bluuebunny/crossref_metadata_2025 huggingface dataset:
Number and Station of Lymph Node Metastasis After Curative-intent Resection of Intrahepatic Cholangiocarcinoma Impact Prognosis
Authors: Zhang Xu-Feng , Xue Feng , Dong Ding-Hui , Weiss Matthew , Popescu Irinel , Marques Hugo P. , Aldrighetti Luca , Maithel Shishir K. , Pulitano Carlo , Bauer Todd W. , Shen Feng , Poultsides George A. , Soubrane Oliver , Martel Guillaume , Koerkamp Bas Groot , Itaru Endo , Lv Yi , Pawlik Timothy M.
Published: January 2020

Objectives:

To determine the prognostic implication of the number and station of LNM, and the minimal number of LNs needed for evaluation to accurately stage patients with intrahepatic cholangiocarcinoma (ICC).

Background:

Impact of the number and station of LNM on long-term survival, and the minimal number of LNs needed for accurate staging of ICC patients remain poorly defined.

Methods:

Data on patients who underwent curative-intent resection for ICC was collected from 15 high-volume centers worldwide. External validation was performed using the SEER registry. Primary outcomes included overall (OS), disease-specific, and recurrence-free survival.

Results:

Among 603 patients who underwent curative-intent resection, median and 5-year OS were 30.6 months and 30.4%. Patients with 1 or 2 LNM had comparable worse OS versus patients with no nodal disease (median OS, 1 LNM 18.0, 2 LNM 20.0 vs no LNM 45.0 months, both P < 0.001), yet better OS versus patients with 3 or more LNM (median OS, 1–2 LNM 19.8 vs ≥3 LNM 16.0 months, P < 0.01). On multivariable analysis, a proposed new nodal staging with N1 (1–2 LNM) (Ref. N0, HR 2.40, P < 0.001) and N2 (≥3 LNM) [Ref. N0, hazard ratio (HR) 3.85, P < 0.001] categories were independently associated with incrementally worse OS. Patients with no nodal metastasis, 1–2 LNM and ≥3 LNM also had an increasingly worse disease-specific survival, and recurrence-free survival (both P < 0.05). Total number of LNs examined ≥6 had the greatest discriminatory power relative to OS among patients with 1–2 LNM, and patients with ≥3 LNM in both the multi-institutional (area under the curve 0.780) and SEER database (area under the curve 0.820) (n = 1036). Among patients who underwent an adequate regional lymphadenectomy (total number of LNs examined ≥6), LNM beyond the HDL was associated with worse OS versus LNM within the HDL only (median OS, 14.0 vs 24.0 months, HR 2.41, P = 0.003).

Conclusion:

Standard lymphadenectomy of at least 6 LNs is strongly recommended and should include examination beyond station 12 to have the greatest chance of accurate staging. The proposed new nodal staging of N0, N1, and N2 should be considered to stratify outcomes among patients after curative-intent resection of ICC.
Lack of Association Between the CCR5-delta32 Polymorphism and Neurodegenerative Disorders
Authors: Wojta Kevin J. , Ayer Ariane H. , Ramos Eliana M. , Nguyen Peter D. , Karydas Anna M. , Yokoyama Jennifer S. , Kramer Joel , Lee Suzee E. , Boxer Adam , Miller Bruce L. , Coppola Giovanni
Published: January 2020

Objective:

Recent studies have suggested that diminished Ccr5 functioning has an effect on synaptic plasticity and hippocampal memory in mouse models. CCR5-delta32, a 32-bp frameshift deletion in human CCR5 encoding a nonfunctional receptor, has been reported to have a protective effect against human immunodeficiency virus infection but its role as a modifier of neurodegenerative disease has been minimally explored. We investigated whether the CCR5-delta32 polymorphism could have an effect in the context of human neurodegenerative diseases.

Methods:

We examined the frequency of the CCR5-delta32 polymorphism in a large and well-characterized cohort including 1425 patients with neurodegenerative dementias and 2032 controls.

Results:

We did not observe a significant association between the CCR5-delta32 polymorphism and any of the neurodegenerative diseases screened in this study. However, we observed an earlier age of onset among neurodegenerative disease patients carrying the CCR5-delta32 allele.

