bluuebunny/crossref_metadata_2025 huggingface dataset:
Recurrent YAP1 and KMT2A Gene Rearrangements in a Subset of MUC4-negative Sclerosing Epithelioid Fibrosarcoma
Authors: Kao Yu-Chien , Lee Jen-Chieh , Zhang Lei , Sung Yun-Shao , Swanson David , Hsieh Tsung-Han , Liu Yun-Ru , Agaram Narasimhan P. , Huang Hsuan-Ying , Dickson Brendan C. , Antonescu Cristina R.
Published: October 2019

Sclerosing epithelioid fibrosarcoma (SEF) is an aggressive soft tissue sarcoma, characterized by a distinctive epithelioid phenotype in a densely sclerotic collagenous stroma, that shows frequent MUC4 immunoreactivity and recurrent gene fusions, often involving EWSR1 gene. A pathogenetic link with low-grade fibromyxoid sarcoma (LGFMS) has been suggested, due to cases with hybrid morphology as well as overlapping genetic signature. However, a small subset of SEF is negative for MUC4 and lacks the canonical EWSR1/FUS gene rearrangements. Triggered by the identification of recurrent YAP1-KMT2A gene fusions by RNA sequencing in 3 index cases of MUC4-negative, EWSR1/FUS fusion-negative SEF, we further investigated a cohort of 14 similar SEF cases (MUC4-negative, EWSR1/FUS fusion-negative) by fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction, and/or DNA-based massively parallel sequencing (MSK-IMPACT) for abnormalities in these genes. Three additional SEFs with KMT2A gene rearrangements and one additional case with YAP1 gene rearrangements were identified by FISH. In addition, one case with YAP1-KMT2A and one with KMT2A-YAP1 fusion were detected by reverse transcription-polymerase chain reaction and MSK-IMPACT, respectively. As a control group, 24 fibromyxoid spindle cell tumors, diagnosed or suspected as fusion-negative LGFMS, were also tested for YAP1 and KMT2A abnormalities by FISH, but none were positive. The YAP1/KMT2A-rearranged SEF group affected patients ranging from 10 to 86 years old (average and median: 45) of both sexes (4 females, 5 males). The tumors involved somatic soft tissues with a wide distribution, including extremities, trunk, neck, and dura. Histologically, the tumors showed variable cellularity, with monotonous ovoid to epithelioid tumor cells and hyalinized collagenous background typical of SEF. More than half of the cases showed infiltrative borders, within fat or skeletal muscle. No LGFMS component was identified. All tumors were negative for MUC4 and had an otherwise nonspecific immunophenotype. Of the 6 cases with available follow-up information, 2 had local recurrences, and 2 developed soft tissue and/or bone metastases, including 1 of them died of the disease.
Transfusion-Free Cranial Vault Remodeling: A Novel, Multifaceted Approach
Authors: Wood Robert J. , Stewart Christopher N. , Liljeberg Katie , Sylvanus Tonye S. , Lim Paul K.
Published: October 2019

Background:

Approximately one in 2000 babies are born with craniosynostosis, and primary open repair is typically performed before 1 year of age. Historically, the procedure has been associated with nearly 100 percent transfusion rates. To decrease the rates of transfusion, the authors’ center has developed a novel multimodal blood conservation protocol.

Methods:

The authors administered their standard of care to children aged 1 year or younger undergoing primary repair of craniosynostosis between 2008 and 2014. In 2014, the authors implemented the following protocol: (1) preoperative erythropoietin and ferrous sulfate, (2) local anesthetic with epinephrine infiltration of the incision, (3) PlasmaBlade incision and subgaleal dissection, (4) hypervolemic hemodilution, and (5) intravenous tranexamic acid. Procedures performed before the protocol implementation served as controls. The authors performed classic fronto-orbital advancement with anterior cranial vault remodeling for coronal and metopic craniosynostosis. For lambdoid and sagittal craniosynostosis, barrel stave osteotomies, cranial base outfracture, and interposition bone grafting were performed.

Results:

A total of 279 children with a mean age of 6 months who had craniosynostosis repairs were included. One hundred forty-five underwent repair before the authors’ protocol, and 134 had repairs during the authors’ blood conservation protocol. Both groups were similar in demographics. Overall blood loss and operative times were significantly reduced by 73 percent and 11 percent, respectively. Blood transfusion rate decreased 92 percent (p < 0.001).

