bluuebunny/crossref_metadata_2025 huggingface dataset:
Does Renal Function Remain Stable after Puberty in Children who underwent Ureteral Reimplantation due to Ureterovesical Junction Obstruction?
Authors: Neeman Binyamin B. , Jaber Jawdat , Kocherov Stanislav , Farkas Amicur , Chertin Boris
Published: May 2020

Introduction Ureteric reimplantation due to ureterovesical junction (UVJ) obstruction enjoys high success in the short term. However, renal function after reimplantation must accommodate the numerous changes in the pediatric urinary tract that occur along with child development that may theoretically cause an occult loss of renal function. The purpose of this study was to evaluate whether improved renal function after ureter reimplantation for antenatal diagnosed UVJ obstruction remains stable after puberty.

Materials and Methods Twenty-one children who underwent open reimplantation using Politano–Leadbetter technique were followed until they completed puberty. Mean age at surgery was 14.3 months (range: 3–60 months). Five (23.8%) of 21 children had right hydronephrosis, 13 (61.9%) had left hydronephrosis, and 3 (14.3%) had bilateral hydronephrosis. The Society for Fetal Urology (SFU) level of the hydronephrosis was 3 (47.6%) in 10 children and 4 (52.4%) in remaining 11. Fourteen (66.6%) patients had poor renal function upon surgery and the remaining seven (33.4%) patients had moderate renal function. The mean renal function upon operation was 28 ± 4.3 (mean ± standard deviation [SD]).

Results Reimplantation led to the increase in the RRF in the short-term period from 28 ± 4.3% prior to the surgery to 36.4 ± 5% (p < 0.001) in all patients and remains stable 35 ± 5% after puberty in all the reviewed patients.

Conclusion Our data demonstrate for the first time that successful ureteral reimplantation following antenatal diagnosis of UVJ obstruction is associated with an improvement in renal function, not only during short- and midterm follow-up but also allows preserving the renal function throughout the puberty period.
Evidence for a food-deceptive pollination system using Hylaeus bees in Caladenia hildae (Orchidaceae)
Authors: Phillips Ryan D. , Batley Michael
Published: May 2020

Numerous orchid species are pollinated by food deception, where rewardless flowers attract foraging pollinators through the mimicry of other flowers or the use of non-specific floral signals. Here we investigate the pollination of Caladenia hildae, a member of a diverse Australian genus containing species pollinated by sexual deception, and species pollinated by food foraging pollinators. Despite eight bee species occurring at the main study site, only food foraging bees of a single species of Hylaeus (Colletidae) were observed to remove and deposit pollen of C. hildae. Spectral reflectance of C. hildae flowers differed from co-flowering rewarding species in terms of both the wavelengths of light reflected, and the pattern of colouration. As such, there was no evidence that C. hildae uses a pollination strategy based on floral mimicry. However, the attraction of only a single bee species at this site suggests that C. hildae may use a deceptive strategy that exploits sensory biases or behaviours that differ between Hylaeus sp. and the remainder of the bee community. While Hylaeus have been recorded visiting orchid flowers in several parts of the world, C. hildae may represent the first documented case of an orchid species specialised on pollination by Hylaeus bees.
Priming exercise increases Wingate cycling peak power output
Authors: Ktenidis Charalabos K. , Margaritelis Nikos V. , Cherouveim Evgenia D. , Stergiopoulos Dimitris C. , Malliou Vassiliki J. , Geladas Nikos D. , Nikolaidis Michalis G. , Paschalis Vassilis
Published: May 2020

Purpose: The aim of the present study was to investigate the effect of priming exercise on Wingate performance and fatigue. Methods: Twelve recreationally active young male volunteers participated in the study (age: 25 ± 5 years; weight: 75.0 ± 7.5 kg; height: 177 ± 6 cm; BMI: 24.0 ± 1.7). During a first visit, participants performed a typical test and a supramaximal assessment of on a cycle ergometer, while during the next three visits, the participants performed in a random order a Wingate test (i) with no priming exercise, (ii) after priming exercise followed by a 15‐min recovery (Priming15) and (iii) after priming exercise followed by a 30‐min recovery (Priming30). Priming exercise lasted 6 min, at work rate corresponding to the gas exchange threshold (GET) plus 70% of the difference between the GET and . Results: The Priming 30 condition exhibited greater peak power output (595 ± 84 W) compared to the control (567 ± 85 W) and the Priming15 condition (569 ± 95 W) (P < .05). Regarding fatigue index, a tendency towards increased resistance to fatigue was observed in the Priming30 condition compared to the control and the Priming15 conditions (P = .072). Pre‐Wingate lactate levels were found to be significantly different between the Priming15 (7.18 ± 3.09 mmol/L) and the Priming30 (4.87 ± 2.11 mmol/L) conditions (P < .05). Conclusions: Priming exercise of high intensity followed by a prolonged recovery leads to increased peak power in a subsequent Wingate test. Moreover, our data are consistent with the idea that a priming exercise‐induced modest increase in blood lactate concentration at the onset of the following criterion bout is a key factor of performance.
Training intensity distribution analysis by race pace vs. physiological approach in world‐class middle‐ and long‐distance runners
Authors: Kenneally Mark , Casado Arturo , Gomez‐Ezeiza Josu , Santos‐Concejero Jordan
Published: May 2020

