensive molecular approaches aimed at understanding MP conformational variations (polymorphism) and their bearing on spreading of MPs, MP toxicity, as well as MP targeting in imaging and therapy. Neurodegenerative disease (ND) represents a major and growing societal challenge, with millions of people worldwide suffering from Alzheimer's or Parkinson's diseases alone. For all NDs, current treatment is palliative without addressing the primary cause and is not curative. Over recent years, particularly the shape‐shifting properties of misfolded proteins and their spreading pathways have been intensively researched. The difficulty in addressing ND has prompted most major pharma companies to severely downsize their nervous system disorder research. Increased academic research is pivotal for filling this void and to translate basic research into tools for medical professionals. Recent discoveries of targeting drug design against MPs and improved model systems to study structure, pathology spreading and toxicity strongly encourage future studies along these lines to provide an opportunity for selective imaging, prognostic diagnosis and therapy.
Peritonitis after percutaneous endoscopic gastrojejunostomy for levodopa–carbidopa intestinal gel treatment despite concomitant use of gastropexy
Authors: Tsuboi Takashi , Watanabe Hirohisa , Funasaka Kouhei , Takebayashi Mikiko , Miyata Kazushi , Katsuno Masahisa 
Published: January 2018

AbstractA 58‐year‐old man with Parkinson's disease experienced peritonitis after percutaneous endoscopic gastrojejunostomy (PEG‐J) for levodopa–carbidopa intestinal gel treatment despite concomitant use of gastropexy. Although gastropexy reduces complications including peritonitis, clinicians should consider structural characteristics of PEG‐J devices and patients’ anatomical differences. We recommend that suture threads are removed 2–4 weeks after PEG‐J and that the PEG‐J tube length outside the body is routinely recorded to assess tube dislocation.
Rubisco is not really so bad
Authors: Bathellier Camille , Tcherkez Guillaume , Lorimer George H. , Farquhar Graham D. 
Published: January 2018

AbstractRibulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) is the most widespread carboxylating enzyme in autotrophic organisms. Its kinetic and structural properties have been intensively studied for more than half a century. Yet important aspects of the catalytic mechanism remain poorly understood, especially the oxygenase reaction. Because of its relatively modest turnover rate (a few catalytic events per second) and the competitive inhibition by oxygen, Rubisco is often viewed as an inefficient catalyst for CO2 fixation. Considerable efforts have been devoted to improving its catalytic efficiency, so far without success. In this review, we re‐examine Rubisco's catalytic performance by comparison with other chemically related enzymes. We find that Rubisco is not especially slow. Furthermore, considering both the nature and the complexity of the chemical reaction, its kinetic properties are unremarkable. Although not unique to Rubisco, oxygenation is not systematically observed in enolate and enamine forming enzymes and cannot be considered as an inevitable consequence of the mechanism. It is more likely the result of a compromise between chemical and metabolic imperatives. We argue that a better description of Rubisco mechanism is still required to better understand the link between CO2 and O2 reactivity and the rationale of Rubisco diversification and evolution.
Arranging ‘facts’ in ‘fiction’ – Presenting categories of knowledge in Antwerp prints and plays (1550–1565)
Authors: Vandommele Jeroen 
Published: January 2018

AbstractThis essay examines the way the artes liberales – the seven disciplines that traditionally categorised the different fields of learning – were publicly envisioned in the commercial metropolis of Antwerp between 1550 and 1565. It will introduce the Antwerp Landjuweel of 1561, a theatre competition organised by chambers of rhetoric that had knowledge as its main theme. Through an in‐depths analysis of the allegorical plays performed during this Landjuweel, the essay shows that these plays had an encyclopaedic purpose. Their goal was to produce a structured system that categorised the various arts and sciences. To help internalise and deliberate the presented knowledge structure, the plays employed a fictional mode of discourse and used a visual language related to rhetorical strategies. Showing the similarities between the plays of 1561 and two print series published around the same time and composed by Frans Floris, an influential Antwerp artist who had strong ties to the chambers of rhetoric, it is argued that both media intended to aid citizens in navigating the existing knowledge system, while at the same time redefining the corpus of knowledge and its necessity, thus propagating their own view of humanity's place in the world.
Does trade weaken product standards?
Authors: Berti Katia , Falvey Rod 
Published: January 2018

