bluuebunny/crossref_metadata_2025 huggingface dataset:
Week 96 results of a phase 3 trial of darunavir/cobicistat/emtricitabine/tenofovir alafenamide in treatment-naive HIV-1 patients
Authors: Orkin Chloe , Eron Joseph J. , Rockstroh Jürgen , Podzamczer Daniel , Esser Stefan , Vandekerckhove Linos , Van Landuyt Erika , Lathouwers Erkki , Hufkens Veerle , Jezorwski John , Opsomer Magda
Published: December 2019

Background:

Darunavir/cobicistat/emtricitabine/tenofovir alafenamide (D/C/F/TAF) 800/150/200/10 mg was investigated through 96 weeks in AMBER (NCT02431247).

Methods:

Treatment-naive, HIV-1-positive adults [screening plasma viral load ≥1000 copies/ml; CD4+ cell count >50 cells/μl) were randomized (1 : 1) to D/C/F/TAF (N = 362) or D/C plus emtricitabine/tenofovir-disoproxil-fumarate (F/TDF) (N = 363) over at least 48 weeks. After week 48, patients could continue on or switch to D/C/F/TAF in an open-label extension phase until week 96.

Results:

At week 96, D/C/F/TAF exposure was 626 patient-years (D/C/F/TAF arm) and 109 patient-years (control arm post switch), week 96 virologic suppression (viral load <50 copies/ml; FDA-Snapshot, from baseline) was 85.1% (308/362) (D/C/F/TAF) and 83.7% (304/363) (control). Week 96 virologic failure (viral load ≥50 copies/ml; FDA-Snapshot) was 5.5% (20/362) and 4.4% (16/363), respectively. No darunavir, primary protease inhibitor or tenofovir resistance-associated mutations (RAMs) were observed post baseline. In one patient in each arm, an M184I and/or V RAM was detected. Few adverse event-related discontinuations (3% D/C/F/TAF; <1% control post switch) and no deaths occurred on D/C/F/TAF. Improved renal and bone parameters were maintained in the D/C/F/TAF arm and observed in the control arm post switch. Increases in total-cholesterol/high-density-lipoprotein--cholesterol rtio at week 96 were +0.25 versus baseline (D/C/F/TAF) and +0.24 versus switch (control).

Conclusion:

At week 96, D/C/F/TAF resulted in high virologic response and low virologic failure rates, with no resistance development to darunavir or TAF/TDF. Bone, renal and lipid safety were consistent with known D/C/F/TAF component profiles. Control arm safety post switch was consistent with the D/C/F/TAF arm. AMBER week 96 results confirm the efficacy, high barrier to resistance and bone/renal safety benefits of D/C/F/TAF for treatment-naive patients.
An Extraordinary Case of Brown Fat Distribution
Authors: Reichel Cedric , Deroose Christophe , Van Laere Koen , Goffin Karolien
Published: December 2019

We report the case of a 27-year-old woman who underwent an 18F-FDG PET/CT, after administration of 20 mg propranolol, 20 minutes preinjection, to investigate B-symptoms as well as right-sided shoulder pain. Unilateral hypermetabolism was seen in the left cervical, thoracic, and paravertebral brown fat, without any uptake on the contralateral side. The patient was born with neuroblastoma in the right thoracic area. She underwent surgery a few days after birth. As brown fat activation is under sympathetic control, we hypothesize that a surgical lesion to the right orthosympathetic trunk resulted in sympathetic denervation, responsible for this distribution.
Esophageal Adenocarcinoma With Subscalp Metastasis as the First Manifestation Detected by 18F-FDG PET/CT
Authors: Xu Tingting , Zhang Xinyi , Fu Wenhui , Zeng Chengrun , Chen Yue
Published: December 2019

Subscalp metastases occur infrequently in malignant tumors but may appear as an initial clinical presentation. This report presents the case of a 53-year-old man who recently found a painless nodule under the right side of his scalp. 18F-FDG PET/CT, endoscopy, and tissue biopsy diagnosed the nodule as a metastasis of esophageal adenocarcinoma.
18F-FDG PET/CT-Guided Diagnosis and Evaluation of Treatment Response to Cyclosporine A in Maldistributed Subcutaneous Panniculitis-like T-Cell Lymphoma Without Typical Skin Rash
Authors: Abe Yoshiaki , Narita Kentaro , Kobayashi Hiroki , Kitadate Akihiro , Takeuchi Masami , Matsue Kosei
Published: December 2019

A 30-year-old woman presented with persistent fever and elevated lactate dehydrogenase levels without skin rash. 18F-FDG PET/CT revealed FDG uptake in subcutaneous tissues in the forearm, buttocks, and lower limbs, whereas the trunk was unaffected. She was diagnosed with subcutaneous panniculitis-like T-cell lymphoma based on a PET/CT-guided subcutaneous tissue biopsy from the thigh. Although conventional cytotoxic agent–based chemotherapies failed to achieve disease remission, subsequent cyclosporine A treatment promptly resolved the fever and laboratory abnormalities. Remarkably, abnormal FDG uptake disappeared entirely on follow-up PET/CT, demonstrating its utility in the evaluations of responses to emerging cyclosporine A–based treatments in subcutaneous panniculitis-like T-cell lymphoma.
False-Positive 18F-FDG and 18F-Fluorothymidine Uptake in a Patient With Round Atelectasis
Authors: Norikane Takashi , Yamamoto Yuka , Mitamura Katsuya , Tani Ryosuke , Nishiyama Yoshihiro
Published: December 2019