This study aimed to analyse the training intensity distribution (TID) of a group of 7 world‐class middle‐ and long‐distance runners over 50 weeks using two different approaches to organise TID zones: (1) based on individual specific race pace and; (2) based on physiological parameters. Analysed training data included training volume, intensity and frequency. The average weekly volume for the group was 135.4 ± 29.4 km·week−1. Training volumes for Z1, Z2 and Z3 were 88.5 ± 1.1%, 7.4 ± 0.8% and 4.1 ± 0.7% respectively for race‐pace based approach, and 87.2 ± 1.2%, 6.1 ± 0.7% and 6.6 ± 0.9% respectively for the physiological approach. Differences were found between the approaches in Z2 (large effect, ES = 1.20) and Z3 (moderate effect, ES = 0.93). The approach based on race‐pace zones produced pyramidal distributions in both middle‐ and long‐distance runners across all phases of the season. The physiological approach produced polarised and pyramidal distributions depending of the phase of the season in the middle‐distance runners, and pyramidal type TID across all phases of the season in the long‐distance runners. The results of this study demonstrate that the training analysis in a world‐class group of runners shows different TID when assessed relative to race pace versus to physiological zones. This highlights a potential deficiency in training analysis and prescription methods which do not make reference to specific performance. An approach which makes reference to both physiological and performance measures may allow for a more consistent and logical analysis.
Enhancement of the photoassociation of ultracold atoms via a non-resonant magnetic field*
Authors: Wu Ji-Zhou , Li Yu-Qing , Liu Wen-Liang , Li Peng , Wang Xiao-Feng , Chen Peng , Ma Jie , Xiao Lian-Tuan , Jia Suo-Tang
Published: May 2020

We report an effective method for enhancing the photoassociation of ultracold atoms using a non-resonant magnetic field, which enables the manipulation of the coupling between the wavefunctions of the colliding atomic pairs and the excited molecules. A series of photoassociation spectra are measured for different magnetic fields. We show that the photoassociation rate is significantly dependent on the non-resonant magnetic field. A qualitatively theoretical explanation is provided, and shows a good agreement with the experimental result.
Lattice deformation in epitaxial Fe3O4 films on MgO substrates studied by polarized Raman spectroscopy*
Authors: Yang Yang , Zhang Qiang , Mi Wenbo , Zhang Xixiang
Published: May 2020

The lattice structures of epitaxial Fe3O4 films deposited on MgO were studied systematically using polarized Raman spectroscopy as a function of film thickness, where interesting phenomena were observed. Firstly, the spectral conflict to the Raman selection rules (RSRs) was observed under cross-sectional configuration, which can be attributed to the tetragonal deformation in the growth direction due to the lattice mismatch between Fe3O4 and MgO. Secondly, the blue shift and broadening of Raman peaks evidenced the decrease of the tensile strain in Fe3O4 films with decreasing thickness. Thirdly, distinct from the other Raman modes, the lowest T
2g mode exhibited asymmetric lineshape, which can be interpreted using the spatial correlation model. The increased correlation length introduced in the model can well explain the enhanced peak asymmetry feature with decreasing thickness. These results provide useful information for understanding the lattice structure of epitaxial Fe3O4 film.
Size effect of He clusters on the interactions with self-interstitial tungsten atoms at different temperatures*
Authors: Wang Jinlong , Dang Wenqiang , Liu Daping , Guo Zhichao
Published: May 2020

The behaviors of helium clusters and self-interstitial tungsten atoms at different temperatures are investigated with the molecular dynamics method. The self-interstitial tungsten atoms prefer to form crowdions which can tightly bind the helium cluster at low temperature. The crowdion can change its position around the helium cluster by rotating and slipping at medium temperatures, which leads to formation of combined crowdions or dislocation loop locating at one side of a helium cluster. The combined crowdions or dislocation loop even separates from the helium cluster at high temperature. It is found that a big helium cluster is more stable and its interaction with crowdions or dislocation loop is stronger.
Audit logs to enforce document integrity in Skyline and Panorama
Authors: Rohde Tobias , Chupalov Rita , Shulman Nicholas , Sharma Vagisha , Eckels Josh , Pratt Brian S , MacCoss Michael J , MacLean Brendan X
Published: May 2020

Skyline is a Windows application for targeted mass spectrometry method creation and quantitative data analysis. Like most graphical user interface (GUI) tools, it has a complex user interface with many ways for users to edit their files which makes the task of logging user actions challenging and is the reason why audit logging of every change is not common in GUI tools. We present an object comparison-based approach to audit logging for Skyline that is extensible to other GUI tools. The new audit logging system keeps track of all document modifications made through the GUI or the command line and displays them in an interactive grid. The audit log can also be uploaded and viewed in Panorama, a web repository for Skyline documents that can be configured to only accept documents with a valid audit log, based on embedded hashes to protect log integrity. This makes workflows involving Skyline and Panorama more reproducible.

