bluuebunny/crossref_metadata_2025_split huggingface dataset:
GABAB receptors enhance excitatory responses in isolated rat retinal ganglion cells
Authors: Garaycochea Jay , Slaughter Malcolm M. 
Published: April 2016

Key points
GABA is an inhibitory transmitter but can sometimes produce paradoxical excitatory effects through synaptic networks.
We found a novel GABA‐mediated excitation within a single retinal cell. It involves a chain of events from receptor stimulation to the sequential modulation of two associated channels, resulting in enhanced neuroexcitability.
GABAB receptor activation selectively suppresses N‐type calcium channels.
The BK‐type potassium channels are exclusively linked to the N‐type calcium channel.
Thus, stimulation of GABAB receptors suppresses an outward current, increasing the excitatory range of single neurons.
AbstractGABAB receptors (GABABRs) suppress voltage‐gated calcium channels and activate G‐protein coupled potassium channels (GIRK and TREK channels), both mechanisms serving to inhibit neurons. In isolated rat retinal spiking neurons, GABABRs produce both actions but the net effect is to enhance excitatory signals. This is because GABABRs selectively suppress N‐type calcium channels, which in turn are specifically linked to BK channels. Consequently, when GABABRs are stimulated there is a reduction in outward current, allowing neurons to extend their level of depolarization. Whereas many retinal neurons use L‐type channels to stimulate vesicle fusion, the suppression of N‐type channels augments dynamic range without affecting transmitter release.
Peptidomimetic Small Molecules Disrupt Type IV Secretion System Activity in Diverse Bacterial Pathogens
Authors: Shaffer Carrie L. , Good James A. D. , Kumar Santosh , Krishnan K. Syam , Gaddy Jennifer A. , Loh John T. , Chappell Joseph , Almqvist Fredrik , Cover Timothy L. , Hadjifrangiskou Maria 
Published: April 2016

ABSTRACT

Bacteria utilize complex type IV secretion systems (T4SSs) to translocate diverse effector proteins or DNA into target cells. Despite the importance of T4SSs in bacterial pathogenesis, the mechanism by which these translocation machineries deliver cargo across the bacterial envelope remains poorly understood, and very few studies have investigated the use of synthetic molecules to disrupt T4SS-mediated transport. Here, we describe two synthetic small molecules (C10 and KSK85) that disrupt T4SS-dependent processes in multiple bacterial pathogens.
Helicobacter pylori
exploits a pilus appendage associated with the
cag
T4SS to inject an oncogenic effector protein (CagA) and peptidoglycan into gastric epithelial cells. In
H. pylori
, KSK85 impedes biogenesis of the pilus appendage associated with the
cag
T4SS, while C10 disrupts
cag
T4SS activity without perturbing pilus assembly. In addition to the effects in
H. pylori
, we demonstrate that these compounds disrupt interbacterial DNA transfer by conjugative T4SSs in
Escherichia coli
and impede
vir
T4SS-mediated DNA delivery by
Agrobacterium tumefaciens
in a plant model of infection. Of note, C10 effectively disarmed dissemination of a derepressed IncF plasmid into a recipient bacterial population, thus demonstrating the potential of these compounds in mitigating the spread of antibiotic resistance determinants driven by conjugation. To our knowledge, this study is the first report of synthetic small molecules that impair delivery of both effector protein and DNA cargos by diverse T4SSs.

IMPORTANCE
Many human and plant pathogens utilize complex nanomachines called type IV secretion systems (T4SSs) to transport proteins and DNA to target cells. In addition to delivery of harmful effector proteins into target cells, T4SSs can disseminate genetic determinants that confer antibiotic resistance among bacterial populations. In this study, we sought to identify compounds that disrupt T4SS-mediated processes. Using the human gastric pathogen
H. pylori
as a model system, we identified and characterized two small molecules that prevent transfer of an oncogenic effector protein to host cells. We discovered that these small molecules also prevented the spread of antibiotic resistance plasmids in
E. coli
populations and diminished the transfer of tumor-inducing DNA from the plant pathogen
A. tumefaciens
to target cells. Thus, these compounds are versatile molecular tools that can be used to study and disarm these important bacterial machines.
Biosynthesis of Conjugate Vaccines Using an O-Linked Glycosylation System
Authors: Pan Chao , Sun Peng , Liu Bo , Liang Haoyu , Peng Zhehui , Dong Yan , Wang Dongshu , Liu Xiankai , Wang Bin , Zeng Ming , Wu Jun , Zhu Li , Wang Hengliang 
Published: April 2016