A 64-year-old man with no significant medical history demonstrated a right lower lobe opacity on routine chest radiography. Transaxial CT showed a round, well-circumscribed, pleural mass with comet-tail sign in the right lower lobe and pleural thickening with pleural effusion. 18F-FDG PET/CT showed hypermetabolic activity in the mass (SUVmax 9.61). 18F-fluorothymidine PET/CT also showed mild increased uptake in the mass (SUVmax 3.26). Lung biopsy and follow-up CT scan revealed round atelectasis.
Near Complete Recovery of Visual Acuity After Calcium Hydroxylapatite Injection–Related Vision Loss
Authors: Liu Ying-Chun , Tsai Ming-Feng , Chen Yu-Fan
Published: December 2019

Injection of fillers has gained popularity over the past decades in aesthetic treatments. Calcium hydroxylapatite (CaHA; Radiesse) was introduced in the year 2003 and received approval from the Food and Drug Administration in 2006 for the treatment of moderate-to-severe wrinkles. The properties of CaHA include biostimulation, neocollagenesis, and stability over a long period. However, similar to other fillers, CaHA is associated with the risk of complications such as ecchymosis, inflammation, local infection, skin necrosis, and vascular occlusion. Iatrogenic vision loss remains the most devastating complication related to vascular occlusion. Development of vision impairment is associated with a relatively high risk of permanent damage to vision acuity and poor prognosis. The current report presents a case of a patient who suffered from skin necrosis, vision impairment, and ophthalmoplegia after the injection of CaHA into the nasal dorsum. Significant improvement in visual acuity was observed during hospitalization after the treatment. The patient recovered to near-normal visual acuity and completely recovered from ophthalmoplegia. We aimed to discuss the current treatment employed and review the literature on CaHA-related vision loss.
Attitudes of Hand Surgeons and Hand Reconstruction Patients Toward Hand Allotransplantation in Taiwan
Authors: Wei Hao-I , Do Nicholas T. , Din Rong-Yao , Lin Chih-Hung , Lin Cheng-Hung
Published: December 2019

Background

Recent advances in immunosuppressive protocols have increasingly made hand allotransplantation a realistic reconstructive option with more than 100 cases performed worldwide. While attitudes toward allotransplantation have been assessed for North American surgeons and patients alike, similar assessments have previously remained unconducted in Asia in general and Taiwan in specific. This study examines the perceptions of both Taiwanese hand surgeons and hand reconstruction patients.

Methods

An email-based survey was sent to all active members of the Taiwanese Society for Surgery of the Hand. Surgeon training backgrounds and practice profiles were gathered as well as current beliefs on indications, risks, ethicality, priority of psychosocial issues, and obstacles to implementation. Patients receiving rehabilitation at Chang Gung Memorial Hospital Linkou after severe upper extremity injuries were invited to complete a patient survey. Demographics, injury characteristics, understanding of allotransplantation and immunosuppression, willingness to donate, and willingness to receive transplantation were assessed.

Results

Forty-four hand surgeons responded (24.3% response rate). The majority (61.4%) considered hand allotransplantation to be a high-risk operation, although 40% supported the development of hand allotransplantation under current techniques and immunosuppression. Bilateral hands loss was the most commonly accepted indication for transplant (90.9%), whereas dominant hand loss was less frequently accepted (43.2%). Treatment compliance and functional outcomes were the most frequent psychosocial issues of concern regarding patient counseling. Patient respondents were mostly in the fifth decade of life (29.5%) with at least a high school education (75.0%). Most were aware of the feasibility of hand transplantation (68.2%). Patients were more likely than surgeons to consider nondominant hand, multiple-digit, and thumb-only amputations as indications for transplantation. Functional outcomes and financial considerations were the most frequent patient concerns.

Conclusions

This study indicates there is support for hand allotransplantation as a solution for limb loss in both hand surgeons and hand patients in Taiwan. This study adds to the lack of knowledge regarding surgeon and patient attitudes toward allotransplantation in Asia, although further work is required to assess the willingness of broader Taiwanese medical to refer candidates and for the general population to donate.
Distant Intramuscular Metastases of Head and Neck Squamous Cell Carcinoma
Authors: Hsu I. , Yen Chao-Wu , Huang Kuo-Feng , Lin Yu-San
Published: December 2019

Objectives

Metastasis of head and neck squamous cell carcinoma (HNSCC) usually occurs regionally in the neck lymph nodes, but also more infrequently at distant organs (eg, the lungs, bone, and liver). Intramuscular metastasis (IMM) has rarely been described. Therefore, we aimed to identify this disease characteristic and to evaluate available medical management options.

Methods

Data of surgically treated HNSCC patients (n = 1150) at the Chi Mei Medical Center, Taiwan (2005–2015), were retrospectively reviewed. Literature searches were also conducted (1985–2015) to analyze the behavior of HNSCC with distant IMMs.

