bluuebunny/crossref_metadata_2025 huggingface dataset:
Objective Assessment of Fitness to Perform (FTOP) After Surgical Night Shifts in the Netherlands
Authors: Tummers Fokkedien H. M. P. , Huizinga Coen R. H. , Stockmann Hein B. A. C. , Hamming Jaap F. , Cohen Adam F. , van der Bogt Koen E. A.
Published: September 2019

Background:

Surgical skills and decision making are influenced by alertness, reaction time, eye-hand coordination, and concentration. Night shift might impair these functions but it is unclear to what extent. The aim of this study was to investigate whether a night shift routinely impairs the surgeon's fitness to perform and whether this reaches a critical limit as compared to relevant frames of reference.

Methods:

Consultants (n = 59) and residents (n = 103) conducted fitness to perform measurements at precall, postcall, and noncall moments. This validated self-test consists of an adaptive tracker that is able to objectively measure alertness, reaction time, concentration, and eye-hand coordination, and multiple visual analog scales to subjectively score alertness. Results are compared to sociolegal (ethanol) and professional (operative skills) frames of reference that refer to a decrease under the influence of 0.06% ethanol.

Results:

Residents spent 1.7 call hours asleep on average as compared to 5.4 for consultants. Subjective alertness decreased in residents after night shifts (−13, P < 0.001) but not in consultants (−1.2, P = NS). The overnight difference in tracker score was −1.17 (P < 0.001) for residents and 0.46 (P = NS) for surgeons. Postcall subjective alertness only correlated to objective alertness in consultants. For residents, hours slept on-call correlated to objective alertness. For consultants, subsequent night calls significantly correlated to objective alertness, with the third subsequent call related to performance below the reference.

Conclusions:

Consultants remain fit to perform after night call, but subsequent calls may compromise clinical activities. This study provides insight and awareness of individual performance with clear frames of reference.
Comparison of Surgical Intervention and Mortality for Seven Surgical Emergencies in England and the United States
Authors: Markar Sheraz R. , Vidal-Diez Alberto , Patel Kirtan , Maynard Will , Tukanova Karina , Murray Alice , Holt Peter J. , Karthikesalingam Alan , Hanna George B.
Published: September 2019

Objective:

To examine differences between England and the USA in the rate of surgical intervention and in-hospital mortality for 7 index surgical emergencies.

Background:

Considerable international variation exists in the configuration, provision, and outcomes of emergency healthcare.

Methods:

Patients aged <80 years hospitalized with 1 of 7 surgical emergencies (ruptured abdominal aortic aneurysm, aortic dissection, appendicitis, perforated esophagus, peptic ulcer, small bowel or large bowel, and incarcerated or strangulated hernias) were identified from English Hospital Episode Statistics and the USA Nationwide Inpatient Sample (2006–2012) and classified by whether they received a corrective surgical intervention. The rates of surgical intervention and population mortality were compared between England and the USA after adjustment for patient demographic factors.

Results:

From 2006 to 2012, there were 136,047 admissions in English hospitals and 1,863,626 admissions in US hospitals due to the index surgical emergencies.

Proportion of patients receiving no surgical intervention, for all 7 conditions was greater in the England (OR 4.25, 1.55, 8.53, 1.92, 2.06, 2.42, 1.75) and population in-hospital mortality was greater in England (OR 1.34, 1.67, 2.22, 1.65, 2.7, 4.46, 3.22) for ruptured abdominal aortic aneurysm, aortic dissection, appendicitis, perforated esophagus, peptic ulcer, small bowel or large bowel, and incarcerated or strangulated hernias respectively.

In England (where follow-up was available), lack of utilization of surgery was also associated with increased in-hospital and long-term mortality for all conditions.

Conclusion:

England and US hospitals differ in the threshold for surgical intervention, which may be associated with increases in mortality in England for these 7 general surgical emergencies.
Penetrating Crohn Disease Is Not Associated With a Higher Risk of Recurrence After Surgery
Authors: Maggiori Léon , Brouquet Antoine , Zerbib Philippe , Lefevre Jérémie H. , Denost Quentin , Germain Adeline , Cotte Eddy , Beyer-Berjot Laura , Munoz-Bongrand Nicolas , Desfourneaux Véronique , Rahili Amine , Duffas Jean-Pierre , Pautrat Karine , Denet Christine , Bridoux Valérie , Meurette Guillaume , Faucheron Jean-Luc , Loriau Jérome , Souche Regis , Vicaut Eric , Panis Yves , Benoist Stéphane
Published: September 2019

Objective:

The aim of this study was to assess recurrence risk factors following ileocolonic resection (ICR) for Crohn disease (CD) in a nationwide cohort study

Summary Background Data:

Recurrence rate after ICR for CD can be up to 60%, but its predictive factors have never been evaluated in large prospective cohort studies.

Methods:

From 2013 to 2015, 346 consecutive patients undergoing ICR for CD and a postoperative ileocoloscopy within 6 to 12 months after surgery at 19 academic French centers were included prospectively.