ABSTRACT Conjugate vaccines are known to be one of the most effective and safest types of vaccines against bacterial pathogens. Previously, vaccine biosynthesis has been performed by using N-linked glycosylation systems. However, the structural specificity of these systems for sugar substrates has hindered their application. Here, we report a novel protein glycosylation system (O-linked glycosylation viaNeisseria meningitidis) that can transfer virtually any glycan to produce a conjugate vaccine. We successfully established this system inShigellaspp., avoiding the construction of an expression vector for polysaccharide synthesis. We further found that different protein substrates can be glycosylated using this system and that the O-linked glycosylation system can also effectively function in other Gram-negative bacteria, including some strains whose polysaccharide structure was not suitable for conjugation using the N-linked glycosylation system. The results from a series of animal experiments show that the conjugate vaccine produced by this O-linked glycosylation system offered a potentially protective antibody response. Furthermore, we elucidated and optimized the recognition motif, named MOOR, for theO-glycosyltransferase PglL. Finally, we demonstrated that the fusion of other peptides recognized by major histocompatibility complex class II around MOOR had no adverse effects on substrate glycosylation, suggesting that this optimized system will be useful for future vaccine development. Our results expand the glycoengineering toolbox and provide a simpler and more robust strategy for producing bioconjugate vaccines against a variety of pathogens.IMPORTANCERecently, the rapid development of synthetic biology has allowed bioconjugate vaccines with N-linked protein glycosylation to become a reality. However, the difficulty of reestablishing the exogenous polysaccharide synthetic pathway inEscherichia colihinders their application. Here, we show that an O-linked protein glycosylation system fromNeisseria meningitidis, which has a lower structure specificity for sugar substrates, could be engineered directly in attenuated pathogens to produce effective conjugate vaccines. To facilitate the further design of next-generation bioconjugate vaccines, we optimized a novel short motif consisting of 8 amino acids that is sufficient for glycosylation. Our results expand the application potential of O-linked protein glycosylation and demonstrate a simpler and more robust strategy for producing bioconjugate vaccines against different pathogens. In the future, bacterial antigenic polysaccharides could be attached to major histocompatibility complex binding peptides to improve immunological memory or attached to protein subunit vaccine candidates to provide double immune stimulation.
Structures of Pathogenic Fungal FKBP12s Reveal Possible Self-Catalysis Function
Authors: Tonthat Nam K. , Juvvadi Praveen Rao , Zhang Hengshan , Lee Soo Chan , Venters Ron , Spicer Leonard , Steinbach William J. , Heitman Joseph , Schumacher Maria A. 
Published: April 2016

ABSTRACTInvasive fungal infections remain difficult to treat and require novel targeting strategies. The 12-kDa FK506-binding protein (FKBP12) is a ubiquitously expressed peptidyl-prolyl isomerase with considerable homology between fungal pathogens and is thus a prime candidate for future targeting efforts to generate a panfungal strategy. Despite decades of research on FKBPs, their substrates and mechanisms of action remain unclear. Here we describe structural, biochemical, andin vivoanalyses of FKBP12s from the pathogenic fungiCandida albicans,Candida glabrata, andAspergillus fumigatus. Strikingly, multiple apoA. fumigatusandC. albicansFKBP12 crystal structures revealed a symmetric, intermolecular interaction involving the deep insertion of an active-site loop proline into the active-site pocket of an adjacent subunit. Such interactions have not been observed in previous FKBP structures. This finding indicates the possibility that this is a self-substrate interaction unique to theA. fumigatusandC. albicansfungal proteins that contain this central proline. Structures obtained with the proline in thecisandtransstates provide more data in support of self-catalysis. Moreover, cysteine cross-linking experiments captured the interacting dimer, supporting the idea that it forms in solution. Finally, genetic studies exploring the impact of mutations altering the central proline and an adjacent residue provide evidence that any dimeric state formedin vivo, where FKBP12 concentrations are low, is transient. Taken together, these findings suggest a unique mechanism of self-substrate regulation by fungal FKBP12s, lending further novel understanding of this protein for future drug-targeting efforts.IMPORTANCEFKBP12 is acis-transpeptidyl-prolyl isomerase that plays key roles in cellular protein homeostasis. FKBP12s also bind the immunosuppressive drug FK506 to inhibit the phosphatase calcineurin (CaN). CaN is required for virulence ofA. fumigatus,C. albicans,C. glabrata, and other deadly fungal pathogens, marking FKBP12 and CaN as potential broad-spectrum drug targets. Here we describe structures of fungal FKBP12s. Multiple apoA. fumigatusandC. albicansFKBP12 structures reveal the insertion of a proline, conspicuously conserved in these proteins, into the active sites of adjacent molecules. This suggests that these proteins might serve as their own substrates. Cysteine disulfide trapping experiments provide support for this self-interaction and hence possible intermolecular catalysis by these enzymes.
Word Sense Clustering and Clusterability
Authors: McCarthy Diana , Apidianaki Marianna , Erk Katrin 
Published: April 2016