Results

We identified 1 HNSCC patient with histopathologically proven IMMs. Ten similar cases were also identified in the available literature. Two-thirds of lesions arose in patients with laryngeal/hypopharyngeal malignancies, and two-thirds of lesions were located in the lower limbs. Lesions were subjectively painful and usually had rim enhancement with central hypoattenuation in contrast-enhanced computed tomography/magnetic resonance imaging. The mean duration between primary tumor diagnosis and secondary lesion detection was 13.7 months. No patient survived more than 2 years after establishing a diagnosis of HNSCC with IMMs.

Conclusions

Distant IMMs are extremely rare in HNSCC patients and have a poor clinical outcome. Differentiating this disease from sarcoma via anatomic distribution or diagnostic imaging studies is not straightforward. Biopsies for histopathologic examination are mandatory. Treatment of HNSCC patients with IMMs is mainly palliative for life quality preservation and not lifetime prolongation. Radiotherapy is established as a first-line treatment for symptom control with surgical intervention usually preserved for refractory cases.
Use of Anterolateral Thigh Flap and Fibula Flap in Oncologic Maxillary Reconstruction
Authors: Chen Szu-Han , Kuo Yao-Lung , Chang Tzu-Yen , Lee Yao-Chou
Published: December 2019

Background

Maxillary defects after oncologic resection can lead to not only cosmetic deformity but also functional problem. Reconstruction of maxillary defects remains the most challenging endeavor for plastic surgeons. An algorithm to guide plastic surgeons in selecting either the anterolateral thigh flap or the fibula flap for oncologic maxillary reconstruction has not been well established.

Methods

Patients who underwent oncologic maxillectomy and free flap reconstruction from August 2012 to April 2018 were enrolled for retrospective chart review. Their operative findings and postoperative outcomes were analyzed as a case series. The reconstructive plan was decided using the 4 essential components in sequence: the anterior maxillary arch, orbital floor, eyeball, and oro-sinonasal communication, which are the main considerations in the established classification systems. Accordingly, when the anterior maxillary arch was lost or when the orbital floor was lost with eyeball preservation, a fibula flap was used. Otherwise, an anterolateral thigh flap was used.

Results

Various maxillectomy defects were successfully reconstructed using an anterolateral thigh flap and a fibula flap. The defect types and corresponding reconstruction were fit into our proposed algorithm and classification. The corresponding outcomes were satisfactory.

Conclusion

The proposed algorithm by using the anterolateral thigh flap and the fibula flap for oncologic maxillary reconstruction is feasible, simple, and effective.
Myotomy In Situ for Essential Blepharospasm Refractory to Botulinum Toxin
Authors: Lai Hsin-Ti , Chen Austin D. , Lee Su-Shin , Lin Yi-Hui , Lai Chung-Sheng
Published: December 2019

Background

Full myectomy is recommended for benign essential blepharospasm (BEB) refractory to botulinum toxin (BT) treatment, but long-term swelling, scar contracture, hollow appearance, and unnatural contour of the eyelids are common postoperative complications. We present myotomy in situ to minimize these adverse outcomes.

Methods

The redundant eyelid skin with its underlying muscle is resected first, and myotomy in situ is performed by completely cutting the residual orbicularis oculi muscles into multiple cubes and down to the subcutaneous layer, and then cutting the procerus and corrugator muscles down to the periosteum. Patient demographics, medical treatment history, BT injection history, blepharoptosis correction techniques, associated surgical procedures, and aesthetic outcomes were analyzed. Preoperative and postoperative BT injection dosage and frequency, as well as modified disability scores, were compared using paired Student t tests.

Results

Twenty-five patients underwent this technique. Their average ± SD age was 64.4 ± 8.9 years, with average postoperative follow-up occurring 17.0 ± 8.0 months. Associated diseases included blepharoptosis (88%) and apraxia of lid opening (44%). There were no postoperative hematoma, seroma, scar contracture, and depressed hollow eyelid contours. Preoperative to postoperative assessments revealed improvements in mean BT injection interval (10.4 ± 2.1 to 14.6 ± 2.9 weeks, P < 0.001), BT injection dosage (44.4 ± 13.3 to 28.1 ± 6.7 units, P < 0.001), and modified disability score (15.3 ± 3.0 to 2.8 ± 2.2, P < 0.001). All patients were highly satisfied with functional and aesthetic surgical outcomes (4.5 ± 0.6 on Likert scale).

Conclusions

Myotomy in situ is effective for patients with BEB who are refractory to BT treatment, with therapeutic benefits similar to that of full myectomy with the ability to maintain favorable cosmetic results. Relative high incidence of blepharoptosis and apraxia of lid opening in patients with refractory BEB was reported. Simultaneous correction of the ptosis can further optimize outcomes.
Vaccine-driven virulence evolution: consequences of unbalanced reductions in mortality and transmission and implications for pertussis vaccines
Authors: Miller Ian F. , Metcalf C. Jessica
Published: December 2019