Conclusions:

Although our findings were inconclusive, the earlier age of onset observed among neurodegenerative disease patients carrying the CCR5-delta32 allele suggests that the deletion may have a detrimental effect in the context of neurodegeneration.
Correlation Between Optic Disc Peripapillary Capillary Network and Papilledema Grading in Patients With Idiopathic Intracranial Hypertension: A Study of Optical Coherence Tomography Angiography
Authors: Rodriguez Torres Yasaira , Lee Patrick , Mihlstin Melanie , Tomsak Robert L.
Published: January 2020

Background:

The continued increase in idiopathic intracranial hypertension (IIH) prevalence has many implications for societal health care. Its potential vision-threatening consequences make ophthalmologists key players in its diagnosis and management. Newer technology such as optical coherence tomography angiography (OCT-A) enables evaluation of the branching complexity of the peripapillary capillary plexus, a region where accurate imaging via fluorescein angiography was previously limited.

Methods:

A cross-sectional, observational study of 23 (46 eyes) consecutive patients with IIH. Peripapillary total vasculature was recorded using commercial OCT-A en face vessel density mapping. In addition, OCT-A blood flow slab was compared with papilledema grading. OCT-A images were analyzed using a customized image analysis protocol using ImageJ software (v1.51w) and Photoshop software (Adobe Systems, CA). SPSS software version 25 was used for statistical analysis (SPSS Inc, IBM, Chicago, IL).

Results:

Skeletonized vessel density peripapillary capillary plexus was significantly associated with Frisen papilledema grades, OCT retinal nerve fiber layer (RNFL), and macular ganglion cell layer (GCL) thickness with a P < 0.001, P = 0.022, and P = 0.006, respectively. Every point increase in grade was correlated with a decrease of 9.1 pixels/mm2 in vessel density (R = 0.512, β = −0.115 ± 0.029; P < 0.001). Increased papilledema was correlated with an increased retinal blood flow percentage (R = 0.300, β = 2.114 ± 1.013; P < 0.05) and decreased choroidal blood flow (CBF) percentage (R = 0.300, β = 2.114 ± 1.013; P < 0.05). Every point increase in grade was correlated with a decrease in CBF by 47.4%, as calculated using a linear best-fit line inclusive for all of the data points.

Conclusions:

OCT-A allows for effective visualization and quantification of the peripapillary retinal vasculature. Our results demonstrate a correlation between skeletonized peripapillary density and papilledema grading, OCT RNFL thickness, and GCL thickness. In addition, we show a significant negative correlation between CBF and papilledema grading. These changes provide key findings regarding the pathophysiology of optic neuropathy in papilledema and highlight the potential of OCT-A as a diagnostic tool for papilledema and a clinical marker for detecting early optic nerve damage.
Optic Disc Drusen Associated Anterior Ischemic Optic Neuropathy: Prevalence of Comorbidities and Vascular Risk Factors
Authors: Rueløkke Lea L. , Malmqvist Lasse , Wegener Marianne , Hamann Steffen
Published: January 2020

Background:

Nonarteritic anterior ischemic optic neuropathy (NA-AION) associated with optic disc drusen (ODD) is termed ODD-AION, where NA-AION with no evidence of ODD is simply termed NA-AION. Patients with ODD-AION have been found to be younger than those with NA-AION but with similar vascular risk factors. This study compares the known risk factors for NA-AION between a group with ODD-AION and a similarly aged group with NA-AION.

Methods:

A case–control study of 13 patients with ODD-AION and 14 patients with NA-AION diagnosed in the period 2008–2017. All patients underwent an interview designed to evaluate history of vascular risk factors and comorbidities and re-examination including enhanced depth imaging optical coherence tomography to confirm the presence or absence of ODD.

Results:

No significant differences were found in demographic or clinical characteristics between the ODD-AION and the NA-AION group. Significantly more ODD-AION patients than NA-AION patients had no vascular risk factors (smoking, arterial hypertension, diabetes mellitus, and dyslipidemia) present (P = 0.047). Significantly fewer patients in the ODD-AION group were diagnosed with arterial hypertension or dyslipidemia than in the NA-AION group.