Word sense disambiguation and the related field of automated word sense induction traditionally assume that the occurrences of a lemma can be partitioned into senses. But this seems to be a much easier task for some lemmas than others. Our work builds on recent work that proposes describing word meaning in a graded fashion rather than through a strict partition into senses; in this article we argue that not all lemmas may need the more complex graded analysis, depending on their partitionability. Although there is plenty of evidence from previous studies and from the linguistics literature that there is a spectrum of partitionability of word meanings, this is the first attempt to measure the phenomenon and to couple the machine learning literature on clusterability with word usage data used in computational linguistics. We propose to operationalize partitionability as clusterability, a measure of how easy the occurrences of a lemma are to cluster. We test two ways of measuring clusterability: (1) existing measures from the machine learning literature that aim to measure the goodness of optimal k-means clusterings, and (2) the idea that if a lemma is more clusterable, two clusterings based on two different “views” of the same data points will be more congruent. The two views that we use are two different sets of manually constructed lexical substitutes for the target lemma, on the one hand monolingual paraphrases, and on the other hand translations. We apply automatic clustering to the manual annotations. We use manual annotations because we want the representations of the instances that we cluster to be as informative and “clean” as possible. We show that when we control for polysemy, our measures of clusterability tend to correlate with partitionability, in particular some of the type-(1) clusterability measures, and that these measures outperform a baseline that relies on the amount of overlap in a soft clustering.
Turning Ocean Mixing Upside Down
Authors: Ferrari Raffaele , Mashayek Ali , McDougall Trevor J. , Nikurashin Maxim , Campin Jean-Michael 
Published: April 2016

AbstractIt is generally understood that small-scale mixing, such as is caused by breaking internal waves, drives upwelling of the densest ocean waters that sink to the ocean bottom at high latitudes. However, the observational evidence that the strong turbulent fluxes generated by small-scale mixing in the stratified ocean interior are more vigorous close to the ocean bottom boundary than above implies that small-scale mixing converts light waters into denser ones, thus driving a net sinking of abyssal waters. Using a combination of theoretical ideas and numerical models, it is argued that abyssal waters upwell along weakly stratified boundary layers, where small-scale mixing of density decreases to zero to satisfy the no density flux condition at the ocean bottom. The abyssal ocean meridional overturning circulation is the small residual of a large net sinking of waters, driven by small-scale mixing in the stratified interior above the bottom boundary layers, and a slightly larger net upwelling, driven by the decay of small-scale mixing in the boundary layers. The crucial importance of upwelling along boundary layers in closing the abyssal overturning circulation is the main finding of this work.
Biomechanics of Pharyngeal Deglutitive Function following Total Laryngectomy
Authors: Zhang Teng , Szczesniak Michal , Maclean Julia , Bertrand Paul , Wu Peter I. , Omari Taher , Cook Ian J. 
Published: April 2016