Many vaccines have heterogeneous effects across individuals. Additionally, some vaccines do not prevent infection, but reduce disease-associated mortality and transmission. Both of these factors will alter selection pressures on pathogens and thus shape the evolution of pathogen virulence. We use a mathematical modelling framework to show that (i) the balance of how vaccines reduce transmission versus mortality and (ii) individual variability in protection conferred both shape the evolution of pathogen virulence. Epidemiological (burden of disease) and evolutionary (pathogen virulence) outcomes are both worse when vaccines confer smaller reductions in transmission than in mortality. Furthermore, outcomes are modulated by variability in vaccine effects, with increased variability limiting the extent of virulence evolution but in some cases preventing eradication. These findings are pertinent to current concerns about the global resurgence of pertussis and the efficacy of pertussis vaccines, as the two classes of these vaccines may reduce disease symptoms without preventing infection and differ in their ability to reduce transmission. Furthermore, these findings point to the importance of generating precise predictions for virulence evolution in
Bordetella pertussis
(and other similar pathogens) by incorporating empirical characterizations of vaccine effects into models capturing the epidemiological details of this system.
High-throughput dense reconstruction of cell lineages
Authors: Espinosa-Medina Isabel , Garcia-Marques Jorge , Cepko Connie , Lee Tzumin
Published: December 2019

The first meeting exclusively dedicated to the ‘High-throughput dense reconstruction of cell lineages' took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.
Pollination treatment affects fruit set and modifies marketable and storable fruit quality of commercial apples
Authors: Samnegård Ulrika , Hambäck Peter A. , Smith Henrik G.
Published: December 2019

Insect-mediated pollination increases yields of many crop species and some evidence suggests that it also influences crop quality. However, the mechanistic linkages between insect-mediated pollination and crop quality are poorly known. In this study, we explored how different pollination treatments affected fruit set, dry matter content (DMC), mineral content and storability of apples. Apple flowers supplementary pollinated with compatible pollen resulted in higher initial fruit set rates, higher fruit DMC and a tendency for lower fruit potassium (K) : calcium (Ca) ratio than flowers that received natural or no pollination. These variables are related to desirable quality aspects, because higher DMC is connected to higher consumer preference and lower K : Ca ratio is related to lower incidence of postharvest disorders during storage. Using structural equation modelling, we showed an indirect effect of pollination treatment on storability, however mediated by complex interactions between fruit set, fruit weight and K : Ca ratio. The concentrations of several elements in apples (K, zinc, magnesium) were affected by the interaction between pollination treatment and apple weight, indicating that pollination affects element allocation into fruits. In conclusion, our study shows that pollination and the availability of compatible pollen needs to be considered in the management of orchard systems, not only to increase fruit set, but also to increase the quality and potentially the storability of apples.
Experimental evaluation of 3D printed spiral phase plates for enabling an orbital angular momentum multiplexed radio system
Authors: Allen B. , Pelham T. , Wu Y. , Drysdale T. , Isakov D. , Gamlath C. , Stevens C. J. , Hilton G. , Beach M. A. , Grant P. S.
Published: December 2019

This paper evaluates the performance of three-dimensionally (3D) printed spiral phase plates (SPPs) for enabling an orbital angular momentum (OAM) multiplexed radio system. The design and realization of the SPPs by means of additive manufacturing exploiting a high-permittivity material is described. Modes 1 and 2 SPPs are then evaluated at 15 GHz in terms of 3D complex radiation pattern, mode purity and beam collimation by means of a 3D printed dielectric lens. The results with the lens yield a crosstalk of −8 dB for between modes 1 and −1, and −11.4 dB for between modes 2 and −2. We suggest a mode multiplexer architecture that is expected to further reduce the crosstalk for each mode. An additional loss of 4.2 dB is incurred with the SPPs inserted into the communication link, which is undesirable for obtaining reliable LTE-based communications. Thus, we suggest: using lower loss materials, seeking ways to reduce material interface reflections or alternative ways of OAM multiplexing to realize a viable OAM multiplexed radio system.
Knowledge about benefits and risks of undergoing cataract surgery among cataract patients in Southern China
Authors: Ye Guofang , Qu Bo , Shi Wen , Chen Xin , Ma Pengjuan , Zhong Yuxin , Chen Shida , Lamoureux Ecosse , Zheng Yingfeng
Published: December 2019

Objective

To develop a theoretical framework for assessing knowledge about the possible outcomes of undergoing cataract surgery, and explore the association of knowledge level with psychological status and decision quality among patients with cataract in Southern China.

Methods

The details of the knowledge scale were based on the health education information booklet provided by National Eye Institute, NIH. We used a theory-based approach to assess gist knowledge, which comprises conceptual and numeric questions related to knowledge of the possible surgical outcomes. The scale was then used in a cross-sectional study to assess the association of knowledge score with psychological status and decision quality of cataract patients, including worry, anxiety, attitudes, intentions, decisional conflict, confidence in decision making, anticipated regret and temporal orientation.

Results

A total of 489 participants with age-related cataract were included in this study, and 10.2% (50/489) of them had adequate level of knowledge. The knowledge scale was significantly associated to the levels of worry (Odds Ratio (OR) = 0.36, 95%CI: 0.18, 0.70; P = 0.003), anxiety (beta coefficient = -5.36, 95%CI: -8.88,-1.84; P = 0.003), inaction regret (OR = 0.49, 95%CI : 0.28, 0.88; P = 0.016) and decision conflict (beta coefficient = -7.93, 95%CI: -12.81, -3.04; P = 0.002) in multivariate analyses adjusted for age, sex, education level and literacy level.