Conclusions:

These results show a strong association between the authors’ blood conservation protocol and significantly reduced transfusion rates. The authors believe this is a significant step forward and can be safely applied in the great majority of children undergoing craniosynostosis repairs.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, III.
Facial Recognition Neural Networks Confirm Success of Facial Feminization Surgery
Authors: Chen Kevin , Lu Stephen M. , Cheng Roger , Fisher Mark , Zhang Ben H. , Di Maggio Marcelo , Bradley James P.
Published: October 2019

Background:

Male-to-female transgender patients desire to be identified, and treated, as female, in public and social settings. Facial feminization surgery entails a combination of highly visible changes in facial features. To study the effectiveness of facial feminization surgery, we investigated preoperative/postoperative gender-typing using facial recognition neural networks.

Methods:

In this study, standardized frontal and lateral view preoperative and postoperative images of 20 male-to-female patients who completed hard- and soft-tissue facial feminization surgery procedures were used, along with control images of unoperated cisgender men and women (n = 120 images). Four public neural networks trained to identify gender based on facial features analyzed the images. Correct gender-typing, improvement in gender-typing (preoperatively to postoperatively), and confidence in femininity were analyzed.

Results:

Cisgender male and female control frontal images were correctly identified 100 percent and 98 percent of the time, respectively. Preoperative facial feminization surgery images were misgendered 47 percent of the time (recognized as male) and only correctly identified as female 53 percent of the time. Postoperative facial feminization surgery images were gendered correctly 98 percent of the time; this was an improvement of 45 percent. Confidence in femininity also improved from a mean score of 0.27 before facial feminization surgery to 0.87 after facial feminization surgery.

Conclusions:

In the first study of its kind, facial recognition neural networks showed improved gender-typing of transgender women from preoperative facial feminization surgery to postoperative facial feminization surgery. This demonstrated the effectiveness of facial feminization surgery by artificial intelligence methods.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Demineralized Bone Matrix and Resorbable Mesh Bilaminate Cranioplasty Is Ineffective for Secondary Reconstruction of Large Pediatric Cranial Defects
Authors: Dvoracek Lucas A. , Lee Jonathan Y. , Ayyash Ali , Losee Joseph E. , Goldstein Jesse A.
Published: October 2019

Replacement of the autologous bone flap after decompressive craniectomy can be complicated by significant osteolysis or infection with large defects over scarred dura. Demineralized bone matrix is an alternative to autologous reconstruction, effective when reconstructing large defects using a resorbable mesh bilaminate technique in primary cranioplasty, but this technique has not been studied for revision cranioplasty and the setting of scarred dura. Retrospective review was performed of patients receiving demineralized bone matrix and resorbable mesh bilaminate cranioplasty for postdecompressive craniectomy defects. Seven patients (mean age, 4.2 years) were identified with a mean follow-up of 4.0 years. Computed tomography before the demineralized bone matrix and resorbable mesh bilaminate cranioplasty and at least 1 year postoperatively were compared. Defects were characterized and need for revision was assessed. All patients had craniectomy with associated hemidural scarring. Five patients had autologous bone flap cranioplasty associated with nearly total osteolysis, and two patients had deferral of bone flap before demineralized bone matrix and resorbable mesh bilaminate cranioplasty. Demineralized bone matrix and resorbable mesh bilaminate cranioplasty demonstrated unpredictable and poor ossification, with bony coverage unchanged at postoperative follow-up. All patients required major revision cranioplasty at a mean time of 2.5 years. Porous polyethylene was successfully used in six of the revisions, whereas exchange cranioplasty was used in the remaining patient, with a mean follow-up of 1.4 years. Although demineralized bone matrix and resorbable mesh bilaminate is appropriate for primary cranioplasty, it should be avoided in the setting of scarred or infected dura in favor of synthetic materials or exchange cranioplasty.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Linking Daily-Life Interpersonal Stressors and Health Problems Via Affective Reactivity in Borderline Personality and Depressive Disorders
Authors: Hepp Johanna , Lane Sean P. , Carpenter Ryan W. , Trull Timothy J.
Published: October 2019

Objective

Borderline personality disorder (BPD) is associated with unstable interpersonal relationships, affective instability, and physical health problems. In individuals with BPD, intense affective reactions to interpersonal stressors may contribute to the increased prevalence of health problems.

Methods

BPD (n = 81) and depressed participants (DD; n = 50) completed six daily ambulatory assessment prompts for 28 days. At each prompt, participants reported interpersonal stressors (disagreements, rejections, feeling let down), negative affect, and health problems in four domains (gastrointestinal, respiratory, aches, depressive symptoms). In multilevel moderated mediation models, we examined the indirect effects of interpersonal stressors on health problems via negative affect, by group.