Availability and implementation

Skyline is freely available at https://skyline.ms.

Supplementary information

Supplementary data are available at Bioinformatics online.
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence
Authors: Sedova Mayya , Jaroszewski Lukasz , Alisoltani Arghavan , Godzik Adam
Published: May 2020

Motivation

As the COVID-19 pandemic is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome.

Results

Coronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context.

Availability and implementation

Coronavirus3D server is freely available at https://coronavirus3d.org.
Broadening the ‘Survivor Capsule’ of Intimate Partner Violence Services
Authors: Baird Stephanie L , Alaggia Ramona , Maiter Sarah
Published: May 2020

This study responds to a need to expand current understandings of the ways in which counselling services for intimate partner violence (IPV) address trauma. From the perspectives of fifteen women who accessed IPV counselling services in Ontario, Canada, this feminist intersectional study used constructivist grounded theory methods to explore how services help women heal from trauma. Specifically, the study aimed to understand how counselling services meet the needs of survivors of IPV and respond to their complex identities and experiences of trauma and oppression. Findings exemplify the theoretical concept of a survivor capsule, illustrating ways in which women’s unique lives often do not fit into current IPV services, showing a need for more complex intersectional understandings of women’s experiences of IPV and trauma. These study findings demonstrate the importance of recognising women’s individual needs for multiple services as well as the harm caused when women have to fight to access the services they need. Findings also illustrate the instrumental role of counsellors who provide validation, are connected with women’s experiences, and are knowledgeable about IPV and trauma. Finally, suggestions are put forward for ways in which service providers can create spaces of acceptance rather than services that are stigmatising.
Message in a bottle: the Mediterranean Sea currents acted as protagonists in shaping the distribution of the sea daffodil (Pancratium maritimum, Amaryllidaceae)
Authors: De Castro Olga , Innangi Michele , Menale Bruno
Published: May 2020

The Mediterranean Basin can be considered as a natural laboratory with which to study the effects of sea currents in the dispersal of coastal plant species that use hydrochory. Pancratium maritimum is a perennial geophyte, with a wide distribution along Mediterranean coasts. We aim to provide a timeframe for the origin of the diversification of this plant, to clarify its phylogeographical structure and to investigate the role of currents in the Mediterranean Sea in influencing spatial patterns of its genetic distribution. The phylogeographic history was analysed using 50 populations. A genetic structure analysis and divergence time estimation was performed using plastid sequences. Five haplotypes were detected, of which two were the most abundant; a third was observed in the central Mediterranean, and two rare haplotypes were present in the eastern Mediterranean. The genetic breaks were concordant with the direction of the major Mediterranean currents. The divergence time estimation for the origin of P. maritimum was located at the end of the Neogene (mid Pliocene to mid Pleistocene). We showed the importance of sea currents in the Mediterranean in acting both as a means of dispersal and as a barrier to the distribution and evolution of P. maritimum due to the special adaptations of its seeds.
High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display
Authors: O’Donovan Brian , Mandel-Brehm Caleigh , Vazquez Sara E , Liu Jamin , Parent Audrey V , Anderson Mark S , Kassimatis Travis , Zekeridou Anastasia , Hauser Stephen L , Pittock Sean J , Chow Eric , Wilson Michael R , DeRisi Joseph L
Published: May 2020

Paraneoplastic neurological disorders are immune-mediated diseases understood to manifest as part of a misdirected anti-tumor immune response. Paraneoplastic neurological disorder-associated autoantibodies can assist with diagnosis and enhance our understanding of tumor-associated immune processes. We designed a comprehensive library of 49-amino-acid overlapping peptides spanning the entire human proteome, including all splicing isoforms and computationally predicted coding regions. Using this library, we optimized a phage immunoprecipitation and sequencing protocol with multiple rounds of enrichment to create high-resolution epitope profiles in serum and cerebrospinal fluid (CSF) samples from patients suffering from two common paraneoplastic neurological disorders, the anti-Yo (n = 36 patients) and anti-Hu (n = 44 patients) syndromes. All (100%) anti-Yo patient samples yielded enrichment of peptides from the canonical anti-Yo (CDR2 and CDR2L) antigens, while 38% of anti-Hu patients enriched peptides deriving from the nELAVL (neuronal embryonic lethal abnormal vision like) family of proteins, the anti-Hu autoantigenic target. Among the anti-Hu patient samples that were positive for nELAVL, we noted a restricted region of immunoreactivity. To achieve single amino acid resolution, we designed a novel deep mutational scanning phage library encoding all possible single-point mutants targeting the reactive nELAVL region. This analysis revealed a distinct preference for the degenerate motif, RLDxLL, shared by ELAVL2, 3 and 4. Lastly, phage immunoprecipitation sequencing identified several known autoantigens in these same patient samples, including peptides deriving from the cancer-associated antigens ZIC and SOX families of transcription factors. Overall, this optimized phage immunoprecipitation sequencing library and protocol yielded the high-resolution epitope mapping of the autoantigens targeted in anti-Yo and anti-Hu encephalitis patients to date. The results presented here further demonstrate the utility and high-resolution capability of phage immunoprecipitation sequencing for both basic science and clinical applications and for better understanding the antigenic targets and triggers of paraneoplastic neurological disorders.
Ligation-assisted endoscopic mucosal resection for esophageal granular cell tumors is safe and effective
Authors: Kumar Shria , Chandrasekhara Vinay , Kochman Michael L , Ahmad Nuzhat , Attalla Sara , Ho Immanuel K , Jaffe David L , Lee Peter J , Panganamamula Kashyap V , Saumoy Monica , Fortuna Danielle , Ginsberg Gregory G
Published: May 2020