Conclusion

The level of knowledge adequacy with cataract surgery outcomes is high in China and was associated with psychological status and decision quality. These findings suggest that strategies targeting knowledge of possible surgical outcomes may reduce psychological stress and improve decision quality among patients with age-related cataract.
Out of hospital cardiac arrests in the Gulf Region: a scoping review
Authors: Batt Alan M. , Lanos Chelsea , Delport Shannon , Al-Hasan Dalal , Knox Shane , Alhmoudi Assim , Anderson Megan , Fares Saleh , Cummins Fergal H.
Published: December 2019

Background

Out-of-hospital cardiac arrest (OHCA) is a major cause of mortality worldwide. Recent studies demonstrated low survival rates in Middle Eastern countries. Anecdotally there are unique demographic, cultural and logistical challenges in this region. However, there remains a paucity of data published on OHCA in the Middle East. In order to address OHCA in a meaningful manner in the region, we first need to quantify the issue.

Methods

We conducted a scoping review of published and grey literature on OHCA in the Gulf Cooperative Council region that utilised Arksey and O’Malley’s framework. Electronic databases and grey literature sources were identified and searched. Subject matter experts in the region were consulted. All types of studies in English and Arabic were included.

Results

A total of 24 studies were included from Saudi Arabia, the UAE, Oman, Kuwait, and Qatar. No literature was identified from the state of Bahrain. OHCA victims in the region are younger, predominantly male, and more co-morbid than other international studies. We observed low Emergency Medical Service utilisation, low bystander cardiopulmonary resuscitation, return of spontaneous circulation, and survival to discharge rates across the region. There are differences in characteristics of OHCA among ethnic groups.

Discussion and conclusions

We identified unique characteristics associated with OHCA in the region, variances in processes and outcomes, and a lack of coordinated effort to research and address OHCA. We recommend creating lead agencies responsible for coordinating and developing strategies such as community response, public education, and reporting databases.
Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries
Authors: Sjögren Karl-Göran , Olalde Inigo , Carver Sophie , Allentoft Morten E. , Knowles Tim , Kroonen Guus , Pike Alistair W.G. , Schröter Peter , Brown Keri A. , Robson-Brown Kate , Harrison Richard J. , Bertemes Francois , Reich David , Kristiansen Kristian , Heyd Volker
Published: December 2019

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.
The experimentally obtained functional impact assessments of GT>GC 5’ splice site variants differ markedly from those predicted
Authors: Chen Jian-Min , Lin Jin-Huan , Masson Emmanuelle , Liao Zhuan , Férec Claude , Cooper David N. , Hayden Matthew
Published: December 2019

GT>GC 5’ splice site (or +2T>C) variants have been frequently reported to cause human genetic disease. However, although we have demonstrated that GT>GC variants in human disease genes may not invariably be pathogenic, none of the currently available splicing prediction tools appear to be capable of reliably distinguishing those GT>GC variants that generate wild-type transcripts from those that do not. Recently, SpliceAI, a novel deep residual neural network tool, has been developed for splicing prediction. Methodologically distinct from previous approaches that either rely on human-engineered features and/or which focus on short nucleotide windows adjoining exon-intron boundaries, SpliceAI assesses splicing determinants by evaluating 10,000 nucleotides of flanking contextual sequence to predict the functional role in splicing of each position in the pre-mRNA transcript. Herein, we evaluated the performance of SpliceAI in the context of three datasets of GT>GC variants, all of which had been characterized functionally in terms of their impact on mRNA splicing. The first two datasets refer to our recently described “in vivo” dataset of 45 disease-causing GT>GC variants and the “in vitro” dataset of 103 GT>GC substitutions. The third dataset comprised 12 BRCA1 GT>GC variants that were recently analyzed by saturation genome editing. We processed all GT>GC variants using the default settings of SpliceAI. Comparison of the SpliceAI-predicted and experimentally obtained functional impact assessments of the analyzed GT>GC variants revealed that although SpliceAI performed rather better than other prediction tools, it was still far from perfect. A key issue is that the impact of GT>GC (as well as GT>GA or +2T>A) variants that generated wild-type transcripts represents a quantitative change that can vary from barely detectable to almost full expression of wild-type transcripts, with wild-type transcripts often co-existing with aberrantly spliced transcripts. Our findings highlight the challenges that we still face in attempting to accurately identify splice-altering variants.
A Highly-ordered and Fail-safe Electrical Network in Cable Bacteria
Authors: Thiruvallur Eachambadi Raghavendran , Bonné Robin , Cornelissen Rob , Hidalgo-Martinez Silvia , Vangronsveld Jaco , Meysman Filip J. R. , Valcke Roland , Cleuren Bart , Manca Jean V.
Published: December 2019