Conclusions:

In this cross-sectional study, the ODD-AION patients more often had no vascular risk factors as compared to NA-AION patients, which supports the hypothesis that ODD are an independent risk factor for AION.
Remote Pontine Hemorrhage After Left Frontal Lobe Meningioma Resection Presenting as Bilateral Internuclear Ophthalmoplegia
Authors: Lee Maxwell , Al Othman Bayan A. , Kini Tonse A. , Lee Andrew G.
Published: January 2020

Postoperative hemorrhages are relatively common complications of surgical procedures including craniotomies, and these typically occur at or near the operative site. Bleeding in remote areas (e.g., posterior fossa) after supratentorial craniotomy can occur and may be associated with a high morbidity and mortality. Although remote cerebellar hemorrhage after craniotomy is well described, remote pontine hemorrhage is less common. We describe a bilateral internuclear ophthalmoplegia due to an RPH after otherwise uncomplicated resection of a frontal meningioma. Clinicians should be aware that neuro-ophthalmic findings can occur from hemorrhages remote from the operative site.
Using clinical registries, administrative data and electronic medical records to improve medication safety and effectiveness in dementia
Authors: Ilomäki Jenni , Lai Edward Chia-Cheng , Bell J. Simon
Published: January 2020

Purpose of review

Clinical registries, routinely collected administrative data and electronic medical records (EMRs) provide new opportunities to investigate medication safety and effectiveness. This review outlines the strengths and limitations of these data, and highlights recent research related to safe and effective medication use in dementia.

Recent findings

Clinical registries, administrative data and EMRs facilitate observational research among people often excluded from randomized controlled trials (RCTs). Larger sample sizes and longer follow-up times permit research into less common adverse events not apparent in RCTs. The validity of diagnoses recorded in administrative data and EMRs remains variable, although positive predictive values are typically high and sensitivity is low. Dispensing records are a rich source of data for estimating medication exposure. Recent research has investigated medications and prescribing patterns as risk factors for incident dementia, strategies to alleviate behavioural symptoms and the management of comorbidity. Common study protocols and common data models are examples of distributed network approaches increasingly used to conduct large and generalizable multi-database studies across different countries.

Greater availability of electronic health data provides important opportunities to address evidence-practice gaps in relation to medication use and safety in people with dementia.
A randomized, double-blind study comparing the efficacy and safety of trazodone once-a-day and venlafaxine extended-release for the treatment of patients with major depressive disorder
Authors: Fagiolini Andrea , Albert Umberto , Ferrando Laura , Herman Erik , Muntean Cosmina , Pálová Eva , Cattaneo Agnese , Comandini Alessandro , Di Dato Giorgio , Di Loreto Giorgio , Olivieri Luisa , Salvatori Enrica , Tongiani Serena , Kasper Siegfried
Published: January 2020

This double-blind, randomized study evaluated the efficacy and safety of trazodone OAD (once-a-day) in comparison with venlafaxine XR (extended-release) in 324 patients (166 trazodone and 158 venlafaxine) with major depressive disorder (MDD). The primary efficacy endpoint was the mean change from baseline in the 17-item Hamilton Depression Rating Scale (HAM-D) at week 8. Both treatments were effective in reducing the HAM-D-17 total score at week 8 vs. baseline (intent-to-treat: trazodone –12.9, venlafaxine –14.7; per protocol: trazodone –15.4, venlafaxine –16.4). Patients in the venlafaxine group achieved better results after 8 weeks, whereas the trazodone group achieved a statistically significant reduction in HAM-D-17 following only 7 days of treatment. The most frequent adverse events (AEs) were dizziness and somnolence in the trazodone group, and nausea and headache in the venlafaxine group. Most AEs were mild-to-moderate in severity. This study confirmed that both venlafaxine XR and trazodone OAD may represent a valid treatment option for patients with MDD.
Evolution, geographic spreading, and demographic distribution of Enterovirus D68
Authors: Hodcroft Emma B. , Dyrdak Robert , Andrés Cristina , Egli Adrian , Reist Josiane , García Martínez de Artola Diego , Alcoba Flórez Julia , Niesters Hubert G. M. , Antón Andrés , Poelman Randy , Reynders Marijke , Wollants Elke , Neher Richard A. , Albert Jan
Published: January 2020

Background

Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease.