Results

Interpersonal stressors were positively associated with negative affect in both groups (β values > 0.12, p values < .001), but more so for participants with BPD (βDay = 0.05, p < .001). Negative affect was positively associated with health problems across all domains (βMoment/Day values > 0.01, p values < .046), but associations were larger at the day level for respiratory symptoms in BPD (β = 0.02, p = .025) and for depressive symptoms in DD (β = 0.04, p < .001). Negative affect mediated the association of interpersonal stressors and health problems in both groups, with larger effects for the DD group for depressive problems (β = 0.02, p = .092) and for the BPD group for the other three domains (β values > 0.02, p values < .090).

Conclusions

Interpersonal stressors may contribute to increased physical health problems via an inability to regulate affective responses to such events. This pathway may be stronger in several health domains for those with BPD and may contribute to an elevated risk of morbidity and mortality in this disorder, suggesting a target for intervention to reduce these risks.
Longer Sleep Duration and Endothelial Cell Health Among a Multiethnic Sample of Adolescents
Authors: Alcántara Carmela , Giorgio Cosenzo Luciana , Leigh Adam K.K. , Shimbo Daichi , Miller Gregory E.
Published: October 2019

Objective

Adverse endothelial cell health, an early pathogenic process underlying atherosclerosis and cardiovascular disease, is evident in childhood and adolescence. Sleep duration, a modifiable cardiovascular health behavior, may be an important cardiovascular disease prevention target that may affect endothelial cell health. We examined the associations of longer sleep duration with endothelial cell injury among youth.

Methods

In a multiethnic sample of 235 children (63.0% female, mean age = 13.9 years), we conducted multivariable linear regressions to test the cross-sectional association of sleep duration and circulating levels of endothelial cell–derived microparticles (EMPs), phenotypic for endothelial cell activation and apoptosis (CD62E+ EMPs, CD31+/CD42b− EMPs, and CD31+/Annexin V+ EMPs). Sleep duration and EMPs were both treated as continuous variables. Models were adjusted for age, sex, race, pubertal status, household economic resources, and waist circumference.

Results

Overall, 69.2% had short sleep duration (<8 hours of sleep per night). Longer sleep duration was significantly associated with lower levels of CD62E+ EMPs and CD31+/CD42b− EMPs. A 60-minute increase in sleep duration was associated with an 8.40 (95% confidence interval = −205.20 to −1.80, p = .046) decrease in CD62E+ EMPs and a 9.00 (95% confidence interval = −153.60 to −9.60, p = .027) decrease in CD31+/CD42b− EMPs. Sleep duration was not associated with CD31+/Annexin V+ EMPs.

Conclusions

Our results support the hypothesis that sleeping longer has beneficial effects on endothelial cell health during childhood. Primordial prevention efforts might incorporate sleep extension to offset cardiovascular risk in youth.
Defining Global Benchmarks in Bariatric Surgery
Authors: Gero Daniel , Raptis Dimitri A. , Vleeschouwers Wouter , van Veldhuisen Sophie L. , Martin Andres San , Xiao Yao , Galvao Manoela , Giorgi Marcoandrea , Benois Marine , Espinoza Felipe , Hollyman Marianne , Lloyd Aaron , Hosa Hanna , Schmidt Henner , Garcia-Galocha José Luis , van de Vrande Simon , Chiappetta Sonja , Menzo Emanuele Lo , Aboud Cristina Mamédio , Lüthy Sandra Gagliardo , Orchard Philippa , Rothe Steffi , Prager Gerhard , Pournaras Dimitri J. , Cohen Ricardo , Rosenthal Raul , Weiner Rudolf , Himpens Jacques , Torres Antonio , Higa Kelvin , Welbourn Richard , Berry Marcos , Boza Camilo , Iannelli Antonio , Vithiananthan Sivamainthan , Ramos Almino , Olbers Torsten , Sepúlveda Matias , Hazebroek Eric J. , Dillemans Bruno , Staiger Roxane D. , Puhan Milo A. , Peterli Ralph , Bueter Marco
Published: October 2019

Objective:

To define “best possible” outcomes for bariatric surgery (BS)(Roux-en-Y gastric bypass [RYGB] and sleeve gastrectomy [SG]).

Background:

Reference values for optimal surgical outcomes in well-defined low-risk bariatric patients have not been established so far. Consequently, outcome comparison across centers and over time is impeded by heterogeneity in case-mix.