Cable Bacteria are an emerging class of electroactive organisms that sustain unprecedented long-range electron transport across centimeter-scale distances. The pathways of the electrical currents in these filamentous microorganisms remain unresolved. Here, the electrical circuitry in a single cable bacterium is visualized with nanoscopic resolution using Conductive Atomic Force Microscopy. Combined with perturbation experiments, it is demonstrated that electrical currents are conveyed through a parallel network of conductive fibers embedded in the cell envelope which are electrically interconnected between adjacent cells. This redundant structural organization of electrical pathways likely forms a crucial adaptive trait for organisms capable of long-distance electron transport. The observed electrical circuit architecture is unique in biology and could inspire future technological applications in bioelectronics.
A proximity-labeling proteomic approach to investigate invadopodia molecular landscape in breast cancer cells
Authors: Thuault Sylvie , Mamelonet Claire , Salameh Joëlle , Ostacolo Kevin , Chanez Brice , Salaün Danièle , Baudelet Emilie , Audebert Stéphane , Camoin Luc , Badache Ali
Published: December 2019

Metastatic progression is the leading cause of mortality in breast cancer. Invasive tumor cells develop invadopodia to travel through basement membranes and the interstitial matrix. Substantial efforts have been made to characterize invadopodia molecular composition. However, their full molecular identity is still missing due to the difficulty in isolating them. To fill this gap, we developed a non-hypothesis driven proteomic approach based on the BioID proximity biotinylation technology, using the invadopodia-specific protein Tks5α fused to the promiscuous biotin ligase BirA* as bait. In invasive breast cancer cells, Tks5α fusion concentrated to invadopodia and selectively biotinylated invadopodia components, in contrast to a fusion which lacked the membrane-targeting PX domain (Tks5β). Biotinylated proteins were isolated by affinity capture and identified by mass spectrometry. We identified known invadopodia components, revealing the pertinence of our strategy. Furthermore, we observed that Tks5 newly identified close neighbors belonged to a biologically relevant network centered on actin cytoskeleton organization. Analysis of Tks5β interactome demonstrated that some partners bound Tks5 before its recruitment to invadopodia. Thus, the present strategy allowed us to identify novel Tks5 partners that were not identified by traditional approaches and could help get a more comprehensive picture of invadopodia molecular landscape.
Effective potential reveals evolutionary trajectories in complex fitness landscapes
Authors: Smerlak Matteo
Published: December 2019

Growing efforts to measure fitness landscapes in molecular and microbial systems are premised on a tight relationship between landscape topography and evolutionary trajectories. This relationship, however, is far from being straightforward: depending on their mutation rate, Darwinian populations can climb the closest fitness peak (survival of the fittest), settle in lower regions with higher mutational robustness (survival of the flattest), or fail to adapt altogether (error catastrophes). These bifurcations highlight that evolution does not necessarily drive populations “from lower peak to higher peak”, as Wright imagined. The problem therefore remains: how exactly does a complex landscape topography constrain evolution, and can we predict where it will go next? Here I introduce a generalization of quasispecies theory which identifies metastable evolutionary states as minima of an effective potential. From this representation I derive a coarse-grained, Markov state model of evolution, which in turn forms a basis for evolutionary predictions across a wide range of mutation rates. Because the effective potential is related to the ground state of a quantum Hamiltonian, my approach could stimulate fruitful interactions between evolutionary dynamics and quantum many-body theory.

SIGNIFICANCE STATEMENT

The course of evolution is determined by the relationship between heritable types and their adaptive values, the fitness landscape. Thanks to the explosive development of sequencing technologies, fitness landscapes have now been measured in a diversity of systems from molecules to micro-organisms. How can we turn these data into evolutionary predictions? I show that preferred evolutionary trajectories are revealed when the effects of selection and mutations are blended in a single effective evolutionary force. With this reformulation, the dynamics of selection and mutation becomes Markovian, bringing a wealth of classical visualization and analysis tools to bear on evolutionary dynamics. Among these is a coarse-graining of evolutionary dynamics along its metastable states which greatly reduces the complexity of the prediction problem.
Evaluation of MALDI-ToF Mass Spectrometry for Rapid Detection of Cereulide from Bacillus cereus Cultures
Authors: Doellinger Joerg , Schneider Andy , Stark Timo , Ehling-Schulz Monika , Lasch Peter
Published: December 2019

1.

Bacillus cereus plays an often unrecognized role in food borne diseases. Food poisoning caused by this pathogen is manifested by either diarrhea or emesis. While different enterotoxins have been linked to the diarrheal type of B. cereus infections, the emetic toxin cereulide is responsible for the second type. Due to the relatively high prevalence of cereulide associated food poisoning, methods for simple and reliable detection of cereulide producing strains are of utmost importance. Currently, liquid-chromatography coupled to mass spectrometry (LC-MS) is used for sensitive, specific and quantitative cereulide detection, but this technique requires specialized LC-MS equipment, which is often not available in microbiology routine diagnostic laboratories.

The last decade has witnessed the advent of matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-ToF MS) as a simple, rapid and cost-efficient technique for identification of microbial pathogens in routine diagnostics. Just recently, two different studies reported on the application of MALDI-ToF MS for either the differentiation of emetic and non-emetic strains of B. cereus or for direct detection of cereulide from bacterial colony smears. However, no method evaluation and optimization was performed in frame of these studies. Thus, additional investigations on the selectivity and sensitivity of MALDI-TOF MS for cereulide detection are needed before implementation of this method in routine diagnostics can be considered. These aspects prompted us to investigate open or controversial issues and to systematically test sample preparation methods, commonly used for microbial identification for their suitability to detect the emetic toxin directly from bacteria.