Results:

Twelve-month postoperative endoscopic (Rutgeerts score ≥i2) and clinical recurrence rates were 57.6% [95% confidence interval (CI), 54.2–61.0] and 11.3% (95% CI, 9–13.6), respectively. A total of 185 patients (54%) had a postoperative CD prophylaxis, comprising thiopurine in 69 (20%), or anti-tumor necrosis factor (TNF) therapy in 93 (27%). In multivariate Cox regression analysis, absence of postoperative smoking {odds ratio [OR] = 0.60 (95% CI, 0.40–0.91); P = 0.016}, postoperative prophylaxis [OR = 0.60 (95% CI, 0.41–0.88); P = 0.009], and penetrating disease behavior [OR = 0.58 (95% CI, 0.39–0.86); P = 0.007] were the only independent predictors of reduced endoscopic recurrence risk. Postoperative prophylaxis [OR 0.31 (95% CI, 0.15–0.66); P = 0.002), and penetrating behavior [OR = 00.36 (95% CI, 0.16–0.81); P = 0.013), were the only independent predictors of reduced clinical recurrence risk. Postoperative anti-TNF therapy was associated with a significant reduction of both 12-month risks of endoscopic (P < 0.001) and clinical (P = 0.019) recurrences.

Conclusion:

Absence of postoperative smoking, CD prophylaxis, and penetrating disease behavior could be independent predictors of reduced postoperative recurrence after ICR for CD. Prophylactic anti-TNF therapy reduces both endoscopic and clinical recurrence rates. It suggests that upfront surgery followed by postoperative anti-TNF therapy is probably the best therapeutic approach for complex CD (penetrating disease behavior).
Variation in the Use of Resection for Colorectal Cancer Liver Metastases
Authors: Fenton Hayley M. , Taylor John C. , Lodge J. Peter A. , Toogood Giles J. , Finan Paul J. , Young Alastair L. , Morris Eva J. A.
Published: September 2019

Objective:

The aim of this study was to investigate variation in the frequency of resections for colorectal cancer liver metastases across the English NHS.

Background:

Previous research has shown significant variation in access to liver resection surgery across the English NHS. This study uses more recent data to identify whether inequalities in access to liver resection still persist.

Methods:

All adults who underwent a major resection for colorectal cancer in an NHS hospital between 2005 and 2012 were identified in the COloRECTal cancer data Repository (CORECT-R). All episodes of care, occurring within 3 years of the initial bowel operation, corresponding to liver resection were identified.

Result:

During the study period 157,383 patients were identified as undergoing major resection for a colorectal tumor, of whom 7423 (4.7%) underwent ≥1 liver resections. The resection rate increased from 4.1% in 2005, reaching a plateau around 5% by 2012. There was significant variation in the rate of liver resection across hospitals (2.1%–12.2%). Patients with synchronous metastases who have their primary colorectal resection in a hospital with an onsite specialist hepatobiliary team were more likely to receive a liver resection (odds ratio 1.22; 95% confidence interval, 1.10–1.35) than those treated in one without. This effect was absent in resection for metachronous metastases.

Conclusions:

This study presents the largest reported population-based analysis of liver resection rates in colorectal cancer patients. Significant variation has been observed in patient and hospital characteristics and the likelihood of patients receiving a liver resection, with the data showing that proximity to a liver resection service is as important a factor as deprivation.
Urethral Injury and Other Urologic Injuries During Transanal Total Mesorectal Excision
Authors: Sylla Patricia , Knol Joep J. , D’Andrea Anthony P. , Perez Rodrigo O. , Atallah Sam B. , Penna Marta , Hompes Roel , Wolthuis Albert , Rouanet Philippe , Fingerhut Abe
Published: September 2019

Objective:

To identify risk factors for urethral and urologic injuries during transanal total mesorectal excision (taTME) and evaluate outcomes.

Background:

Urethral injury is a rare complication of abdominoperineal resection (APR) that has not been reported during abdominal proctectomy. The Low Rectal Cancer Development Program international taTME registry recently reported a 0.8% incidence, but actual incidence and mechanisms of injury remain largely unknown.

Methods:

A retrospective analysis of taTME cases complicated by urologic injury was conducted. Patient demographics, tumor characteristics, intraoperative details, and outcomes were analyzed, along with surgeons’ experience and training in taTME. Surgeons’ opinion of contributing factors and best approaches to avoid injuries were evaluated.

Results:

Thirty-four urethral, 2 ureteral, and 3 bladder injuries were reported during taTME operations performed over 7 years by 32 surgical teams. Twenty injuries occurred during the teams’ first 8 taTME cases (“early experience”), whereas the remainder occurred between the 12th to 101st case. Injuries resulted in a 22% conversion rate and 8% rate of unplanned APR or Hartmann procedure. At median follow-up of 27.6 months (range, 3–85), the urethral repair complication rate was 26% with a 9% rate of failed urethral repair requiring permanent urinary diversion. In patients with successful repair, 18% reported persistent urinary dysfunction.

Conclusions:

Urologic injuries result in substantial morbidity. Our survey indicated that those occurring in surgeons’ early experience might best be reduced by implementation of structured taTME training and proctoring, whereas those occurring later relate to case complexity and may be avoided by more stringent case selection.
Endocrinopathies and cancer cachexia
Authors: Dev Rony , Del Fabbro Egidio , Dalal Shalini
Published: September 2019

Purpose of review

Cancer cachexia cannot be easily reversed by standard nutritional support and interventions directed at underlying metabolic derangements may be needed to prevent or reverse cachexia and maintain healthy body composition. The following review will highlight the contribution and potential therapeutic interventions for insulin resistance, alterations in ghrelin signaling, and hypogonadism in cancer patients.