Methods:

Out of 39,424 elective BS performed in 19 high-volume academic centers from 3 continents between June 2012 and May 2017, we identified 4120 RYGB and 1457 SG low-risk cases defined by absence of previous abdominal surgery, concomitant procedures, diabetes mellitus, sleep apnea, cardiopathy, renal insufficiency, inflammatory bowel disease, immunosuppression, anticoagulation, BMI>50 kg/m2 and age>65 years. We chose clinically relevant endpoints covering the intra- and postoperative course. Complications were graded by severity using the comprehensive complication index. Benchmark values were defined as the 75th percentile of the participating centers’ median values for respective quality indicators.

Results:

Patients were mainly females (78%), aged 38±11 years, with a baseline BMI 40.8 ± 5.8 kg/m2. Over 90 days, 7.2% of RYGB and 6.2% of SG patients presented at least 1 complication and no patients died (mortality in nonbenchmark cases: 0.06%). The most frequent reasons for readmission after 90-days following both procedures were symptomatic cholelithiasis and abdominal pain of unknown origin. Benchmark values for both RYGB and SG at 90-days postoperatively were 5.5% Clavien-Dindo grade ≥IIIa complication rate, 5.5% readmission rate, and comprehensive complication index ≤33.73 in the subgroup of patients presenting at least 1 grade ≥II complication.

Conclusion:

Benchmark cutoffs targeting perioperative outcomes in BS offer a new tool in surgical quality-metrics and may be implemented in quality-improvement cycle.

ClinicalTrials.gov Identifier NCT03440138
Novel Real-time Prediction of Liver Graft Function During Hypothermic Oxygenated Machine Perfusion Before Liver Transplantation
Authors: Muller Xavier , Schlegel Andrea , Kron Philipp , Eshmuminov Dilmurodjon , Würdinger Michael , Meierhofer David , Clavien Pierre-Alain , Dutkowski Philipp
Published: October 2019

Objective:

The aim of this study was to determine the predictive value of machine perfusate analysis on graft outcome.

Background:

Ex situ machine perfusion (MP) is gaining increasing interest to potentially repair injured organs and to assess organ function. In the field of liver transplantation, however, no studies exist on reliable prediction of graft function during MP.

Methods:

We have used hypothermic oxygenated perfusion (HOPE) for donation after circulatory death (DCD) or extended criteria donation after brain death (DBD) human liver grafts during the last 7 years. Our series includes 100 HOPE-treated liver-transplanted patients with an overall tumor-censored 5-year graft survival of 89%. We monitored 54 livers during HOPE in terms of fluorometric analysis of released mitochondrial flavin (flavin mononucleotide, FMN) in the machine perfusate.

Results:

Real-time optical measurement of mitochondrial FMN release in machine perfusates of livers disclosed a strong correlation with lactate clearance and coagulation factors at day 1 and 2 after transplantation. Receiver-operating characteristic curve analysis revealed an area under the curve (AUROC) of 0.79 [95% confidence interval (CI), 0.62–0.97] for severe allograft dysfunction and for early graft loss (AUROC 0.93, 95% CI, 0.84–1.0).

Conclusions:

Assessment of flavin, a marker of mitochondrial complex I injury, in the perfusate provides a fast prediction of liver graft function and loss during ex situ MP before implantation. This finding may have high clinical relevance, as liver grafts from extended DBD or DCD donors carry considerable risks for recipients. On-line estimation of outcome before implantation would therefore substantially increase safe utilization of liver grafts.
Intracorporeal or Extracorporeal Ileocolic Anastomosis After Laparoscopic Right Colectomy
Authors: Allaix Marco E. , Degiuli Maurizio , Bonino Marco A. , Arezzo Alberto , Mistrangelo Massimiliano , Passera Roberto , Morino Mario
Published: October 2019

Objectives:

The aim of the study was to determine whether there are clinically relevant differences in outcomes between laparoscopic right colectomy (LRC) with intracorporeal ileocolic anastomosis (IIA) and LRC with extracorporeal IA (EIA).

Background:

IIA and EIA are 2 well-established techniques for restoration of bowel continuity after LRC. There are no high-quality studies demonstrating the superiority of one anastomotic technique over the other.

Methods:

This is a double-blinded randomized controlled trial comparing the outcomes of LRC with IIA and LRC with EIA in patients with a benign or malignant right-sided colon neoplasm. Primary endpoint was length of hospital stay (LOS). This trial was registered with ClinicalTrials.gov, number NCT03045107.