Based on our experimental findings we propose a MALDI-ToF MS workflow that allows identification of B. cereus and sensitive detection of cereulide in parallel, using standard, linear-mode MALDI-ToF MS equipment. The experimental protocol is based on the well-established ethanol/formic acid extraction method and offers, if required, possibilities for further characterization by more sophisticated LC-MS-based methods. In summary, the ease of use and the achieved level of analytical sensitivity as well as the wide-spread availability of standard MALDI-ToF MS equipment in clinical microbiological laboratories provides a promising tool to improve and to facilitate routine diagnostics of B. cereus associated food intoxications.
Alcohol intake triggers aberrant synaptic pruning leading to synapse loss and anxiety-like behavior
Authors: Socodato Renato , Henriques Joana F. , Portugal Camila C. , Almeida Tiago O. , Tedim-Moreira Joana , Alves Renata L. , Canedo Teresa , Silva Cátia , Magalhães Ana , Summavielle Teresa , Relvas João B.
Published: December 2019

Alcohol use adversely impacts the life of millions of people worldwide. Deficits in synaptic transmission and in microglial function are common findings in human alcohol users and in animal models of alcohol intoxication. Here, we show that alcohol intake over ten consecutive days resulted in substantial loss of excitatory synapse in the prefrontal cortex, a consequence of aberrant synaptic pruning, which led to increased anxiety-like behavior. Mechanistically, these effects of alcohol intake were mediated by a detrimental increase of microglia engulfment capacity via Src-dependent activation of NFkB and consequent TNF production. Accordingly, pharmacological blockade of Src activation or TNF production by microglia, genetic ablation of TNF, or diphtheria toxin-mediated conditional ablation of microglia attenuated aberrant synaptic pruning preventing excitatory synapse loss and anxiety-like behavior. Overall, our data suggest that aberrant pruning of excitatory synapses by microglia might disrupt synaptic transmission during alcohol use.
A mean-field approach to the dynamics of networks of complex neurons, from nonlinear Integrate-and-Fire to Hodgkin-Huxley models
Authors: Carlu M. , Chehab O. , Dalla Porta L. , Depannemaecker D. , Héricé C. , Jedynak M. , Köksal Ersöz E. , Muratore P. , Souihel S. , Capone C. , Zerlaut Y. , Destexhe A. , di Volo M.
Published: December 2019

We present a mean-field formalism able to predict the collective dynamics of large networks of conductance-based interacting spiking neurons. We apply this formalism to several neuronal models, from the simplest Adaptive Exponential Integrate-and-Fire model to the more complex Hodgkin-Huxley and Morris-Lecar models. We show that the resulting mean-field models are capable of predicting the correct spontaneous activity of both excitatory and inhibitory neurons in asynchronous irregular regimes, typical of cortical dynamics. Moreover, it is possible to quantitatively predict the populations response to external stimuli in the form of external spike trains. This mean-field formalism therefore provides a paradigm to bridge the scale between population dynamics and the microscopic complexity of the individual cells physiology.

NEW & NOTEWORTHY

Population models are a powerful mathematical tool to study the dynamics of neuronal networks and to simulate the brain at macroscopic scales. We present a mean-field model capable of quantitatively predicting the temporal dynamics of a network of complex spiking neuronal models, from Integrate-and-Fire to Hodgkin-Huxley, thus linking population models to neurons electrophysiology. This opens a perspective on generating biologically realistic mean-field models from electrophysiological recordings.
Extrinsic Activin signaling cooperates with an intrinsic temporal program to increase mushroom body neuronal diversity
Authors: Rossi Anthony M. , Desplan Claude
Published: December 2019

Temporal patterning of neural progenitors leads to the sequential production of diverse neuronal types. To better understand how extrinsic cues interact with intrinsic temporal programs to contribute to temporal patterning, we studied theDrosophilamushroom body neural progenitors (neuroblasts). Each of these four neuroblasts divides ~250 times to sequentially produce only three main neuronal types over the course of ~9 days of development: γ, followed by α’β’, and finally αβ neurons. The intrinsic temporal clock is composed of two RNA-binding proteins, IGF-II mRNA binding protein (Imp) and Syncrip (Syp), that are expressed in opposing temporal gradients. Activin signaling affects the production of α’β’ neurons but whether and how this extrinsic cue interacts with the intrinsic temporal program was not known. We show that the Activin ligand Myoglianin produced from glia regulates the levels of the intrinsic temporal factor Imp in mushroom body neuroblasts. In neuroblasts mutant for the Activin signaling receptorbaboon,Imp levels are higher than normal during the α’β’ temporal window, leading to the specific loss of the α’β’ neurons. The intrinsic temporal clock still progresses but with a delay, skipping the α’β’ window without affecting the total number of neurons produced: The number of γ neurons increases, α’β’ disappear and the number of αβ neurons decreases. Our results illustrate that an extrinsic cue modifies an intrinsic temporal program to increase neuronal diversity.
Hierarchical assembly of the MLL1 core complex within a biomolecular condensate regulates H3K4 methylation
Authors: Namitz Kevin E.W. , Tan Song , Cosgrove Michael S.
Published: December 2019