AbstractWe investigate the effects of trade on national minimum quality standards for a product whose quality is unobservable to consumers prior to purchase. Two standard‐setting regimes are considered: (1) where the regulatory authority takes the trade share as given; and (2) where the regulatory authority takes full account of its ability to influence the trade share. We find that standards are not a protectionist instrument in this model, the usual gains from trade apply if standards are maintained at their autarky values, trade can cause private standards to be adjusted in a welfare reducing way, and the welfare of a country is higher if its regulatory authority adopts regime (2) rather than (1).
Recent morphology and sedimentary processes along the western slope of Great Bahama Bank (Bahamas)
Authors: Principaud Melanie , Mulder Thierry , Hanquiez Vincent , Ducassou Emmanuelle , Eberli Gregor P. , Chabaud Ludivine , Borgomano Jean 
Published: January 2018

AbstractCarbonate slopes and associated resedimented deposits have recently gained renewed interest because they represent volumetrically significant parts of carbonate platforms. Carbonate slopes are highly variable compositionally, architecturally and spatially due to a spectrum of sediment sources, resedimentation processes and controlling factors. Here, new high resolution acoustic data (including EM302 multi‐beam echo‐sounder and very high resolution seismic) and piston cores document highly diverse and complex morphological features along the north‐western slope of Great Bahama Bank. The recent morphology of the slope is the result of the interplay between depositional and erosive processes that vary through time and along strike. The different sedimentary processes are recorded as a Pleistocene lowstand surface, characterized by many erosional features and a Holocene sedimentary wedge along the upper to middle slope that partially covers the underlying Pleistocene surface. Sedimentary processes during the Holocene are dominated by density cascading flows, which export muddy aragonitic sediment from the platform top towards the slope. Sedimentation rates, however, vary along strike due to platform top morphology combined with the variable strength of the basinal current. Reefs and islands in the Bimini area block off‐bank sediment export, and shoals and tidal deltas from Cat Cay to the south reduce the density cascading processes. Numerous small and large slope failure scars show the instability of the steep slopes of Great Bahama Bank. Bottom currents dominate the lower slope and the basin. Striations and moats are the morphological expressions of current directions, while areas of non‐deposition document strong current and concomitant removal of off‐bank transported sediment along parts of the slope, while the Santaren Drift and the drift on the north‐western edge of Great Bahama Bank act as the depositional locus for the fine‐grained sediments transported in the current.
Mycobacterium abscessus infections in lung transplant recipients: 15‐year experience from a single institution
Authors: Osmani Morsal , Sotello David , Alvarez Salvador , Odell John A. , Thomas Mathew 
Published: January 2018

AbstractPurposeTo evaluate our institutional experience with Mycobacterium abscessus infections occurring in lung transplant recipients (LTR).MethodsWe retrospectively reviewed our prospectively collected institutional adult lung transplant database from 2001 to 2015 to identify patients with M. abscessus or Mycobacterium chelonae/abscessus infection before or after transplantation. Untreated, colonized patients were excluded from the study. Electronic health records of nine out of 516 lung recipients (1.74%) with clinical infection were reviewed to determine outcomes.ResultsSeven patients acquired the infection after transplantation. Indications for transplantation were: idiopathic pulmonary fibrosis (in 6), chronic obstructive pulmonary disease (in 2), and cystic fibrosis (in 1). Five patients (55.5%) underwent bilateral lung transplantation; one patient required bilateral re‐transplantation for complications from infection. M. abscessus was isolated from the respiratory tract with a median time of 7.5 months (range: 3 days to 13 months) from transplantation. All patients were treated using a multidrug regimen, with durations ranging from 3 days to 12 months. Complications from infection included death in one patient, bronchial anastomotic dehiscence in one patient, delayed bronchial occlusions in two patients, and osteomyelitis of the knee in one patient. Median survival time from transplantation was 39 months (range: 11‐96 months) and from the date of first positive culture was 58 months (range: 3‐91 months). Five patients (55.5%) were cured but two had re‐infections >1 year later.ConclusionsMycobacterium abscessus infection in LTR is rare and can lead to severe complications. Eradication is difficult and usually requires prolonged combination antibiotic therapy and occasionally surgical management.
Creutzfeldt‐Jakob disease and blood transfusion safety
Authors: Seed C. R. , Hewitt P. E. , Dodd R. Y. , Houston F. , Cervenakova L. 
Published: January 2018