Recent findings

In addition to decreased caloric intake, chronic inflammation, and altered metabolism of glucose, proteins and lipids, endocrine abnormalities can propagate weight loss or changes in body composition in cancer patients.

Cancer cachexia, loss of muscle mass with or without the loss of fat mass, is a multifactorial syndrome, which is associated with increased morbidity and mortality. Currently, limited therapeutic options for the treatment of weight loss in cancer patients exist, which lead to clinically meaningful improvements in weight gain and performance status. Treatment directed at underlying insulin resistance, low testosterone, and altered ghrelin sensitivity, in the future, may lead to potential therapeutic options for loss of lean body mass and cancer cachexia.
Novel sensory paradigms for neuromodulation in disorders of consciousness in traumatic brain injury
Authors: Padua Luca , Cuccagna Cristina , Pazzaglia Costanza
Published: September 2019

Purpose of review

Traumatic brain injury (TBI) represents a major cause of mortality and disability worldwide. In cases of severe TBI, disorders of consciousness (DoC) can occur and therapeutic options for these conditions are few and of limited efficacy. Sensory stimulation, an instrument to improve arousal and awareness, is frequently applied in the neurorehabilitation of DoC, but scientific evidence supporting its efficacy is limited. Our aim is to review the recent literature concerning novel sensory paradigms used in sensory stimulation protocols in DoC following TBI.

Recent findings

Recent studies on sensory stimulation have investigated different types of stimulation protocols, focusing on the issue of how to demonstrate that improvements are related to the treatment applied and not to spontaneous recovery. Moreover, these studies have also shown that paraclinical tests should be useful not only to discover signs of awareness when behavioural assessment fails to do so, but also to measure the effects of sensory stimulation.

Future studies about novel types of sensory stimulation, whose effects should be possibly measured through paraclinical approaches, are recommended in order to increase the probability that the proper individualized stimulation is administered for each patient.
Alternative routes for recovery of hand functions after corticospinal tract injury in primates and rodents
Authors: Isa Tadashi , Mitsuhashi Masahiro , Yamaguchi Reona
Published: September 2019

Purpose of review

Recent studies on various corticospinal tract (CST) lesions have shown the plastic changes at a variety of motor systems after the lesion. This review provides the alternative routes associated with the motor functional recovery after the CST lesions at various levels in nonhuman primates and rodents.

Recent findings

In the case of the motor cortical lesions, the perilesional area compensates for the lesion. In contrast, sprouting of the corticoreticular tracts was observed after the lesions involving sensorimotor cortical areas. After the internal capsule lesion, sprouting in the cortico-rubral pathway contributes to the recovery. In case of the pyramidal lesion, rubrospinal and reticulospinal tracts play a role of the functional recovery. After the dorsolateral funiculus (DLF) lesion at C4/C5, the indirect pathway via propriospinal tract contributes to the recovery. In case of the hemisection at lower cervical cord, the CST fibers sprouted from the bilateral motor cortex and descended to the contralesional DLF and crossed below the lesion area.

The central pathways can change their structure and activity dynamically depending on the lesion sites and size. Revealing the difference of the alternative pathways should be crucial to understand the whole recovery mechanism and develop the further neurorehabilitative treatment.
Evaluation of the JBI scoping reviews methodology by current users
Authors: Khalil Hanan , Bennett Marsha , Godfrey Christina , McInerney Patricia , Munn Zac , Peters Micah
Published: September 2019

Background:

In 2014, JBI Database of Systematic Reviews and Implementation Reports published a comprehensive methodology for the conduct and reporting of scoping reviews based on previous frameworks and guidance. Further work on scoping review methodology and particularly reporting is needed. To assist with refinements to the methodology, this survey was undertaken to evaluate users’ experiences of following the process methodology. An electronic survey was generated to explore authors’ experiences with the methodology and to seek feedback on the stages of scoping review development.

Method:

An online survey administered using Qualtrics – a secure survey platform – was distributed through invitations to a total of 51 registered users in the Joanna Briggs Database of Systematic reviews and Implementation reports. We analysed the questionnaire data using descriptive statistics. The qualitative data were grouped together, and free text comments were inductively themed and coded by the authors.

Results:

Thirty-one participants completed the survey (response rate of 61%). The majority of the participants identified themselves as researchers (55%) followed by educators (25%). Most participants were university employees (77%) and only 10% were based in hospitals. Forty-two percent of the participants reported that the scoping review they had been involved with had taken between 6 and 12 months, and 32% of participants spent over a year completing their reviews. Eighty-seven percent of participants stated that their scoping reviews led to further work such as developing a systematic review, a basis for a grant application, formation of a part of students’ doctoral studies, and informing further work in a research project. Some of the limitations listed by the participants were the lack of examples in each section of the methodology, especially in the inclusion criteria, and presentation of the results sections.

Conclusion:

The overall evaluation by the participants of the JBI scoping review methodology highlighted the need for additional detailed guidance for inclusion criteria and presentation of the results. Provision of clear examples for each step was also requested for future improvement.
The fragility of randomized trial outcomes underlying management of dyspepsia and Helicobacter pylori infections
Authors: Meyer Chase , Bowers Aaron , Tritz Daniel , Fuller Kaleb , Wayant Cole , Cook Courtney , Torgerson Trevor , Som Mousumi , Vassar Matt
Published: September 2019

Aim:

The fragility index is calculated by changing one outcome event to a nonevent within a trial until the associated P value exceeds 0.05. In this study, we assessed the robustness, risk of bias (RoB), and power of randomized controlled trials that underlie recommendations set forth by the American College of Gastroenterology (ACG) on managing dyspepsia and Helicobacter pylori infections.