Results:

A total of 140 patients were randomized and analyzed. Median operative time was comparable in IIA versus EIA group {130 [interquartile range (IQR) 105–195] vs 130 (IQR 110–180) min; P = 0.770} and no intraoperative complications occurred. The quicker recovery of bowel function after IIA than EIA [gas: 2 (IQR 2–3) vs 3 (IQR 2–3) days, P = 0.003; stool: 4 (IQR 3–5) vs 4.5 (IQR 3–5) days, P = 0.032] was not reflected in any advantage in the primary endpoint: median LOS was similar in the 2 groups [6 (IQR 5–7) vs 6 (IQR 5–8) days; P = 0.839]. No significant differences were observed in the number of lymph nodes harvested, length of skin incision, 30-day morbidity (17.1% vs 15.7%, P = 0.823), reoperation rate, and readmission rate between the 2 groups.

Conclusions:

LRC with IIA is associated with earlier recovery of postoperative bowel function than LRC with EIA; however, it does not reflect into a shorter LOS.
Perioperative Interstitial Fluid Expansion Predicts Major Morbidity Following Pancreatic Surgery
Authors: Sandini Marta , Paiella Salvatore , Cereda Marco , Angrisani Marco , Capretti Giovanni , Casciani Fabio , Famularo Simone , Giani Alessandro , Roccamatisi Linda , Viviani Elena , Caccialanza Riccardo , Montorsi Marco , Zerbi Alessandro , Bassi Claudio , Gianotti Luca
Published: October 2019

Objective:

To evaluate whether perioperative bioimpedance vector analysis (BIVA) predicts the occurrence of surgery-related morbidity.

Summary Background Data:

BIVA is a reliable tool to assess hydration status and compartimentalized fluid distribution.

Methods:

The BIVA of patients undergoing resection for pancreatic malignancies was prospectively measured on the day prior to surgery and on postoperative day (POD)1. Postoperative morbidity was scored per the Clavien-Dindo classification (CDC), and the Comprehensive Complication Index (CCI).

Results:

Out of 249 patients, the overall and major complication rates were 61% and 16.5% respectively. The median CCI was 24 (IQR 0.0–24.2), and 24 patients (9.6%) had a complication burden with CCI≥40. At baseline the impedance vectors of severe complicated patients were shorter compared to the vectors of uncomplicated patients only for the female subgroup (P=0.016). The preoperative extracellular water (ECW) was significantly higher in patients who experienced severe morbidity according to the CDC or not [19.4L (17.5–22.0) vs. 18.2L (15.6–20.6), P=0.009, respectively] and CCI≥40, or not [20.3L (18.5–22.7) vs. 18.3L (15.6–20.6), P=0.002, respectively]. The hydration index on POD1 was significantly higher in patients who experienced major complications than in uncomplicated patients (P=0.020 and P=0.025 for CDC and CCI, respectively).

At a linear regression model, age (β=0.14, P=0.035), sex female (β=0.40, P<0.001), BMI (β=0.30, P<0.001), and malnutrition (β=0.14, P=0.037) were independent predictors of postoperative ECW.

Conclusion:

The amount of extracellular fluid accumulation predicts major morbidity after pancreatic surgery. Female, obese and malnourished patients were at high risk of extracellular fluid accumulation.
Effect of Sleeve Gastrectomy on Ghrelin, GLP-1, PYY, and GIP Gut Hormones
Authors: McCarty Thomas R. , Jirapinyo Pichamol , Thompson Christopher C.
Published: October 2019

Objective:

To perform a structured systematic review and meta-analysis to evaluate changes in ghrelin, glucagon-like peptide-1 (GLP-1), peptide YY (PYY), and gastric inhibitory peptide (GIP) gut hormone levels in patients after sleeve gastrectomy.

Background:

Despite sleeve gastrectomy becoming the most common surgical weight loss procedure, weight loss mechanisms remain less clear.

Methods:

Searches of PubMed, EMBASE, Web of Science, and Cochrane Library databases were performed through April 1, 2019, in accordance with PRISMA and MOOSE guidelines. Randomized controlled trials and prospective observational studies evaluating pre and post-procedure hormones fasting ghrelin, postprandial GLP-1, postprandial PYY, and fasting GIP levels were included. Hedge g with random-effects models were used to determine pooled effect size and corresponding 95% confidence intervals (CIs).

Results:

A total of 28 studies (n = 653; 29.56% male) were included. Mean age was 42.00 ± 5.48 years, with average follow-up of 11.70 ± 11.38 months. Pre-procedure body mass index (BMI) was 46.01 ± 4.07 kg/m2 with a postsleeve gastrectomy BMI of 34.07 ± 3.73 kg/m2, representing total body weight loss of 25.13 ± 4.44% and excess weight loss of 57.48 ± 9.64% (P < 0.001). Ghrelin decreased (Hedge g −1.486, 95% CI −1.884 to −1.089, I
2 = 91.95%), whereas GLP-1 and PYY increased post-procedure (Hedge g 1.095, 95% CI 0.509 to 1.642, I
2 = 84.38%; and Hedge g 1.396, 95% CI 0.781 to 2.011, I
2 = 84.02%, respectively). GIP did not significantly change (Hedge g −0.213, 95% CI −1.019 to 0.592, I
2 = 79.65%).