Methods

We collected samples from several European countries during the 2018 out-break and determined 53 near full-length genome (‘whole genome’) sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences.

Findings

In 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68 season. EV-D68 displays strong signs of continuous antigenic evolution and all 2018 A2 strains had novel patterns in the putative neutralizing epitopes in the BC- and DE-loops. The pattern in the BC-loop of the USA B3 subgroup had not been detected on that continent before. Patients with EV-D68 in subclade A2 were significantly older than patients with a B3 subclade virus. In contrast to other subclades, the age distribution of A2 is distinctly bimodal and was found primarily among children and in the elderly.

Interpretation

We hypothesize that EV-D68’s rapid evolution of surface proteins, extensive diversity, and high rate of geographic mixing could be explained by substantial reinfection of adults.

Funding

University of Basel and Swedish Foundation for Research and Development in Medical Microbiology
Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods
Authors: Menke Joe , Roelandse Martijn , Ozyurt Burak , Martone Maryann , Bandrowski Anita
Published: January 2020

The reproducibility crisis in science is a multifaceted problem involving practices and incentives, both in the laboratory and in publication. Fortunately, some of the root causes are known and can be addressed by scientists and authors alike. After careful consideration of the available literature, the National Institutes of Health identified several key problems with the way that scientists conduct and report their research and introduced guidelines to improve the rigor and reproducibility of pre-clinical studies. Many journals have implemented policies addressing these same criteria. We currently have, however, no comprehensive data on how these guidelines are impacting the reporting of research. Using SciScore, an automated tool developed to review the methods sections of manuscripts for the presence of criteria associated with the NIH and other reporting guidelines, e.g., ARRIVE, RRIDs, we have analyzed ~1.6 million PubMed Central papers to determine the degree to which articles were addressing these criteria. The tool scores each paper on a ten point scale identifying sentences that are associated with compliance with criteria associated with increased rigor (5 pts) and those associated with key resource identification and authentication (5 pts). From these data, we have built the Rigor and Transparency Index, which is the average score for analyzed papers in a particular journal. Our analyses show that the average score over all journals has increased since 1997, but remains below five, indicating that less than half of the rigor and reproducibility criteria are routinely addressed by authors. To analyze the data further, we examined the prevalence of individual criteria across the literature, e.g., the reporting of a subject’s sex (21-37% of studies between 1997 and 2019), the inclusion of sample size calculations (2-10%), whether the study addressed blinding (3-9%), or the identifiability of key biological resources such as antibodies (11-43%), transgenic organisms (14-22%), and cell lines (33-39%). The greatest increase in prevalence for rigor criteria was seen in the use of randomization of subjects (10-30%), while software tool identifiability improved the most among key resource types (42-87%). We further analyzed individual journals over time that had implemented specific author guidelines covering rigor criteria, and found that in some journals, they had a big impact, whereas in others they did not. We speculate that unless they are enforced, author guidelines alone do little to improve the number of criteria addressed by authors. Our Rigor and Transparency Index did not correlate with the impact factors of journals.
Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities
Authors: Kleiner Manuel , Bushnell Brian , Sanderson Kenneth E. , Hooper Lora V. , Duerkop Breck A.
Published: January 2020

Horizontal gene transfer (HGT) plays a central role in microbial evolution. Our understanding of the mechanisms, frequency and taxonomic range of HGT in polymicrobial environments is limited, as we currently rely on historical HGT events inferred from genome sequencing and studies involving cultured microorganisms. We lack approaches to observe ongoing HGT in microbial communities. To address this knowledge gap, we developed a DNA sequencing based “transductomics” approach that detects and characterizes microbial DNA transferred via transduction. We validated our approach using model systems representing a range of transduction modes and show that we can detect numerous classes of transducing DNA. Additionally, we show that we can use this methodology to obtain insights into DNA transduction among all major taxonomic groups of the intestinal microbiome. This work extends the genomic toolkit for the broader study of mobile DNA within microbial communities and could be used to understand how phenotypes spread within microbiomes.