Methods:

All citations referenced in the guidelines were screened for inclusion criteria. The fragility indexes for eligible trials were then calculated. The likelihood and sources of bias in the included trials were evaluated by the Cochrane ‘RoB’ Tool 2.0.

Results:

The median fragility index for the 52 trials was three events. Five studies (9.6%) resulted in a fragility index of 0 when statistical analysis was applied. For the 52 trials, 12 (23.1%) were at a low RoB, 15 (28.8%) had some concerns, and 25 (48.1%) were at a high RoB. High RoB was most commonly due to bias of selection in the reported result (15.5%).

Conclusion:

A median of three events was needed to nullify statistical significance in 52 trials that underpin guideline recommendations on the management of dyspepsia and H. pylori infections. In addition, concerns for RoB were found for these trials.
Effect of respiratory muscle training session on ankle muscle activity in athletes with chronic low back pain performing overhead squats: a randomized controlled trial
Authors: Borujeni Behnam Gholami , Yalfani Ali
Published: September 2019

Aim:

The current study was conducted to evaluate the effect of a respiratory muscle training session on ankle muscle activity in athletes with chronic low back pain performing overhead squats.

Methods:

The current double-blind, randomized, controlled trial was conducted on 24 patients randomly selected as the training group and 23 patients as the control group. The training group received the respiratory muscle training protocol. The electromyography activity of the tibialis anterior, peroneus longus, gastrocnemius medialis and gastrocnemius lateralis muscles of the dominant leg was recorded in the participants.

Results:

The findings showed that a session of respiratory muscle training reduced the activities of some ankle joint muscles when performing overhead squats, including tibialis anterior in the static and dynamic overhead squat tests and peroneus longus in the ascending phase. In the dynamic test, the angle to reach peak activity changed in tibialis anterior in the descending phase and also in tibialis anterior and peroneus longus in the ascending phase.

Conclusion:

Effects of respiratory muscle training prevented excessive ankle joint muscle activity through stimulating local muscles while performing overhead squats, which had indicated an improved postural control and multisectional proprioception to maintain postural stability and stimulated the local muscles of the core area.
Bayesian estimation of IVW and MR-Egger models for two-sample Mendelian randomization studies
Authors: Uche-Ikonne Okezie , Dondelinger Frank , Palmer Tom
Published: September 2019

We present our package,mrbayes,for the open source software environment R. The package implements Bayesian estimation for IVW and MR-Egger models, including the radial MR-Egger model, for summary-level data in Mendelian randomization analyses. Users have the option of fitting the models using either JAGS or Stan software packages. We have implemented a choice of prior distributions for the model parameters, namely; weakly informative, non-informative, a joint prior for the MR-Egger model slope and intercept, and an informative prior (pseudo-horseshoe prior), or the user can specify their own prior. Similar prior distributions are included using the Stan software with the exception of a user-defined prior. We include We show how to use the package through an applied example investigating the causal effect of BMI on acute ischemic stroke. In future work, we plan to provide functions for Multivariable MR estimation.
Beyond target-decoy competition: stable validation of peptide and protein identifications in mass spectrometry-based discovery proteomics
Authors: Couté Yohann , Bruley Christophe , Burger Thomas
Published: September 2019

In bottom-up discovery proteomics, target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control. Despite unquestionable statistical foundations, this method has drawbacks, including its hitherto unknown intrinsic lack of stabilityvis-à-vispractical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinter-preted. This article provides evidence that TDC has become less reliable as the accuracy of modern mass spectrometers improved. We therefore propose to replace TDC by a totally different method to control the FDR at spectrum, peptide and protein levels, while benefiting from the theoretical guarantees of the Benjamini-Hochberg framework. As this method is simpler to use, faster to compute and more stable than TDC, we argue that it is better adapted to the standardization and throughput constraints of current proteomic platforms.
Polarity protein distribution on the metaphase furrow regulates hexagon dominated plasma membrane organization in syncytialDrosophilaembryos
Authors: Dey Bipasha , Mitra Debasmita , Das Tirthasree , Sherlekar Aparna , Balaji Ramya , Rikhy Richa
Published: September 2019

Epithelial cells have a polarised distribution of protein complexes on the lateral membrane and are present as a polygonal array dominated by hexagons. Metazoan embryogenesis enables the study of temporal formation of the polygonal array and mechanisms that regulate its distribution. The plasma membrane of the syncytialDrosophilablastoderm embryo is organized as a polygonal array during cortical division cycles with an apical membrane and lateral furrow in between adjacent nuclei. We find that polygonal plasma membrane organization arises in syncytial division cycle 11 and hexagon dominance occurs with increase in furrow length in cycle 12. This is coincident with DE-cadherin and Bazooka enrichment at edges and the septin, Peanut enrichment at vertices of the base of the furrow. DE-cadherin depletion leads to loss of hexagon dominance. Bazooka and Peanut depletion leads to a delay in occurrence of hexagon dominance from nuclear cycle 12 to 13. Hexagon dominance in Bazooka and Peanut mutants occurs with furrow extension and correlates with increase in DE-cadherin in syncytial cycle 13. We conclude that a change in polarity complex distribution leads to loss of furrow stability thereby changing the polygonal organization of the blastoderm embryo.