Conclusions:

Fasting ghrelin levels decreased, whereas postprandial GLP-1 and PYY increased after sleeve gastrectomy. Fasting GIP levels remained unchanged. Future studies are needed to assess the role of these gut hormones and relationship to weight loss and metabolic outcomes.
Bacterial ageing in the absence of external stressors
Authors: Łapińska Urszula , Glover Georgina , Capilla-Lasheras Pablo , Young Andrew J. , Pagliara Stefano
Published: October 2019

Evidence of ageing in the bacterium
Escherichia coli
was a landmark finding in senescence research, as it suggested that even organisms with morphologically symmetrical fission may have evolved strategies to permit damage accumulation. However, recent work has suggested that ageing is only detectable in this organism in the presence of extrinsic stressors, such as the fluorescent proteins and strong light sources typically used to excite them. Here we combine microfluidics with brightfield microscopy to provide evidence of ageing in
E. coli
in the absence of these stressors. We report (i) that the doubling time of the lineage of cells that consistently inherits the ‘maternal old pole’ progressively increases with successive rounds of cell division until it reaches an apparent asymptote, and (ii) that the parental cell divides asymmetrically, with the old pole daughter showing a longer doubling time and slower glucose accumulation than the new pole daughter. Notably, these patterns arise without the progressive accumulation or asymmetric partitioning of observable misfolded-protein aggregates, phenomena previously hypothesized to cause the ageing phenotype. Our findings suggest that ageing is part of the naturally occurring ecologically-relevant phenotype of this bacterium and highlight the importance of alternative mechanisms of damage accumulation in this context.

This article is part of a discussion meeting issue ‘Single cell ecology’.
Visualization is crucial for understanding microbial processes in the ocean
Authors: Sebastián Marta , Gasol Josep M.
Published: October 2019

Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and theirin situlevel of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems.

This article is part of a discussion meeting issue ‘Single cell ecology’.
Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes
Authors: Keeling Patrick J.
Published: October 2019

Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour.

This article is part of a discussion meeting issue ‘Single cell ecology'.
Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes
Authors: Needham David M. , Poirier Camille , Hehenberger Elisabeth , Jiménez Valeria , Swalwell Jarred E. , Santoro Alyson E. , Worden Alexandra Z.
Published: October 2019

Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant
Mimiviridae
, incorporating the
Cafeteria roenbergensis
virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (
e
-value < 10
−5
), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.

This article is part of a discussion meeting issue ‘Single cell ecology’.
Uncovering microbial inter-domain interactions in complex communities
Authors: Florenza Javier , Tamminen Manu , Bertilsson Stefan
Published: October 2019

Interactions between unicellular eukaryotes and bacteria are difficult to characterize in the environment owing to their large number and inherently microscopic scale. Although particular co-occurrences can be recovered through targeted approaches, e.g. single-cell sequencing or fluorescence
in situ
hybridization, the vast majority of the interactions remain unseen. Here, we discuss Emulsion, Paired Isolation and Concatenation polymerase chain reaction (epicPCR) as a tool to uncover these interactions in very high throughput. Originally developed for taxonomy-to-function linkage in bacterial communities, epicPCR has the potential to recover the complete interaction network in a given environment at single-cell resolution. This approach relies on the encapsulation of protistan single cells in emulsion droplets that can subsequently be gelified into beads. In this way, encapsulated cells can be exposed to lysis reagents and further phylogenetic paired marker amplification. A bacterium that physically co-occurs with the eukaryote will be jointly trapped, and the amplification will generate a concatenated PCR product containing physically coupled taxonomic markers from both partners, creating a link. Further amplification and sequencing enable the construction of an association pattern with statistically verified physical co-occurrences. Here, we discuss the potential, challenges and limitations of epicPCR. We argue that the microscopic scale at which epicPCR operates, the high throughput it delivers and its exploratory nature make it an unparalleled approach to unravel associations between microbes directly from environmental samples.

This article is part of a discussion meeting issue ‘Single cell ecology’.
Contributions of single-cell genomics to our understanding of planktonic marine archaea
Authors: Santoro A. E. , Kellom M. , Laperriere S. M.
Published: October 2019

Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes—the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening.