The enzymes that regulate histone H3 lysine 4 (H3K4) methylation are required for cellular differentiation and development and are often mutated in human disease. Mixed Lineage Leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 methyltransferases, which require interaction with a conserved sub-complex consisting ofWDR5,RbBP5,Ash2L andDPY30 (WRAD2) for maximal activity. It is currently unclear how assembly of SET1 family complexes is involved in the spatiotemporal control of H3K4 methylation in eukaryotic genomes. In this investigation, we systematically characterized the hydrodynamic and kinetic properties of a reconstituted human MLL1 core complex and found that its assembly is highly concentration and temperature dependent. Consistent with a hierarchical assembly pathway, we found that the holo-complex assembles through interactions between the MW and RAD2sub-complexes, which is correlated with enzymatic activity. Surprisingly, we found that the disassembled state is favored at physiological temperatures, and that this thermodynamic barrier can be overcome under conditions that induce high-local concentrations of subunits in phase separated compartments. Combining this data with the observation that MLL1 primary sequence contains large regions of intrinsic disorder, we propose a “swinging-domain” model in which the interaction between a tethered MW subcomplex and multiple nucleosome-RAD2complexes is regulated by the rapid formation or dissolution of biomolecular condensates, such as occurs in transcription factories. This model provides an elegant “switch-like” mechanism for spatiotemporal control of H3K4 methylation within eukaryotic genomes.
Spatially Varying Trophic Effects of Reservoir-Derived Plankton on Stream Macroinvertebrates Among Heterogeneous Habitats Within Reaches
Authors: Takahashi Shinji , Takemon Yasuhiro , Omura Tatsuo , Watanabe Kozo
Published: December 2019

Dam reservoirs often supply high amounts of plankton to downstream reaches, leading to a critical shift of trophic origins of stream ecosystems from natural sources (e.g. attached algae and terrestrial inputs) to reservoir-oriented plankton. Although this is a widely observed phenomenon, previous studies focused only on lotic habitats (e.g. riffles) rather than lentic habitats such as backwaters and isolated ponds (IP).

Using a stable isotope three-source mixing model, we evaluated trophic contributions of reservoir-derived plankton, epilithon and terrestrial leaves to stream macroinvertebrates at four dam outlet reaches and two reference reaches in the Natori River catchment, Japan. We compared four different habitat types co-occurring within the reaches: lotic habitat (riffle and pool), bar-head (BH) lentic habitat, bar-tail (BT) lentic habitat (backwater) and isolated pond (IP) on sandy bars.

The trophic contributions of reservoir-derived plankton were significantly lower in lentic habitats (BH, 15.4%; BT, 10.4%; IP, 9.1%) than in lotic habitats (mean, 27.7%). This was especially notable for filter feeders that feed on suspended fine particulate organic matter (SFPOM). The three-source model analysis indicated a lower biomass proportion of dam plankton in lentic SFPOM (mean, 21.2%) than in lotic SFPOM (mean, 35.6%). This difference in SFPOM composition was reflected in the lower trophic contribution of dam plankton to lentic filter feeders.

The abundance ratio of filter feeders in the community was decreased in lentic habitats, while the abundance ratios of collector-gatherers, scrapers and shredders were increased. Macroinvertebrates in lentic habitats fed on sources less mixed with reservoir-derived plankton (e.g. benthic coarse particulate organic matter [BCPOM], benthic fine particulate organic matter [BFPOM] and epilithon); therefore, the trophic impact of reservoirs was indistinctive at the community level, indicating that lentic habitats can function as trophic refugia to mitigate the trophic impact of reservoirs.

Because lentic habitats were decreased in area (accounting for 5.7% of average total area) in the downstream reaches of dams due to riverbed degradation, lentic habitats must be created in order to restore the trophic impact of reservoirs in river ecosystems.
Parkinson’s disease associated mutation E46K of α-synuclein triggers the formation of a novel fibril structure
Authors: Zhao Kun , Li Yaowang , Liu Zhenying , Long Houfang , Zhao Chunyu , Luo Feng , Sun Yunpeng , Tao Youqi , Su Xiao-dong , Li Dan , Li Xueming , Liu Cong
Published: December 2019

α-Synuclein (α-syn) amyloid fibril, as the major component of Lewy bodies and pathological entity spreading in human brain, is closely associated with Parkinson’s disease (PD) and other synucleinopathies. Several single amino-acid mutations (e.g. E46K) of α-syn have been identified causative to the early onset of familial PD. Here, we determined the cryo-EM structure of a full-length α-syn fibril formed by N-terminal acetylated E46K mutant α-syn (Ac-E46K). The fibril structure represents a new fold of α-syn, which demonstrates that the E46K mutation breaks the electrostatic interactions in the wild type (WT) α-syn fibril and thus triggers the rearrangement of the overall structure. Furthermore, we show that the Ac-E46K fibril is less resistant to harsh conditions and protease cleavage, and more prone to be fragmented with a higher capability of seeding fibril formation than that of the WT fibril. Our work provides a structural view to the severe pathology of the PD familial mutation E46K of α-syn and highlights the importance of electrostatic interactions in defining the fibril polymorphs.