Highlight Summary for TOC

Metazoan embryogenesis starts with the formation of polygonal epithelial-like cells. We show that hexagon dominance in polygonal epithelial-like plasma membrane organization occurs in nuclear cycle 12 in the syncytial blastodermDrosophilaembryo. DE-cadherin and Bazooka distribution along the lateral furrow regulates this hexagon dominance.
Rare Variants in theOTOGGene Are a Frequent Cause of Familial Meniere’s Disease
Authors: Roman-Naranjo Pablo , Gallego-Martinez Alvaro , Soto-Varela Andrés , Aran Ismael , Moleon Maria del Carmen , Espinosa-Sanchez Juan Manuel , Amor-Dorado Juan Carlos , Batuecas-Caletrio Angel , Perez-Vazquez Paz , Lopez-Escamez Jose A.
Published: September 2019

Objectives

Meniere’s disease (MD) is a rare inner ear disorder characterized by sensorineural hearing loss, episodic vertigo and tinnitus. Familial MD has been reported in 6-9% of sporadic cases, and few genes includingFAM136A, DTNA, PRKCB, SEMA3DandDPThave been involved in single families, suggesting genetic heterogeneity. In this study, the authors recruited 46 families with MD to search for relevant candidate genes for hearing loss in familial MD.

Design

Exome sequencing data from MD patients were analyzed to search for rare variants in hearing loss genes in a case-control study. A total of 109 patients with MD (73 familial cases and 36 early-onset sporadic patients) diagnosed according to the diagnostic criteria defined by the Barany Society were recruited in 11 hospitals. The allelic frequencies of rare variants in hearing loss genes were calculated in individuals with familial MD. A single rare variant analysis (SRVA) and a gene burden analysis (GBA) were conducted in the dataset selecting one patient from each family. Allelic frequencies from European and Spanish reference datasets were used as controls.

Results

A total of 5136 single nucleotide variants in hearing loss genes were considered for SRVA in familial MD cases, but only one heterozygous variant in theOTOGgene (rs552304627) was found in two unrelated families. The GBA found an enrichment of rare missense variants in theOTOGgene in familial MD. So, 15/46 families (33%) showed at least one rare missense variant in theOTOGgene, suggesting a key role in familial MD.

Conclusions

The authors found an enrichment of multiplex rare missense variants in theOTOGgene in familial MD. This finding supportsOTOGas a relevant gene in familial MD and set the groundwork for genetic testing in MD.
Transthyretin-stabilizing mutation T119M is not associated with protection against vascular disease or death in the UK Biobank
Authors: Parker Margaret M. , Ticau Simina , Butler James , Erbe David , Merkel Madeline , Aldinc Emre , Hinkle Gregory , Nioi Paul
Published: September 2019

Background

Destabilized transthyretin (TTR) can result in the progressive, fatal disease transthyretin-mediated (ATTR) amyloidosis. A stabilizingTTRmutation, T119M, is the basis for a therapeutic strategy to reduce destabilized TTR. Recently, T119M was associated with extended lifespan and lower risk of cerebrovascular disease in a Danish cohort. We aimed to determine whether this finding could be replicated in the UK Biobank.

Methods

TTRT119M carriers were identified in the UK Biobank, a large prospective cohort of ∼500,000 individuals. Association between T119M genotype and inpatient diagnosis of vascular disease, cardiovascular disease, cerebrovascular disease, and mortality was analyzed.

Results

Frequency of T119M within the white UK Biobank population (n=337,148) was 0.4%. Logistic regression comparing T119M carriers to non-carriers found no association between T119M and vascular disease (odds ratio [OR]=1.08;p=.27), cardiovascular disease (OR=1.08;p=.31), cerebrovascular disease (OR=1.1;p=.42), or death (OR=1.2;p=.06). Cox proportional hazards regression showed similar results (hazard ratio>1,p>.05). Age at death and vascular disease diagnosis were similar between T119M carriers and non-carriers (p=.12 andp=.38, respectively).

Conclusions

There was no association between theTTRT119M genotype and risk of vascular disease or death in a large prospective cohort study, indicating that TTR tetramer stabilization through T119M is not protective in this setting.
A simple, versatile and robust centrifugation-based filtration protocol for the isolation and quantification of α-synuclein monomers, oligomers and fibrils: towards improving experimental reproducibility in α-synuclein research
Authors: Kumar Senthil T. , Donzelli Sonia , Chiki Anass , Syed Muhammed Muazzam Kamil , Lashuel Hilal A.
Published: September 2019