This article is part of a discussion meeting issue ‘Single cell ecology’.
A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure
Authors: Wideman Jeremy G. , Lax Gordon , Leonard Guy , Milner David S. , Rodríguez-Martínez Raquel , Simpson Alastair G. B. , Richards Thomas A.
Published: October 2019

Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive
trans
-splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive
trans
-splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and
trans
-splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes.

This article is part of a discussion meeting issue ‘Single cell ecology’.
Paulinella micropora KR01 holobiont genome assembly for studying primary plastid evolution
Authors: Lhee Duckhyun , Lee JunMo , Cho Chung Hyun , Ha Ji-San , Jeong Sang Eun , Jeon Che Ok , Zelzion Udi , Price Dana C. , Chan Ya-Fan , Gabr Arwa , Bhattacharya Debashish , Yoon Hwan Su
Published: October 2019

The widespread algal and plant (Archaeplastida) plastid originated >1 billion years ago, therefore relatively little can be learned about plastid integration during the initial stages of primary endosymbiosis by studying these highly derived species. Here we focused on a unique model for endosymbiosis research, the photosynthetic amoeba Paulinella micropora KR01 (Rhizaria) that underwent a more recent independent primary endosymbiosis about 124 Mya. A total of 149 Gbp of PacBio and 19 Gbp of Illumina data were used to generate the draft assembly that comprises 7,048 contigs with N50=143,028 bp and a total length of 707 Mbp. Genome GC-content was 44% with 76% repetitive sequences. We predicted 32,358 genes that contain 73% of the complete, conserved genes in the BUSCO database. The mean intron length was 882 bp, which is significantly greater than in other Rhizaria (86∼184 bp). Symbiotic bacteria from the culture were isolated and completed genomes were generated from three species (Mesorhizobium amorphae Pch-S, Methylibium petroeiphilum Pch-M, Polaromonas sp. Pch-P) with one draft genome (Pimelobacter simplex Pch-N). Our holobiont data establish P. micropora KR01 as a model for studying plastid integration and the role of bacterial symbionts in Paulinella biology.
Structural Basis and Designing of Peptide Vaccine using PE-PGRS Family Protein of Mycobacterium ulcerans – An Integrated Vaccinomics Approach
Authors: Nain Zulkar , Karim Mohammad Minnatul , Sen Monokesh Kumer , Adhikari Utpal Kumar
Published: October 2019

Buruli ulcer is an emerging-necrotizing skin infection, responsible for permanent deformity if untreated, caused by the pathogen Mycobacterium ulcerans (M. ulcerans). Despite this debilitating condition, no specific disease-modifying therapeutics or vaccination is available. Therefore, we aimed to design an effective multi-epitope vaccine against M. ulcerans through an integrated vaccinomics approach. Briefly, the highest antigenic PE-PGRS protein was selected from which the promiscuous T- and B-cell epitopes were predicted. After rigorous assessment, 15 promising CTL, HTL and LBL epitopes were selected. The identified T-cell epitopes showed marked interactions towards the HLA binding alleles and provided 99.8% world population coverage. Consequently, a vaccine chimera was designed by connecting these epitopes with suitable linkers and adjuvant (LprG). The vaccine construct was antigenic and immunogenic as well as non-allergenic; hence, subjected to homology modelling. The molecular docking and dynamic simulation revealed strong and stable binding affinity between the vaccine and TLR2 receptor. The binding energy (ΔG) and dissociation constant (Kd) were −15.3 kcal/mol and 5.9×10−12 M, respectively. Further, disulfide engineering was applied to improve vaccine’ stability and higher expression in Escherichia coli K12 system was ensured by codon optimization and cloning in silico. The computer-simulated immune responses were characterized by higher levels of IgM and IgG antibodies, helper T-cells with increased IFN-γ production, and macrophage activity crucial for immunity against M. ulcerans. Therefore, our data suggest that, if the designed vaccine is validated experimentally, it will prevent Buruli ulcer by generating robust immune response against M. ulcerans.
Crystallography of three-dimensional fluid flows with chirality in hexagonal cases
Authors: Nishiyama Takahiro
Published: October 2019

Magnetic groups are applied to three-dimensional fluid flows with chirality, which are called Beltrami flows (or force-free fields in plasma physics). First, six Beltrami flows are derived so that their symmetries and antisymmetries are described by six different hexagonal magnetic groups. The general Wyckoff positions are used to derive the flows. Special Wyckoff positions are shown to be useful for finding the zero points of the flows. Tube-like surfaces called invariant tori are observed to interlace and form various crystal-like structures when streamlines winding around the surfaces are numerically plotted. Next, two simpler hexagonal Beltrami flows are derived, and their zero points and invariant tori are studied. Some families of the invariant tori have arrangements similar to those observed in materials science.
X-ray interference fringes from a weakly bent plane-parallel crystal with negative strain gradient
Authors: Fukamachi Tomoe , Jongsukswat Sukswat , Ju Dongying , Negishi Riichirou , Hirano Keiichi , Kawamura Takaaki
Published: October 2019