ObjectivePostlaryngectomy, pharyngeal weakness, and pharyngoesophageal junction (PEJ) restriction are the candidate mechanisms of dysphagia. The aims were, in laryngectomees, whether (1) hypopharyngeal propulsion is reduced and/or PEJ resistance is increased, (2) dilatation improves dysphagia, and (3) whether symptomatic improvement correlates with reduced PEJ resistance.DesignMultidisciplinary cross‐sectional study.SettingTertiary academic hospital.Subjects and MethodsSwallow biomechanics were assessed in 30 laryngectomees. Patients were stratified into severe dysphagia (Sydney Swallow Questionnaire >500) and mild/nil dysphagia (Sydney Swallow Questionnaire ≤500). Average hypopharyngeal peak (contractile) pressure (hPP) and hypopharyngeal intrabolus pressure (hIBP) were measured from high‐resolution manometry with concurrent videofluoroscopy based on barium swallows (2.5 and 10 mL). In consecutive 5 patients, measurements were repeated after dilatation.ResultsDysphagia was reported by 87%, and 57% had severe and 43% had mild/nil dysphagia. hIBP increased with larger bolus volumes (P <. 0001), while hPP stayed stable and PEJ diameter plateaued at 9 mm. Laryngectomees had lower hPP (110 ± 14 vs 170 ± 15 mm Hg; P =. 0162) and higher hIBP (29 ± 5 vs 6 ± 5 mm Hg; P =. 156) than controls. There were no differences in hPP between patient groups. However, hIBP was higher in severe than in mild/nil dysphagia (41 ± 10 vs 13 ± 3 mm Hg; P =. 02). Predilation hIBP (R2 = 0.97) and its decrement postdilatation (R2 = 0.98) well predicted symptomatic improvement.ConclusionsPEJ resistance correlates better with dysphagia severity than peak pharyngeal pressure and is more sensitive to bolus sizes than PEJ diameter. Both baseline PEJ resistance and its decrement following dilatation are strong predictors of treatment outcome. PEJ resistance is vital to detect, as it is reversible and can predict the response to dilatation regimens.
Are Pulley Exercises Initiated 6 Weeks After Rotator Cuff Repair a Safe and Effective Rehabilitative Treatment?
Authors: Baumgarten Keith M. , Osborn Roy , Schweinle Will E. , Zens Matthew J. , Helsper Elizabeth A. 
Published: April 2016

Background: There are few level 1 or 2 evidence studies that examine rehabilitation after rotator cuff repair. Pulleys have been used in postoperative shoulder rehabilitation with the intention of improving range of motion and developing strength. There is a concern that the use of pulleys in rehabilitation of rotator cuff repairs may contribute to excessive scapular motion (scapular substitution) and potentially inferior outcomes. Hypothesis: Rotator cuff repair patients treated with pulley exercises would have increased scapular substitution and inferior patient-determined outcome scores, range of motion, and strength compared with patients treated with an alternative rehabilitation program without pulleys. Study Design: Randomized controlled trial; Level of evidence, 1. Methods: A total of 27 patients who underwent rotator cuff repair were randomized to a rehabilitation group that used pulleys initiated 6 weeks postoperatively, and 26 patients followed a rehabilitation protocol without pulleys. Inclusion criteria were patients undergoing arthroscopic rotator cuff repair. Exclusion criteria were large to massive rotator cuff tears, revision rotator cuff repair, glenohumeral osteoarthritis, adhesive capsulitis, and a symptomatic contralateral shoulder. Outcomes of intervention were patient-determined outcome scores (Western Ontario Rotator Cuff Index [WORC], American Shoulder and Elbow Surgeons [ASES] Shoulder Score, Single Assessment Numeric Evaluation [SANE], Shoulder Activity Level, and Simple Shoulder Test [SST]), range of motion, scapular substitution, and strength. Outcomes were determined at 6, 12, 18, 26, and 52 weeks. A power analysis determined that 22 patients were needed per group to have a power of 0.80, α = 0.05, and effect size of f = 0.5. Results: Both groups had statistically significant improvements in WORC, ASES Shoulder Score, SST, and SANE scores over time after rotator cuff repair ( P < .0001). There were no differences between the interventions for WORC ( P = .18), ASES Shoulder Score ( P = .73), SANE ( P = .5), Shoulder Activity Level ( P = .39), or SST ( P = .36). Both interventions demonstrated improvements in shoulder flexion ( P = .002), abduction ( P = .0001), external rotation ( P = .02), strength ( P ≤ .0002), and scapular substitution ( P ≤ .07) over time after rotator cuff repair. However, there was no difference in range of motion ( P ≥ .26), strength ( P ≥ .20), or scapular substitution ( P ≥ .17) between interventions. Conclusion: A rotator cuff repair rehabilitation program that uses pulleys does not result in inferior outcomes, as determined by patient-determined outcome scores, measurements of scapular substitution, range of motion, and scaption strength. Registration: ClinicalTrials.gov NCT01819909
Coagulation, Fibrinolysis, and Platelet Activation Following Open Surgical or Percutaneous Angioplasty Revascularization for Symptomatic Lower Limb Chronic Ischemia
Authors: Rayt Harjeet S. , Merker L. , Davies Robert S. M. 
Published: April 2016