Transmissible spongiform encephalopathies (TSEs) are untreatable, fatal neurologic diseases affecting mammals. Human disease forms include sporadic, familial and acquired Creutzfeldt‐Jakob disease (CJD). While sporadic CJD (sCJD) has been recognized for near on 100 years, variant CJD (vCJD) was first reported in 1996 and is the result of food‐borne transmission of the prion of bovine spongiform encephalopathy (BSE, ‘mad cow disease’). Currently, 230 vCJD cases have been reported in 12 countries, the majority in the UK (178) and France (27). Animal studies demonstrated highly efficient transmission of natural scrapie and experimental BSE by blood transfusion and fuelled concern that sCJD was potentially transfusion transmissible. No such case has been recorded and case–control evaluations and lookback studies indicate that, if transfusion transmission occurs at all, it is very rare. In contrast, four cases of apparent transfusion transmission of vCJD infectivity have been identified in the UK. Risk minimization strategies in response to the threat of vCJD include leucodepletion, geographically based donor deferrals and deferral of transfusion recipients. A sensitive and specific, high‐throughput screening test would provide a potential path to mitigation but despite substantial effort no such test has yet appeared. The initial outbreak of vCJD appears to be over, but concern remains about subsequent waves of disease among those already infected. There is considerable uncertainty about the size of the infected population, and there will be at least a perception of some continuing risk to blood safety. Accordingly, at least some precautionary measures will remain in place and continued surveillance is necessary.
ACOUSTICAL STANDARDS NEWS
Authors: Stremmel Neil B. , Struck Christopher J. 
Published: January 2018

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, S3/SC 1, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, animal bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes a catalog of Acoustical American National Standards. To receive a copy of the latest Standards catalog, please contact Neil Stremmel.
Comments are welcomed on all material in Acoustical Standards News.
This Acoustical Standards News section in JASA and other information on the Standards Program of the Acoustical Society of America are available via the ASA home page: http://acousticalsociety.org.
Shaping Substrate Selectivity in a Broad-Spectrum Metallo-β-Lactamase
Authors: González Lisandro J. , Stival Cintia , Puzzolo Juan L. , Moreno Diego M. , Vila Alejandro J. 
Published: January 2018

ABSTRACT
Metallo-β-lactamases (MBLs) are the major group of carbapenemases produced by bacterial pathogens. The design of MBL inhibitors has been limited by, among other issues, incomplete knowledge about how these enzymes modulate substrate recognition. While most MBLs are broad-spectrum enzymes, B2 MBLs are exclusive carbapenemases. This narrower substrate profile has been attributed to a sequence insertion present in B2 enzymes that limits accessibility to the active site. In this work, we evaluate the role of sequence insertions naturally occurring in the B2 enzyme Sfh-I and in the broad-spectrum B1 enzyme SPM-1. We engineered a chimeric protein in which the sequence insertion of SPM-1 was replaced by the one present in Sfh-I. The chimeric variant is a selective cephalosporinase, revealing that the substrate profile of MBLs can be further tuned depending on the protein context. These results also show that the stable scaffold of MBLs allows a modular engineering much richer than the one observed in nature.
Salt Stress-Induced Loss of Iron Oxidoreduction Activities and Reacquisition of That Phenotype Depend on
rus
Operon Transcription in Acidithiobacillus ferridurans
Authors: Bonnefoy Violaine , Grail Barry M. , Johnson D. Barrie 
Published: January 2018

ABSTRACT

The type strain of the mineral-oxidizing acidophilic bacterium
Acidithiobacillus ferridurans
was grown in liquid medium containing elevated concentrations of sodium chloride with hydrogen as electron donor. While it became more tolerant to chloride, after about 1 year, the salt-stressed acidophile was found to have lost its ability to oxidize iron, though not sulfur or hydrogen. Detailed molecular examination revealed that this was due to an insertion sequence, IS
Afd1
, which belongs to the IS
Pepr1
subgroup of the IS
4
family, having been inserted downstream of the two promoters PI and PII of the
rus
operon (which codes for the iron oxidation pathway in this acidophile), thereby preventing its transcription. The ability to oxidize iron was regained on protracted incubation of the culture inoculated onto salt-free solid medium containing ferrous iron and incubated under hydrogen. Two revertant strains were obtained. In one, the insertion sequence IS
Afd1
had been excised, leaving an 11-bp signature, while in the other an ∼2,500-bp insertion sequence (belonging to the IS
66
family) was detected in the downstream inverted repeat of IS
Afd1
. The transcriptional start site of the
rus
operon in the second revertant strain was downstream of the two ISs, due to the creation of a new “hybrid” promoter. The loss and subsequent regaining of the ability of
A. ferridurans
T
to reduce ferric iron were concurrent with those observed for ferrous iron oxidation, suggesting that these two traits are closely linked in this acidophile.