Under the anomalous transmission condition in the Bragg mode, X-ray interference fringes were observed between two beams with different hyperbolic trajectories in a very weakly bent plane-parallel perfect crystal with negative strain gradient. The origin of the fringes was analysed based on the dynamical theory of diffraction for a distorted crystal. In the reflected beam from the entrance surface, the interference fringes were observed between once- and twice-reflected beams from the back surface. In the transmitted beam from the back surface, the interference fringes were observed between the direct beam and once-reflected beam from the entrance surface. In the emitted beam from the lateral surface, the interference fringes were observed between the beams after different numbers of reflections in the crystal. The multiply reflected beams were formed by a combined result of long propagation length along the beam direction with large divergence of the refracted beams when the strain gradient was negative. The period of these interference fringes was sensitive to very weak strain, of the order of 10−7.
Career sustainability during manufacturing innovation
Authors: Chin Tachia , Li Genyi , Jiao Hao , Addo Frederick , Jawahar I.M.
Published: October 2019

Purpose

Given advances in digitalization and automation, manufacturing employees are facing the increasing threat of being substituted by smart machines and robots. The purpose of this paper is to propose a framework that explains as well as can be used to study career sustainability of workers in the fast-paced, continuously changing manufacturing landscape.

Design/methodology/approach

After tracing the evolution of manufacturing sector in China, the authors review existing literature on career sustainability and then propose a new framework. The authors then describe two fictive cases and illustrate the applicability of the four-dimensional framework in helping understand the lived experience of objects in these fictive cases.

Findings

The proposed dynamic framework of career sustainability constituted by four intricately interconnected dimensions (i.e. resourceful, flexible, renewable and integrative) is useful in understanding the fictive cases and hopefully will guide future research on career sustainability in manufacturing or similarly fast-past, dynamically changing environments.

Practical implications

The framework of career sustainability facilitates manufacturing employees to accurately evaluate the sustainability of their careers, whereby they can choose to continue, shift or re-orient their career paths during the transitional period toward digitalized manufacturing; it also enlightens employers to think about how to enhance the job security and engagement of workers by helping prolong their careers and re-design their career plans.

Originality/value

This paper proposes a novel yet context-specific framework to understand and study sustainability of careers. In addition to helping us understand how careers evolve during transformational periods, it also offers fruitful avenues for further research.
Interaction Facilitation and Task Facilitation need optimization in higher education institutions
Authors: Daly Edward , Mohammed Denelle , Boglarsky Cheryl , Blessinger Patrick , Zeine Rana
Published: October 2019

Purpose

Facilitation and Task Facilitation are important components of healthy supervisory/managerial relationships among higher education professionals. Juniors are guided by superiors who play a supervisory/managerial role in professional development. The purpose of this paper is to examine the impact of Interaction Facilitation and Task Facilitation on supervisory/managerial relationships among higher education professionals.

Design/methodology/approach

The Human Synergistics International Organizational Effectiveness Inventory® was used to survey faculty and administrators at public and private higher education institutions. The authors analyze Interaction Facilitation and Task Facilitation, which focuses on people-oriented and task-oriented skills, respectively.

Findings

The authors demonstrated the negativity of current organizational cultures on organizational effectiveness measures in higher education institutions. The authors analyze Interaction Facilitation and Task Facilitation, which focuses on people-oriented and task-oriented skills, respectively. Results revealed average scores for both measures fell undesirably below the Historical Averages and Constructive Benchmarks in private and public not-for-profits, private for-profits, faculty, administrators, males and females.

Practical implications

To increase follower satisfaction and improve task and contextual performance in higher education institutions, the authors recommend defining the leader’s influence within supervisory/managerial relationships, increasing flexibility in contextual/situational factors, clarifying the role of supervisors, aligning individual and organizational goals in millennials, and maintaining collegiality.

Social implications

The findings suggest that organizational effectiveness in higher education institutions may benefit from thoughtful revision of leadership strategies, better alignment of individual with organizational goals, and continuous cultivation of constructive organizational cultures.

Originality/value

This study has identified the need to ameliorate the practice of Interactive Facilitation and Task Facilitation styles in higher education institutions. Ineffective supervisory/management styles in higher education have a negative impact on the organization cultures reducing the practice of constructive work behaviors.