Introduction: Critical limb ischemia (CLI) is associated with a prothrombotic diathesis that involves a complex balance between the coagulation and fibrinolytic systems. Knowledge of this is essential when considering revascularization procedures but is often overlooked. The aim of this review is to summarize the available literature and provide an overview of the effects of lower limb angioplasty and open surgical revascularization on coagulation, fibrinolysis, and platelet activation. Methods: A MEDLINE and EMBASE search was conducted between 1973 and 2014 for articles relating to the effects of revascularization for patients with CLI on the fibrinolytic and coagulation pathways. Studies with a small cohort of patients (<5) were rejected. Results: Many of the studies included in this analysis had small cohorts. Multiple markers were assessed across the published literature including von Willebrand factor, tissue factor, prothrombin fragments 1 and 2, platelets, soluble platelet selectin, plasminogen activator inhibitor 1, tissue plasminogen activator, and thrombin–antithrombin complex. Percutaneous intervention causes an exaggerated prothrombotic and a disturbed fibrinolytic effect. Surgery seems to cause a similar prothrombotic derangement with reduced fibrinolysis and platelet hyperactivity, but this appears to be maintained for a considerable amount of time postoperatively. Conclusion: There is a sparse amount published on the effects of the coagulation and fibrinolytic systems in patients undergoing intervention for CLI. Much of these studies are small, historical, and completely heterogeneous, making it difficult to draw meaningful conclusions. The literature does identify a prothrombotic state in patients with CLI, which appears to be exacerbated by any form of intervention and prolonged in those having surgery. Understanding this may allow us to tailor the intervention offered to patients and prevent limb loss.
Impact of Type 1 Diabetes Technology on Family Members/Significant Others of People With Diabetes
Authors: Barnard Katharine , Crabtree Vincent , Adolfsson Peter , Davies Melanie , Kerr David , Kraus Amy , Gianferante Danielle , Bevilacqua Elizabeth , Serbedzija George 
Published: April 2016

Background: The aim was to explore the impact of diabetes-related technology to ensure that such devices are used in a way that returns maximum benefit from a medical and psychological perspective. Method: Spouses and caregivers of people with type 1 diabetes were invited to complete an online questionnaire about their experiences with diabetes technologies used by their family members. Participants were recruited via the Glu online community website. Questions explored impact on daily living, frequency and severity of hypoglycemia, and diabetes-related distress. Results: In all, 100 parents/caregivers and 74 partners participated in this survey. Average (mean) duration of living with a person with type 1 diabetes was 16 years (SD = 13) for partners, with duration of diabetes for children being 4.2 ± 3.2 years. Average duration of current therapy was 8.3 ± 7.3 years for adults and 3.4 ± 2.9 years for children. Of the participants, 86% partners and 82% parents/caregivers reported diabetes technology had made it easier for their family members to achieve blood glucose targets. Compared to partners, parents/caregivers reported more negative emotions ( P < .001) and decreased well-being ( P < .001) related to their family members type 1 diabetes. Diabetes-related distress was common, as was sleep disturbance associated with device alarms and fear of hypoglycemia. Reduced frequency and severity of hypoglycemia related to device use was reported by approximately half of participants. Conclusion: There is little doubt about the medical benefit of diabetes technologies and their uptake is increasing but some downsides were reported. Barriers to uptake of technologies lie beyond the mechanics of diabetes management. Supporting users in using diabetes technology to achieve the best possible glycemic control, in the context of their own life, is crucial. Furthermore, understanding these issues with input from the type 1 diabetes community including family members and caregivers will help innovation and design of new technology.