Increasing evidence suggests that the process of alpha-synuclein (aSyn) aggregation from monomers into amyloid fibrils via oligomeric intermediates plays an essential role in the pathogenesis of different synucleinopathies, including Parkinson’s disease (PD), multiple system atrophy and dementia with Lewy bodies. However, the nature of the toxic species and the mechanisms by which they contribute to neurotoxicity and disease progression remain elusive. Over the past two decades, significant efforts and resources have been invested in studies aimed at identifying the putative toxic species along the pathway of aSyn fibrillization, and to develop small molecule drugs or antibodies that target toxic aSyn oligomeric intermediates. Although this approach has helped to advance the field and provide insights into the biological properties and toxicity of different aSyn species, many of the fundamental questions regarding the role of aSyn aggregation in PD remain unanswered, and no therapeutic compounds targeting aSyn oligomers have passed clinical trials. Several factors have contributed to this slow progress, including the complexity of the aggregation pathways and the heterogeneity and dynamic nature of aSyn aggregates. In the majority of experiment, the aSyn samples used contain mixtures of aSyn species that exist in an equilibrium and their ratio changes upon modifying experimental conditions. The failure to quantitatively account for the distribution of different aSyn species in different studies has contributed not only to experimental irreproducibility but also to misinterpretation of results and misdirection of valuable resources. Towards addressing these challenges and improving experimental reproducibility in Parkinson’s research, we describe here a simple centrifugation-based filtration protocol for the isolation, quantification and assessment of the distribution of of aSyn monomers, oligomers and fibrils, in heterogeneous aSyn samples of increasing complexity. The protocol is simple, does not require any special instrumentation and can be performed rapidly on multiple samples using small volumes. Here, we present and discuss several examples that illustrate the applications of this protocol and how it could contribute to improving the reproducibility of experiments aimed at elucidating the structural basis of aSyn aggregation, seeding activity, toxicity and pathology spreading. This protocol is applicable, with slight modifications, to other amyloid-forming proteins.

Table of Content Figure
The Curli Accessory Protein CsgF Influences the Aggregation of Human Islet Amyloid Polypeptide
Authors: Meza-Barajas Osmar , Aranda Isamar , Binmahfooz Ashwag , Newell Alliosn , Jayasinghe Sajith
Published: September 2019

Gram-negative bacteria, such as E. coli and Salmonella, contain proteinaceous, hair-like, cell surface filaments known as curli. Curli serve to facilitate cell-cell interactions and are essential for host cell colonization. Curli assembly involves six proteins, CsgA, CsgB, CsgC, CsgE, CsgF, and CsgG. CsgE and CsgF are thought to act as chaperones to help prevent the premature aggregation of CsgA and/or CsgB, and to help transport these proteins, through the outer-membrane protein CsgG, to the cell surface where they assemble to form Curli. It has been observed that CsgF is able to inhibit the aggregation of CsgA, the major protein component of Curli. This article describes CsgF’s ability to influence the aggregation of human islet amyloid polypeptide (hIAPP), an amyloidogenic polypeptide that is unrelated to Curli. In the presence of CsgF no increase in Thioflavin T fluorescence was observed for freshly solubilized hIAPP monitored as a function of time, suggesting that CsgF prevents the aggregation of hIAPP during the time period of observation. An analog of CsgF lacking the N-terminal unstructured region retained the ability to inhibit the aggregation of hIAPP. The nature of the CsgF-hIAPP interaction was probed via fluorescence quenching using a series of single cysteine mutants of CsgF labeled via the individual cysteine side chains with the fluorophore IAEDANS. In the presence of hIAPP, but not in the presence of the non-amyloidogenic rat islet amyloid polypeptide, the fluorophore attached to position of 23 of CsgF was found to be less exposed the quencher acrylamide suggesting that the interaction of hIAPP changes the solvent exposure of the N-terminus of CsgF. Taken together these data suggest that the structured region of CsgF, between residues 66 and 128, is involved in the protein’s interaction with hIAPP and that upon interaction structural changes make the N-terminus less solvent exposed.
Perceptual metacognition of human faces is causally supported by function of the lateral prefrontal cortex
Authors: Lapate Regina C. , Samaha Jason , Rokers Bas , Postle Bradley R. , Davidson Richard J.
Published: September 2019

Metacognitive visual awareness—the ability to know that one is having a particular visual experience—is thought to optimally guide behavior and help us accurately navigate our complex social environments. Yet the neural underpinnings of visual metacognition continue to be the subject of vigorous debate: While prior work identified correlations between perceptual metacognitive ability and the structure and function of lateral prefrontal cortex (LPFC), evidence for a causal role of this region in promoting metacognition is controversial—in fact, some question whether the prefrontal cortex plays any role in supporting conscious visual experiences. Moreover, whether LPFC function promotes metacognitive awareness of perceptual and emotional features of complex, yet ubiquitous socio-emotional face stimuli is unknown. Using model-based analyses following a causal intervention to LPFC in humans, we demonstrate that LPFC promotes metacognitive awareness of the orientation of emotional faces—although not of their emotional expressions. Effects were specific to metacognition, as LPFC perturbation did not alter stimulus discrimination performance. Collectively, these data support the causal involvement of the prefrontal cortex in metacognitive awareness, and indicate that the role of LPFC function in metacognition encompasses perceptual experiences of naturalistic social stimuli.
Structural requirements of the phytoplasma effector protein SAP54 for causing homeotic transformation of floral organs
Authors: Aurin Marc-Benjamin , Haupt Michael , Görlach Matthias , Rümpler Florian , Theißen Günter
Published: September 2019