Given their malignant potential, resection of esophageal granular cell tumors (GCTs) is often undertaken, yet the optimal technique is unknown. We present a large series of dedicated endoscopic resection using band ligation (EMR-B) of esophageal GCTs. Patients diagnosed with esophageal GCTs between 2002 and 2019 were identified using a prospectively collected pathology database. Endoscopic reports were reviewed, and patients who underwent dedicated EMR-B of esophageal GCTs were included. Medical records were queried for demographics, findings, adverse events, and follow-up. We identified 21 patients who underwent dedicated EMR-B for previously identified esophageal GCT. Median age was 39 years; 16 (76%) were female. Eight (38%) had preceding signs or symptoms, potentially attributable to the GCT. Upon endoscopic evaluation, 12 (57%) were found in the distal esophagus. Endoscopic ultrasound was used in 15 cases (71%). Median lesion size was 7 mm, interquartile range 4 mm—8 mm. The largest lesion was 12 mm. A total of 20 (95%) had en bloc resection confirmed with pathologic examination. The only patient with tumor extending to the resection margin underwent surveillance endoscopy that showed no residual tumor. No patients experienced bleeding, perforation, or stricturing in our series. No patients have had known recurrence of their esophageal GCT. EMR-B of esophageal GCT achieves complete histopathologic resection with minimal adverse events. EMR-B is safe and effective and seems prudent compared with observation for what could be an aggressive and malignant tumor. EMR-B should be considered first-line therapy when resecting esophageal GCT up to 12 mm in diameter.
Prevalence of Early- and Late-Season Pest Damage to Corn in Cover Crop-Based Reduced-Tillage Organic Systems
Authors: Regan Karly H , Voortman Christina A , Wallace John M , Barbercheck Mary E
Published: May 2020

In organic agronomic cropping systems, the use of synthetic insecticides and transgenic varieties are prohibited and producers rely mainly on biological control, tillage, crop rotation, and other cultural practices to manage pests. We measured damage to organic corn (Zea mays L.) from multiple invertebrate pests, including slugs (Gastropoda: Mollusca), European corn borer (Ostrinia nubilalis Hübner), corn earworm (Helicoverpa zea Boddie), and fall armyworm (Spodoptera frugiperda Smith), early and late in the growing season in four cropping systems that varied in tillage frequency and intensity and in winter cover crop species. Specific management tactics included two cover crop mixtures preceding corn, the use of a roller-crimper or tillage to terminate cover crops preceding corn, and the establishment of interseeded cover crops after corn emergence. Prevalence of early-season damage was high, but severity of damage was very low and unrelated to corn yield. The proportion of corn plants affected by chewing pests early in the season was lower in plots in which tillage compared to a roller-crimper was used to terminate cover crops. Cropping system did not affect the numbers of late-season caterpillar pests or corn yield. Predation by natural enemies appeared to effectively maintain damage from chewing pests below yield-damaging levels. These results support the inclusion of winter and interseeded cover crops in organic agronomic crop rotations to gain environmental benefits without increasing risks of damage by insect pests.
The implications of catheter ablation for solitary atrial flutter in preventing stroke risk: a nationwide population-based cohort study
Authors: Lin Yu-Sheng , Wu Victor Chien-Chia , Wang Hui-Ting , Chen Huang-Chung , Chen Mien-Cheng , Chang Shih-Tai , Chu Pao-Hsien , Chen Yung-Lung
Published: May 2020

Aims

The implications of ablation for atrial fibrillation in preventing stroke are controversial, and no studies have investigated whether ablation prevents ischaemic stroke (IS) in atrial flutter (AFL).

Methods and results

This study analysed data contained in the Taiwan National Health Insurance Research Database for 16 765 patients with a first diagnosis of solitary AFL during 2001–2013. Eligible patients were divided into two groups according to whether or not they had received ablation. Propensity score matching (PSM) was performed to mitigate the effects of potential confounding factors. The primary outcome was occurrence of IS during follow-up. After 1:2 PSM, the analysis included 1037 patients in the ablation group and 2074 patients in the non-ablation group. The incidence of IS was lower in the ablation group compared to the non-ablation group [subdistribution hazard ratio (SHR) 0.61, 95% confidence interval (CI) 0.41–0.90] during the 2-year follow-up period but not thereafter (SHR 1.03, 95% CI 0.72–1.48). When grouping by stroke history, it revealed that ablation affected the incidence of stroke in patients without history of stroke (SHR 0.59, 95% CI 0.38–0.91) but not in patients with history of stroke. When each group was stratified by CHA2DS2-VASc score, ablation lowered the incidence of stroke in patients with CHA2DS2-VASc ≤3 (SHR 0.31, 95% CI 0.16–0.60) but not in patients with CHA2DS2-VASc ≥4 in the initial 2-year follow-up.