Significance Statement

Microbes can rapidly evolve new capabilities by acquiring genes from other organisms through a process called horizontal gene transfer (HGT). HGT occurs via different routes, one of which is by the transfer of DNA carried by microbe infecting viruses (phages) or virus-like agents. This process is called transduction and has primarily been studied in the lab using pure cultures or indirectly in environmental communities by analyzing signatures in microbial genomes revealing past transduction events. The transductomics approach that we present here, allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer.
Functional interaction between Fanconi anemia and mTOR pathways during stalled replication fork recovery
Authors: Nolan Matthew , Knudson Kenneth , Holz Marina K. , Chaudhury Indrajit
Published: January 2020

We have previously demonstrated that Fanconi Anemia (FA) proteins work in concert with other FA and non-FA proteins to mediate stalled replication fork restart. Previous studies suggest a connection between FA protein FANCD2 and a non-FA protein mechanistic target of rapamycin (mTOR). A recent study showed that mTOR is involved in actin-dependent DNA replication fork restart, suggesting possible roles in FA DNA repair pathway. In this study, we demonstrate that during replication stress mTOR interacts and cooperates with FANCD2 to provide cellular stability, mediates stalled replication fork restart and prevents nucleolytic degradation of the nascent DNA strands. Taken together, this study unravels a novel functional cross-talk between two important mechanisms: mTOR and FA DNA repair pathways that ensure genomic stability.
Asymmetrical myofiber architecture along the murine tibialis anterior suggests distinct functional regions
Authors: Bindellini Davide , Voortman Lenard M. , Olie Cyriel S. , van Putten Maaike , van den Akker Erik , Raz Vered
Published: January 2020

Skeletal muscle function is inferred from the spatial arrangement of myofiber architecture and the molecular and metabolic features of myofibers. Features of myofiber types can be distinguished by the expression of myosin heavy chain (MyHC) isoforms, indicating contraction properties. In most studies, a local sampling, typically obtained from the median part of the muscle, is used to represent the whole muscle. It remains largely unknown to what extent this local sampling represents the entire muscle. Here we studied myofiber architecture over the entire wild type mouse tibialis anterior muscle, using a high-throughput procedure combining automatic imaging and image processing analyses. We reconstructed myofiber architecture from consecutive cross-sections stained for laminin and MyHC isoforms. The data showed a marked variation in myofiber geometric features, as well as MyHC expression and the distribution of neuromuscular junctions, and suggest that muscle regions with distinct properties can be defined along the entire muscle. We show that in these muscle regions myofiber geometric properties align with biological function and propose that future studies on muscle alterations in pathological or physiological conditions should consider the entire muscle.
Trans-ethnic and ancestry-specific blood-cell genetics in 746,667 individuals from 5 global populations
Authors: Chen Ming-Huei , Raffield Laura M. , Mousas Abdou , Sakaue Saori , Huffman Jennifer E. , Jiang Tao , Akbari Parsa , Vuckovic Dragana , Bao Erik L. , Moscati Arden , Zhong Xue , Manansala Regina , Laplante Véronique , Chen Minhui , Lo Ken Sin , Qian Huijun , Lareau Caleb A. , Beaudoin Mélissa , Akiyama Masato , Bartz Traci M. , Ben-Shlomo Yoav , Beswick Andrew , Bork-Jensen Jette , Bottinger Erwin P. , Brody Jennifer A. , van Rooij Frank J.A. , Chitrala Kumaraswamynaidu , Cho Kelly , Choquet Hélène , Correa Adolfo , Danesh John , Di Angelantonio Emanuele , Dimou Niki , Ding Jingzhong , Elliott Paul , Esko Tõnu , Evans Michele K. , Floyd James S. , Broer Linda , Grarup Niels , Guo Michael H. , Greinacher Andreas , Haessler Jeff , Hansen Torben , Howson Joanna M. M. , Huang Wei , Jorgenson Eric , Kacprowski Tim , Kähönen Mika , Kamatani Yoichiro , Kanai Masahiro , Karthikeyan Savita , Koskeridis Fotis , Lange Leslie A. , Lehtimäki Terho , Lerch Markus M. , Linneberg Allan , Liu Yongmei , Lyytikäinen Leo-Pekka , Manichaikul Ani , Matsuda Koichi , Mohlke Karen L. , Mononen Nina , Murakami Yoshinori , Nadkarni Girish N. , Nauck Matthias , Nikus Kjell , Ouwehand Willem H. , Pankratz Nathan , Pedersen Oluf , Preuss Michael , Psaty Bruce M. , Raitakari Olli T. , Roberts David J. , Rich Stephen S. , Rodriguez Benjamin A.T. , Rosen Jonathan D. , Rotter Jerome I. , Schubert Petra , Spracklen Cassandra N. , Surendran Praveen , Tang Hua , Tardif Jean-Claude , Ghanbari Mohsen , Völker Uwe , Völzke Henry , Watkins Nicholas A. , Zonderman Alan B. , Million Veteran Program VA , Wilson Peter W.F. , Li Yun , Butterworth Adam S. , Gauchat Jean-François , Chiang Charleston W.K. , Li Bingshan , Loos Ruth J.F. , Astle William J. , Evangelou Evangelos , Sankaran Vijay G. , Okada Yukinori , Soranzo Nicole , Johnson Andrew D. , Reiner Alexander P. , Auer Paul L. , Lettre Guillaume
Published: January 2020