Phytoplasmas are intracellular bacterial plant pathogens that cause devastating diseases in crops and ornamental plants by the secretion of effector proteins. One of these effector proteins, termed SECRETED ASTER YELLOWS-WITCHES’ BROOM PROTEIN 54 (SAP54), leads to the degradation of a specific subset of floral homeotic proteins of the MIKC-type MADS-domain family via the ubiquitin-proteasome pathway. In consequence, the developing flowers show the homeotic transformation of floral organs into vegetative leaf-like structures. The molecular mechanism of SAP54 action involves physical binding to the keratin-like K-domain of MIKC-type proteins, and to some RAD23 proteins, which translocate ubiquitylated substrates to the proteasome. The structural requirements and specificity of SAP54 function are poorly understood, however. Here we report, based on biophysical and molecular biological analyses, that SAP54 folds into α-helical structures. We also show that the insertion of helix-breaking mutations disrupts correct folding of SAP54, which interferes with the ability of SAP54 to bind to its target proteins and to cause disease phenotypesin vivo. Surprisingly, dynamic light scattering data together with electrophoretic mobility shift assays suggest that SAP54 preferentially binds to multimeric complexes of MIKC-type proteins rather than to dimers or monomers of these proteins. Together with literature data this finding suggests that MIKC-type proteins and SAP54 constitute multimeric α-helical coiled-coils, possibly also involving other partners such as RAD23 proteins. Our investigations clarify the structure-function relationship of an important phytoplasma effector protein and thus may ultimately help to develop treatments against some devastating plant diseases.

SIGNIFICANCE STATEMENT

Phytoplasmas are bacterial plant pathogens that cause devastating diseases in crops and ornamental plants by the secretion of effector proteins such as SAP54, which leads to the degradation of some floral homeotic proteins. Our study clarifies the structural requirements of SAP54 function and illuminates the molecular mode of interaction and thus may ultimately help to develop treatments against some devastating plant diseases.
Reduction of spontaneous cortical beta bursts in Parkinson’s disease is linked to symptom severity
Authors: Vinding Mikkel C. , Tsitsi Panagiota , Waldthaler Josefine , Oostenveld Robert , Ingvar Martin , Svenningsson Per , Lundqvist Daniel
Published: September 2019

Parkinson’s disease is characterized by a gradual loss of dopaminergic neurons, which are associated with altered neuronal activity in the beta band (13-30 Hz). Assessing beta band activity typically involves transforming the time-series to get the power of the signal in the frequency-domain. Such transformation assumes that the time-series can be reduced to a combination of steady-state sine-and cosine waves. However, recent studies have suggested that this approach masks relevant biophysical features in the beta band activity—for example, that the beta band exhibits transient bursts of high-amplitude activity.

In an exploratory study we used magnetoencephalography (MEG) to record cortical beta band activity to characterize how spontaneous cortical beta bursts manifest in Parkinson’s patients ON and OFF dopaminergic medication, and compare this to matched healthy controls. From three minutes of MEG data, we extracted the time-course of beta band activity from the sensorimotor cortex and characterized high-amplitude epochs in the signal to test if they exhibited burst like properties. We then compared the rate, duration, inter-burst interval, and peak amplitude of the high-amplitude epochs between the Parkinson’s patients and healthy controls.

Our results show that Parkinson’s patients OFF medication had a 6-17% lower beta bursts rate compared to healthy controls, while both the duration and the amplitude of the bursts were the same for Parkinson’s patients and healthy controls and medicated state of the Parkinson’s patients. These data thus support the view that beta bursts are fundamental underlying features of beta band activity, and show that changes in cortical beta band power in PD can be explained primarily by changes in the underlying burst rate. Importantly, our results also revealed a relationship between beta bursts rate and motor symptom severity in PD: a lower burst rate scaled with increased in severity of bradykinesia and postural/kinetic tremor. Beta burst rate might thus serve as neuromarker for Parkinson’s disease that can help in the assessment of symptom severity in Parkinson’s disease or evaluate treatment effectiveness.
The effects of e-cigarette vapor exposure on the transcriptome and virulence of Streptococcus pneumoniae
Authors: Bagale Kamal , Paudel Santosh , Cagle Hayden , Sigel Erin , Kulkarni Ritwij
Published: September 2019

The effects of e-cigarette vapor (EV) exposure on the physiology of respiratory microflora are not fully defined. We analyzed the effects of exposure to vapor from nicotine-containing and nicotine-free e-liquid formulations on virulence and transcriptome of Streptococcus pneumoniae strain TIGR4, a pathogen that asymptomatically colonizes human nasopharyngeal mucosa. TIGR4 was pre-exposed for 2h to nicotine-containing EV extract (EVE+NIC), nicotine-free EV extract (EVE−NIC), cigarette smoke extract (CSE), or nutrient-rich TS broth (control). The differences in the treatment and control TIGR4 were explored using transcriptome sequencing, in vitro virulence assays, and in vivo mouse model of acute pneumonia. The analysis of RNASeq profiles revealed modest changes in the expression of 14 genes involved in sugar transport and metabolism in EVE−NIC pre-exposed TIGR4 compared to the control. While, EVE+NIC or CSE exposure altered expression of 264 and 982 genes, respectively, most of which were involved in metabolism and stress response. Infection in a mouse model of acute pneumonia with control TIGR4 or with TIGR4 pre-exposed to EVE+NIC, EVE−NIC, or CSE did not show significant differences in disease parameters, such as bacterial organ burden and respiratory cytokine response. Interestingly, TIGR4 exposed to CSE or EVE+NIC (but not EVE−NIC) exhibited moderate induction of biofilm formation. However, none of the treatment groups showed significant alterations in pneumococcal hydrophobicity or epithelial cell adherence. In summary, our study reports that exposure to EV significantly alters the S. pneumoniae transcriptome in a nicotine-dependent manner without affecting pneumococcal virulence.