Conclusion

The different incidence of IS in patients with/without ablation indicates that ablation reduces the risk of IS in AFL patients.
Electrocardiographic imaging for cardiac arrhythmias and resynchronization therapy
Authors: Pereira Helder , Niederer Steven , Rinaldi Christopher A
Published: May 2020

Use of the 12-lead electrocardiogram (ECG) is fundamental for the assessment of heart disease, including arrhythmias, but cannot always reveal the underlying mechanism or the location of the arrhythmia origin. Electrocardiographic imaging (ECGi) is a non-invasive multi-lead ECG-type imaging tool that enhances conventional 12-lead ECG. Although it is an established technology, its continuous development has been shown to assist in arrhythmic activation mapping and provide insights into the mechanism of cardiac resynchronization therapy (CRT). This review addresses the validity, reliability, and overall feasibility of ECGi for use in a diverse range of arrhythmias. A systematic search limited to full-text human studies published in peer-reviewed journals was performed through Medline via PubMed, using various combinations of three key concepts: ECGi, arrhythmia, and CRT. A total of 456 studies were screened through titles and abstracts. Ultimately, 42 studies were included for literature review. Evidence to date suggests that ECGi can be used to provide diagnostic insights regarding the mechanistic basis of arrhythmias and the location of arrhythmia origin. Furthermore, ECGi can yield valuable information to guide therapeutic decision-making, including during CRT. Several studies have used ECGi as a diagnostic tool for atrial and ventricular arrhythmias. More recently, studies have tested the value of this technique in predicting outcomes of CRT. As a non-invasive method for assessing cardiovascular disease, particularly arrhythmias, ECGi represents a significant advancement over standard procedures in contemporary cardiology. Its full potential has yet to be fully explored.
Orthostatic Blood Pressure Recovery Is Associated With the Rate of Cognitive Decline and Mortality in Clinical Alzheimer’s Disease
Authors: de Heus Rianne A A , de Jong Daan L K , Rijpma Anne , Lawlor Brian A , Olde Rikkert Marcel G M , Claassen Jurgen A H R
Published: May 2020

Background

Impaired recovery of blood pressure (BP) after standing has been shown to be related to cognitive function and mortality in people without dementia, but its role in people with Alzheimer’s disease (AD) is unknown. The aim of this study was to investigate the association of the orthostatic BP response with cognitive decline and mortality in AD.

Methods

In this post hoc analysis of a randomized controlled trial (Nilvad), we measured the beat-to-beat response of BP upon active standing in mild-to-moderate AD. This included the initial drop (nadir within 40 seconds) and recovery after 1 minute, both expressed relative to resting values. We examined the relationship between a small or large initial drop (median split) and unimpaired (≥100%) or impaired recovery (<100%) with 1.5-year change in Alzheimer’s Disease Assessment—cognitive subscale (ADAS-cog) scores and all-cause mortality.

Results

We included 55 participants (age 73.1 ± 6.2 years). Impaired BP recovery was associated with higher increases in ADAS-cog scores (systolic: β [95% confidence interval] = 5.6 [0.4–10.8], p = .035; diastolic: 7.6 [2.3–13.0], p = .006). During a median follow-up time of 49 months, 20 participants died. Impaired BP recovery was associated with increased mortality (systolic: HR [95% confidence interval] = 2.9 [1.1–7.8], p = .039; diastolic: HR [95% confidence interval] = 5.5 [1.9–16.1], p = .002). The initial BP drop was not associated with any outcome. Results were adjusted for age, sex, and intervention group.

Conclusions

Failure to fully recover BP after 1 minute of standing is associated with cognitive decline and mortality in AD. As such, BP recovery can be regarded as an easily obtained marker of progression rate of AD.
CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
Authors: Kuhl Heiner , Li Ling , Wuertz Sven , Stöck Matthias , Liang Xu-Fang , Klopp Christophe
Published: May 2020

Background

Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.

Result

Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads.

Conclusions

CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.
Erythema Nodosum: As an Extraintestinal Manifestation or Complication in Ulcerative Colitis?
Authors: Valdés Delgado Teresa , Maldonado Pérez Belén , Castro Laria Luisa
Published: May 2020

In our case, we want to highlight the importance of screening for opportunistic infectious diseases in these immunosuppressed patients. We present the case of an erythema nodosum triggered by reactivation of Herpes Simplex Virus (HSV) in a patient with ulcerative colitis.
IBD in the Times of COVID-19
Authors: Hernández Benabe Stefany , Langshaw Amber H
Published: May 2020

We discuss the impact that COVID-19 has had on the care of patients with inflammatory bowel disease and the use of telemedicine after the pandemic resolves.
Identification of compounds active against quiescent artemisinin-resistant Plasmodium falciparum parasites via the quiescent-stage survival assay (QSA)
Authors: Reyser Thibaud , Paloque Lucie , Ouji Manel , Nguyen Michel , Ménard Sandie , Witkowski Benoit , Augereau Jean-Michel , Benoit-Vical Françoise
Published: May 2020

Background

Quiescence is an unconventional mechanism of Plasmodium survival, mediating artemisinin resistance. This phenomenon increases the risk of clinical failures following artemisinin-based combination therapies (ACTs) by slowing parasite clearance and allowing the selection of parasites resistant to partner drugs.