Most loci identified by GWAS have been found in populations of European ancestry (EA). In trans-ethnic meta-analyses for 15 hematological traits in 746,667 participants, including 184,535 non-EA individuals, we identified 5,552 trait-variant associations atP<5×10−9, including 71 novel loci not found in EA populations. We also identified novel ancestry-specific variants not found in EA, including anIL7missense variant in South Asians associated with lymphocyte countin vivoand IL7 secretion levelsin vitro. Fine-mapping prioritized variants annotated as functional, and generated 95% credible sets that were 30% smaller when using the trans-ethnic as opposed to the EA-only results. We explored the clinical significance and predictive value of trans-ethnic variants in multiple populations, and compared genetic architecture and the impact of natural selection on these blood phenotypes between populations. Altogether, our results for hematological traits highlight the value of a more global representation of populations in genetic studies.
A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets
Authors: Ekim Barış , Berger Bonnie , Orenstein Yaron
Published: January 2020

As the volume of next generation sequencing data increases, an urgent need for algorithms to efficiently process the data arises.Universal hitting sets(UHS) were recently introduced as an alternative to the central idea of minimizers in sequence analysis with the hopes that they could more efficiently address common tasks such as computing hash functions for read overlap, sparse suffix arrays, and Bloom filters. A UHS is a set ofk-mers that hit every sequence of lengthL, and can thus serve as indices toL-long sequences. Unfortunately, methods for computing small UHSs are not yet practical for real-world sequencing instances due to their serial and deterministic nature, which leads to long runtimes and high memory demands when handling typical values ofk(e.g.k> 13). To address this bottleneck, we present two algorithmic innovations to significantly decrease runtime while keeping memory usage low: (i) we leverage advanced theoretical and architectural techniques to parallelize and decrease memory usage in calculatingk-mer hitting numbers; and (ii) we build upon techniques from randomized Set Cover to select universalk-mers much faster. We implemented these innovations in PASHA, the first randomized parallel algorithm for generating near-optimal UHSs, which newly handlesk> 13. We demonstrate empirically that PASHA produces sets only slightly larger than those of serial deterministic algorithms; moreover, the set size is provably guaranteed to be within a small factor of the optimal size. PASHA’s runtime and memory-usage improvements are orders of magnitude faster than the current best algorithms. We expect our newly-practical construction of UHSs to be adopted in many high-throughput sequence analysis pipelines.
Metalign: Efficient alignment-based metagenomic profiling via containment min hash
Authors: LaPierre Nathan , Alser Mohammed , Eskin Eleazar , Koslicki David , Mangul Serghei
Published: January 2020