Importance

With the increasing popularity of e-cigarettes amongst cigarette smoking and non-smoking adults and children, and the recent reports of vaping related lung illnesses and deaths, further analysis of the adverse health effects of e-cigarette vapor (EV) exposure is warranted. Since pathogenic bacteria such as Streptococcus pneumoniae can colonize the human nasopharynx as commensals, they may be affected by the exposure to bioactive chemicals in EV. Hence in this study we examined the effects of EV exposure on the physiology of S. pneumoniae strain TIGR4. In order to differentiate between the effects of nicotine and non-nicotine components, we specifically compared RNASeq profiles and virulence of TIGR4 exposed to vapor from nicotine-containing and nicotine-free e-liquid formulations. We observed that nicotine-containing EV augmented TIGR4 biofilms and altered expression of TIGR4 genes predominantly involved in metabolism and stress response. However, neither nicotine-containing nor nicotine-free EV affected TIGR4 virulence in a mouse model.
Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase
Authors: da Silva Richard Cardoso , Villar-Fernández María Ascensión , Vader Gerben
Published: September 2019

Pch2 is an AAA+ protein that controls DNA break formation, recombination and checkpoint signaling during meiotic G2/prophase. Chromosomal association of Pch2 is linked to these processes, and several factors influence the association of Pch2 to euchromatin and the specialized chromatin of the ribosomal (r)DNA array of budding yeast. Here, we describe a comprehensive mapping of Pch2 localization across the budding yeast genome during meiotic G2/prophase. Within non-rDNA chromatin, Pch2 associates with a subset of actively RNA Polymerase II (RNAPII)-dependent transcribed genes. Chromatin immunoprecipitation (ChIP)- and microscopy-based analysis reveals that active transcription is required for chromosomal recruitment of Pch2. Similar to what was previously established for association of Pch2 with rDNA chromatin, we find that Orc1, a component of the Origin Recognition Complex (ORC), is required for the association of Pch2 to these euchromatic, transcribed regions, revealing a broad connection between chromosomal association of Pch2 and Orc1/ORC function. Ectopic mitotic expression is insufficient to drive recruitment of Pch2, despite the presence of active transcription and Orc1/ORC in mitotic cells. This suggests meiosis-specific ‘licensing’ of Pch2 recruitment to sites of transcription, and accordingly, we find that the synaptonemal complex (SC) component Zip1 is required for the recruitment of Pch2 to transcription-associated binding regions. Interestingly, Pch2 binding patterns are distinct from meiotic axis enrichment sites (as defined by Red1, Hop1 and Rec8). This suggests that although Pch2 is linked to axis/SC-directed recruitment and function, the chromosomal population of Pch2 described here is not directly associated with chromosomal axis sites. In line with this observation, interfering with the pool of Pch2 that associates with active RNAPII transcription does not lead to effects on the chromosomal abundance of Hop1, a known axial client of Pch2. We thus report characteristics and dependencies for Pch2 recruitment to meiotic chromosomes, and reveal an unexpected link between Pch2, SC formation, chromatin and active transcription.
Host circadian clocks do not set the schedule for the within-host replication of malaria parasites
Authors: O’Donnell Aidan J. , Prior Kimberley F. , Reece Sarah E.
Published: September 2019

Circadian clocks coordinate organisms’ activities with daily cycles in their environment. Parasites are subject to daily rhythms in the within-host environment, resulting from clock-control of host behaviours and physiologies, including immune responses. Parasites also exhibit rhythms in within-host activities; the timing of host feeding sets the timing of the within-host replication of malaria parasites. Why host feeding matters to parasites and how coordination with feeding is achieved are unknown. Determining whether parasites coordinate with clock-driven food-related rhythms of their hosts matters because rhythmic replication underpins disease symptoms and fuels transmission.

We find that parasite rhythms became coordinated with the time of day that hosts feed in both wild type and clock-mutant mice, whereas parasite rhythmicity was lost in clock-mutant mice that fed continuously. These patterns occurred regardless of whether infections were initiated with synchronous or with desynchronised parasites.

Malaria parasite rhythms are not driven by canonical clock-controlled host rhythms. Instead, we propose parasites coordinate with a temporally-restricted nutrient that becomes available through host digestion or are influenced by a separate clock-independent host process that directly responds to feeding. Thus, interventions could disrupt parasite rhythms to reduce their fitness, without interference by host clock-controlled-homeostasis.
Photosystem II does not convert nascent oxygen to the poisonous singlet form
Authors: Mattila Heta , Tyystjärvi Esa
Published: September 2019

In the light, the Mn4CaO5complex of Photosystem II (PSII) splits water producing O2and the triplet state of the primary donor (3P680) of PSII generates reactive singlet oxygen (1O2). We show that nascent O2is not converted to1O2, but originates exclusively from ambient O2, indicating that the sensitivity of PSII to oxidative damage is not a consequence of the water-splittingper se, and showing that the suggested oxygen channels function nearly perfectly, conveying nascent O2out of the reach of3P680. This may have been crucial during evolution of oxygenic photosynthesis, as3P680cannot be quenched by carotenoids that protect non- oxygenic photosystems. In addition, the data indicate that a1O2-independent mechanism contributes to the light-induced damage of PSII.