Objectives

To thwart this multiresistance, the quiescent state of artemisinin-resistant parasites must be taken into consideration from the very early stages of the drug discovery process.

Methods

We designed a novel phenotypic assay we have named the quiescent-stage survival assay (QSA) to assess the antiplasmodial activity of drugs on quiescent parasites. This assay was first validated on quiescent forms from different artemisinin-resistant parasite lines (laboratory strain and field isolates), using two reference drugs with different mechanisms of action: chloroquine and atovaquone. Furthermore, the efficacies of different partner drugs of artemisinins used in ACTs were investigated against both laboratory strains and field isolates from Cambodia.

Results

Our results highlight that because of the mechanism of quiescence and the respective pharmacological targets of drugs, drug efficacies on artemisinin-resistant parasites may be different between quiescent parasites and their proliferating forms.

Conclusions

These data confirm the high relevance of adding the chemosensitivity evaluation of quiescent parasites by the specific in vitro QSA to the antiplasmodial drug development process in the current worrisome context of artemisinin resistance.
Establishing a Framework for the Clinical Translation of Germline Findings in Precision Oncology
Authors: Dixon Katherine , Young Sean , Shen Yaoqing , Thibodeau My Linh , Fok Alexandra , Pleasance Erin , Zhao Eric , Jones Martin , Aubert Geraldine , Armstrong Linlea , Virani Alice , Regier Dean , Gelmon Karen , Renouf Dan , Chia Stephen , Bosdet Ian , Rassekh S Rod , Deyell Rebecca J , Yip Stephen , Fisic Ana , Titmuss Emma , Abadi Shirin , Jones Steven J M , Sun Sophie , Karsan Aly , Marra Marco , Laskin Janessa , Lim Howard , Schrader Kasmintan A
Published: May 2020

Inherited genetic variation has important implications for cancer screening, early diagnosis, and disease prognosis. A role for germline variation has also been described in shaping the molecular landscape, immune response, microenvironment, and treatment response of individual tumors. However, there is a lack of consensus on the handling and analysis of germline information that extends beyond known or suspected cancer susceptibility in large-scale cancer genomics initiatives. As part of the Personalized OncoGenomics program in British Columbia, we performed whole-genome and transcriptome sequencing in paired tumor and normal tissues from advanced cancer patients to characterize the molecular tumor landscape and identify putative targets for therapy. Overall, our experience supports a multidisciplinary and integrative approach to germline data management. This includes a need for broader definitions and standardized recommendations regarding primary and secondary germline findings in precision oncology. Here, we propose a framework for identifying, evaluating, and returning germline variants of potential clinical significance that may have indications for health management beyond cancer risk reduction or prevention in patients and their families.
Genetic basis of phenotypic plasticity and genotype × environment interactions in a multi-parental tomato population
Authors: Diouf Isidore , Derivot Laurent , Koussevitzky Shai , Carretero Yolande , Bitton Frédérique , Moreau Laurence , Causse Mathilde
Published: May 2020

Deciphering the genetic basis of phenotypic plasticity and genotype × environment interactions (G×E) is of primary importance for plant breeding in the context of global climate change. Tomato (Solanum lycopersicum) is a widely cultivated crop that can grow in different geographical habitats and that displays a great capacity for expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore G×E and plasticity for multiple traits measured in a multi-environment trial (MET) comprising optimal cultural conditions together with water deficit, salinity, and heat stress over 12 environments. Substantial G×E was observed for all the traits measured. Different plasticity parameters were estimated by employing Finlay–Wilkinson and factorial regression models and these were used together with genotypic means for quantitative trait loci (QTL) mapping analyses. In addition, mixed linear models were also used to investigate the presence of QTL × environment interactions. The results highlighted a complex genetic architecture of tomato plasticity and G×E. Candidate genes that might be involved in the occurrence of G×E are proposed, paving the way for functional characterization of stress response genes in tomato and for breeding climate-adapted cultivars.
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases
Authors: Zhao Mengge , Havrilla James M , Fang Li , Chen Ying , Peng Jacqueline , Liu Cong , Wu Chao , Sarmady Mahdi , Botas Pablo , Isla Julián , Lyon Gholson J , Weng Chunhua , Wang Kai
Published: May 2020

Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene–disease databases and gene–gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPacket descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model and output gene–disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed and acts as a real-time phenotype-driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients’ de-identified HPO term data from the Children’s Hospital of Philadelphia.
Where are G-quadruplexes located in the human transcriptome?
Authors: Vannutelli Anaïs , Belhamiti Sarah , Garant Jean-Michel , Ouangraoua Aida , Perreault Jean-Pierre
Published: May 2020