IMPORTANCE
Iron-oxidizing acidophilic bacteria have primary roles in the oxidative dissolution of sulfide minerals, a process that underpins commercial mineral-processing biotechnologies (“biomining”). Most of these prokaryotes have relatively low tolerance to chloride, which limits their activities when only saline or brackish waters are available. The study showed that it was possible to adapt a typical iron-oxidizing acidophile to grow in the presence of salt concentrations similar to those in seawater, but in so doing they lost their ability to oxidize iron, though not sulfur or hydrogen. The bacterium regained its capacity for oxidizing iron when the salt stress was removed but simultaneously reverted to tolerating lower concentrations of salt. These results suggest that the bacteria that have the main roles in biomining operations could survive but become ineffective in cases where saline or brackish waters are used for irrigation.
Validation of Active Surveillance Testing for Clostridium difficile Colonization Using the cobas Cdiff Test
Authors: Patel Parul A. , Schora Donna M. , Singh Kamaljit , Peterson Lance R. 
Published: January 2018

ABSTRACT

Clostridium difficile
infection (CDI) is not declining in the United States. Nucleic acid amplification tests (NAAT) are used as part of active surveillance testing programs to prevent health care-associated infection. The objective of this study was to validate the cobas Cdiff Test on the cobas 4800 System (cobas) within a four-hospital system using prospectively collected perirectal swabs from asymptomatic patients at admission and during monthly intensive care unit (ICU) screening in an infection control CDI reduction program. Performance of the cobas was compared to that of toxigenic culture. Each positive cobas sample and the next following negative patient swab were cultured. The study design gave 273 samples processed by both cobas (137 positive and 136 negative) and culture (one negative swab was not cultured). Discrepant analysis was performed using a second NAAT, the Xpert
C. difficile
Epi test (Xpert). This strategy was compared to a medical record review for antibiotic receipt that would inhibit growth of
C. difficile
in colonic stool. None of the cobas-negative samples were culture positive. The cobas positive predictive value was 75.2% (95% confidence interval [CI], 66.9% to 82%) and positive percent agreement was 100% (95% CI, 96.0% to 100%). Overall agreement between cobas and direct toxigenic culture was 87.6% (95% CI, 83.1% to 91%). For the cobas-positive/culture-negative (discrepant) samples, 7 Xpert-positive samples were from patients receiving inhibitory antimicrobials; only 4 of 23 Xpert-negative samples received these agents (
P
= 0.00006). Our results support use of the cobas as a reliable assay for an active surveillance testing program to detect asymptomatic carriers of toxigenic
C. difficile
.
Stress-Induced Reorganization of the Mycobacterial Membrane Domain
Authors: Hayashi Jennifer M. , Richardson Kirill , Melzer Emily S. , Sandler Steven J. , Aldridge Bree B. , Siegrist M. Sloan , Morita Yasu S. 
Published: January 2018

ABSTRACT

Cell elongation occurs primarily at the mycobacterial cell poles, but the molecular mechanisms governing this spatial regulation remain elusive. We recently reported the presence of an intracellular membrane domain (IMD) that was spatially segregated from the conventional plasma membrane in
Mycobacterium smegmatis
. The IMD is enriched in the polar region of actively elongating cells and houses many essential enzymes involved in envelope biosynthesis, suggesting its role in spatially restricted elongation at the cell poles. Here, we examined reorganization of the IMD when the cells are no longer elongating. To monitor the IMD, we used a previously established reporter strain expressing fluorescent IMD markers and grew it to the stationary growth phase or exposed the cells to nutrient starvation. In both cases, the IMD was delocalized from the cell pole and distributed along the sidewall. Importantly, the IMD could still be isolated biochemically by density gradient fractionation, indicating its maintenance as a membrane domain. Chemical and genetic inhibition of peptidoglycan biosynthesis led to the delocalization of the IMD, suggesting the suppression of peptidoglycan biosynthesis as a trigger of spatial IMD rearrangement. Starved cells with a delocalized IMD can resume growth upon nutrient repletion, and polar enrichment of the IMD coincides with the initiation of cell elongation. These data reveal that the IMD is a membrane domain with the unprecedented capability of subcellular repositioning in response to the physiological conditions of the mycobacterial cell.

IMPORTANCE
Mycobacteria include medically important species, such as the human tuberculosis pathogen
Mycobacterium tuberculosis
. The highly impermeable cell envelope is a hallmark of these microbes, and its biosynthesis is a proven chemotherapeutic target. Despite the accumulating knowledge regarding the biosynthesis of individual envelope components, the regulatory mechanisms behind the coordinated synthesis of the complex cell envelope remain elusive. We previously reported the presence of a metabolically active membrane domain enriched in the elongating poles of actively growing mycobacteria. However, the spatiotemporal dynamics of the membrane domain in response to stress have not been examined. Here, we show that the membrane domain is spatially reorganized when growth is inhibited in the stationary growth phase, under nutrient starvation, or in response to perturbation of peptidoglycan biosynthesis. Our results suggest that mycobacteria have a mechanism to spatiotemporally coordinate the membrane domain in response to metabolic needs under different growth conditions.