It has been demonstrated that RNA G-quadruplexes (G4) are structural motifs present in transcriptomes and play important regulatory roles in several post-transcriptional mechanisms. However, the full picture of RNA G4 locations and the extent of their implication remain elusive. Solely computational prediction analysis of the whole transcriptome may reveal all potential G4, since experimental identifications are always limited to specific conditions or specific cell lines. The present study reports the first in-depth computational prediction of potential G4 region across the complete human transcriptome. Although using a relatively stringent approach based on three prediction scores that accounts for the composition of G4 sequences, the composition of their neighboring sequences, and the various forms of G4, over 1.1 million of potential G4 (pG4) were predicted. The abundance of G4 was computationally confirmed in both 5′ and 3′UTR as well as splicing junction of mRNA, appreciate for the first time in the long ncRNA, while almost absent of most of the small ncRNA families. The present results constitute an important step toward a full understanding of the roles of G4 in post-transcriptional mechanisms.
CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions
Authors: Stuart William D , Guo Minzhe , Fink-Baldauf Iris M , Coleman Alan M , Clancy John P , Mall Marcus A , Lim Foong-Yen , Brewington John J , Maeda Yutaka
Published: May 2020

Genome-wide association studies have identified lung disease-associated loci; however, the functions of such loci are not well understood in part because the majority of such loci are located at non-coding regions. Hi-C, ChIP-seq and eQTL data predict potential roles (e.g. enhancer) of such loci; however, they do not elucidate the molecular function. To determine whether these loci function as gene-regulatory regions, CRISPR interference (CRISPRi; CRISPR/dCas9-KRAB) has been recently used. Here, we applied CRISPRi along with Hi-C, ChIP-seq and eQTL to determine the functional roles of loci established as highly associated with asthma, cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Notably, Hi-C, ChIP-seq and eQTL predicted that non-coding regions located at chromosome 19q13 or chromosome 17q21 harboring single-nucleotide polymorphisms (SNPs) linked to asthma/CF/COPD and chromosome 11p15 harboring an SNP linked to IPF interact with nearby genes and function as enhancers; however, CRISPRi indicated that the regions with rs1800469, rs2241712, rs12603332 and rs35705950, but not others, regulate the expression of nearby genes (single or multiple genes). These data indicate that CRISPRi is useful to precisely determine the roles of non-coding regions harboring lung disease-associated loci as to whether they function as gene-regulatory regions at a genomic level.
Deep soft K-means clustering with self-training for single-cell RNA sequence data
Authors: Chen Liang , Wang Weinan , Zhai Yuyao , Deng Minghua
Published: May 2020

Single-cell RNA sequencing (scRNA-seq) allows researchers to study cell heterogeneity at the cellular level. A crucial step in analyzing scRNA-seq data is to cluster cells into subpopulations to facilitate subsequent downstream analysis. However, frequent dropout events and increasing size of scRNA-seq data make clustering such high-dimensional, sparse and massive transcriptional expression profiles challenging. Although some existing deep learning-based clustering algorithms for single cells combine dimensionality reduction with clustering, they either ignore the distance and affinity constraints between similar cells or make some additional latent space assumptions like mixture Gaussian distribution, failing to learn cluster-friendly low-dimensional space. Therefore, in this paper, we combine the deep learning technique with the use of a denoising autoencoder to characterize scRNA-seq data while propose a soft self-training K-means algorithm to cluster the cell population in the learned latent space. The self-training procedure can effectively aggregate the similar cells and pursue more cluster-friendly latent space. Our method, called ‘scziDesk’, alternately performs data compression, data reconstruction and soft clustering iteratively, and the results exhibit excellent compatibility and robustness in both simulated and real data. Moreover, our proposed method has perfect scalability in line with cell size on large-scale datasets.
Simultaneous changes in seed size, oil content and protein content driven by selection of SWEET homologues during soybean domestication
Authors: Wang Shoudong , Liu Shulin , Wang Jie , Yokosho Kengo , Zhou Bin , Yu Ya-Chi , Liu Zhi , Frommer Wolf B , Ma Jian Feng , Chen Li-Qing , Guan Yuefeng , Shou Huixia , Tian Zhixi
Published: May 2020

Soybean accounts for more than half of the global production of oilseed and more than a quarter of the protein used globally for human food and animal feed. Soybean domestication involved parallel increases in seed size and oil content, and a concomitant decrease in protein content. However, science has not yet discovered whether these effects were due to selective pressure on a single gene or multiple genes. Here, re-sequencing data from >800 genotypes revealed a strong selection during soybean domestication on GmSWEET10a. The selection of GmSWEET10a conferred simultaneous increases in soybean-seed size and oil content as well as a reduction in the protein content. The result was validated using both near-isogenic lines carrying substitution of haplotype chromosomal segments and transgenic soybeans. Moreover, GmSWEET10b was found to be functionally redundant with its homologue GmSWEET10a and to be undergoing selection in current breeding, leading the the elite allele GmSWEET10b, a potential target for present-day soybean breeding. Both GmSWEET10a and GmSWEET10b were shown to transport sucrose and hexose, contributing to sugar allocation from seed coat to embryo, which consequently determines oil and protein contents and seed size in soybean. We conclude that past selection of optimal GmSWEET10a alleles drove the initial domestication of multiple soybean-seed traits and that targeted selection of the elite allele GmSWEET10b may further improve the yield and seed quality of modern soybean cultivars.
Access Through the Anatomical Snuffbox for Neuroendovascular Procedures: A Single Institution Series
Authors: Weinberg Joshua H , Sweid Ahmad , Khanna Omaditya , Mouchtouris Nikolaos , Asada Ashlee , Das Somnath , Curtis Darcy , Kim Julie , Romo Victor , Gooch Michael Reid , Herial Nabeel , Tjoumakaris Stavropoula , Zarzour Hekmat , Rosenwasser Robert H , Jabbour Pascal
Published: May 2020

BACKGROUND

Distal transradial catheterization in the anatomic snuffbox is an alternate route of access that has started to gain consideration for neuroendovascular procedures.

OBJECTIVE

To assess the feasibility and outcomes and present our institution's experience in performing neuroendovascular procedures via distal transradial access (dTRA).

METHODS

We conducted a retrospective analysis and identified 120 patients who underwent consecutive neuroendovascular procedures via dTRA in the anatomic snuffbox. Data collection was performed on indication for procedure, sheath size, number of vessels selectively catheterized, fluoroscopy time, procedure duration, radiation exposure, conversion to femoral approach, access site complication, and procedure success.

RESULTS

Of 120 patients with an average age of 54.7 yr ± 14.7, 73 (60.8%) underwent diagnostic angiograms, 38 (31.7%) underwent follow-up angiograms, and 9 (7.5%) underwent therapeutic procedures. The overall mean number of vessels catheterized was 2.5 ± 0.1 per procedure, the mean procedure time was 68.3 min ± 43.4, the mean fluoroscopy time was 10.8 min ± 7.6, the mean contrast dose was 70.6 mL ± 39.1, and the mean radiation exposure was 27 672.2 mGycm2 ± 42 728.4. Successfully completed therapeutic procedures included aneurysm 1 (0.8%), arteriovenous malformation (AVM)/arteriovenous fistula/carotid cavernous fistula 7 (5.8%), and 1 (0.8%) other treatment. Three patients (2.5%) required adjunct transfemoral endovenous access for AVM embolization. Two minor complications (1.67%) were a local wrist hematoma and a radial artery vasospasm without any sequelae.

CONCLUSION

Distal radial artery catheterization in the anatomic snuffbox is a safe and effective access site to perform neuroendovascular procedures. Complications and conversion rate are low making it a safe alternative.
Triggered high-mass star formation in the H iiregion W 28 A2: A cloud–cloud collision scenario
Authors: Hayashi Katsuhiro , Yoshiike Satoshi , Enokiya Rei , Fujita Shinji , Yamada Rin , Sano Hidetoshi , Torii Kazufumi , Kohno Mikito , Nishimura Atsushi , Ohama Akio , Yamamoto Hiroaki , Tachihara Kengo , Wong Graeme , Maxted Nigel , Braiding Catherine , Rowell Gavin , Burton Michael , Fukui Yasuo
Published: May 2020

We report on a study of the high-mass star formation in the H ii region W 28 A2 by investigating the molecular clouds that extend over ∼5–10 pc from the exciting stars using the 12CO and 13CO (J = 1–0) and 12CO (J = 2–1) data taken by NANTEN2 and Mopra observations. These molecular clouds consist of three velocity components with CO intensity peaks at VLSR ∼ −4 km s−1, 9 km s−1, and 16 km s−1. The highest CO intensity is detected at VLSR ∼ 9 km s−1, where the high-mass stars with spectral types O6.5–B0.5 are embedded. We found bridging features connecting these clouds toward the directions of the exciting sources. Comparisons of the gas distributions with the radio continuum emission and 8 μm infrared emission show spatial coincidence/anti-coincidence, suggesting physical associations between the gas and the exciting sources. The 12CO J = 2–1 to 1–0 intensity ratio shows a high value (≳0.8) toward the exciting sources for the −4 km s−1 and +9 km s−1 clouds, possibly due to heating by the high-mass stars, whereas the intensity ratio at the CO intensity peak (VLSR ∼ 9 km s−1) decreases to ∼0.6, suggesting self absorption by the dense gas in the near side of the +9 km s−1 cloud. We found partly complementary gas distributions between the −4 km s−1 and +9 km s−1 clouds, and the −4 km s−1 and +16 km s−1 clouds. The exciting sources are located toward the overlapping region in the −4 km s−1 and +9 km s−1 clouds. Similar gas properties are found in the Galactic massive star clusters RCW 38 and NGC 6334, where an early stage of cloud collision to trigger the star formation is suggested. Based on these results, we discuss the possibility of the formation of high-mass stars in the W 28 A2 region being triggered by cloud–cloud collision.