Whole-genome shotgun sequencing enables the analysis of microbial communities in unprecedented detail, with major implications in medicine and ecology. Predicting the presence and relative abundances of microbes in a sample, known as “metagenomic profiling”, is a critical first step in microbiome analysis. Existing profiling methods have been shown to suffer from poor false positive or false negative rates, while alignment-based approaches are often considered accurate but computationally infeasible. Here we present a novel method, Metalign, that addresses these concerns by performing efficient alignment-based metagenomic profiling. We use a containment min hash approach to reduce the reference database size dramatically before alignment and a method to estimate organism relative abundances in the sample by resolving reads aligned to multiple genomes. We show that Metalign achieves significantly improved results over existing methods on simulated datasets from a large benchmarking study, CAMI, and performs well onin vitromock community data and environmental data from the Tara Oceans project. Metalign is freely available athttps://github.com/nlapier2/Metalign, along with the results and plots used in this paper, and a docker image is also available athttps://hub.docker.com/repository/docker/nlapier2/metalign.
The human and mouse synaptome architecture of excitatory synapses show conserved features
Authors: Curran Olimpia E. , Qiu Zhen , Smith Colin , Grant Seth G. N.
Published: January 2020

Large-scale mapping of the location of synapses and their molecular properties in the mouse has shown that diverse synapse types are spatially distributed across the brain. The diversity of synapses is known as the synaptome and the spatial distribution as the synaptome architecture. Synaptome maps in the mouse show each brain region has a characteristic compositional signature. The signature can store behavioral representations and is modified in mouse genetic models of human disease. The human synaptome remains unexplored and whether it has any conserved features with the mouse synaptome is unknown.

As a first step toward creating a human synaptome atlas, we have labelled and imaged synapses expressing the excitatory synapse protein PSD95 in twenty human brain regions in four phenotypically normal individuals. We quantified the number, size and intensity of approximately a billion individual synaptic puncta and compared their regional distributions. We found that each region showed a distinct signature of synaptic puncta parameters. Comparison of brain regions showed the synaptome of cortical and hippocampal structures were similar but distinct to the synaptome of cerebellum and brainstem. Comparison of human and mouse synaptome revealed conservation of synaptic puncta parameters, hierarchical organization of brain regions and network architecture. These data show that the synaptome of humans and mouse share conserved features despite the 1000-fold difference in brain size and 90 million years since a common ancestor. This first draft human synaptome atlas illustrates the feasibility of generating a systematic atlas of the human synaptome in health and disease.
Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution
Authors: Wolny Adrian , Cerrone Lorenzo , Vijayan Athul , Tofanelli Rachele , Vilches Barro Amaya , Louveaux Marion , Wenzl Christian , Steigleder Susanne , Pape Constantin , Bailoni Alberto , Duran-Nebreda Salva , Bassel George , Lohmann Jan U. , Hamprecht Fred A. , Schneitz Kay , Maizel Alexis , Kreshuk Anna
Published: January 2020

Quantitative analysis of plant and animal morphogenesis requires accurate segmentation of individual cells in volumetric images of growing organs. In the last years, deep learning has provided robust automated algorithms that approach human performance, with applications to bio-image analysis now starting to emerge. Here, we present PlantSeg, a pipeline for volumetric segmentation of plant tissues into cells. PlantSeg employs a convolutional neural network to predict cell boundaries and graph partitioning to segment cells based on the neural network predictions. PlantSeg was trained on fixed and live plant organs imaged with confocal and light sheet microscopes. PlantSeg delivers accurate results and generalizes well across different tissues, scales, and acquisition settings. We present results of PlantSeg applications in diverse developmental contexts. PlantSeg is free and open-source, with both a command line and a user-friendly graphical interface.
Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation
Authors: Fang Celestia , Wang Zhenjia , Han Cuijuan , Safgren Stephanie L. , Helmin Kathryn A. , Adelman Emmalee R. , Eagen Kyle P. , Gaspar-Maia Alexandre , Figueroa Maria E. , Singer Benjamin D. , Ratan Aakrosh , Ntziachristos Panagiotis , Zang Chongzhi
Published: January 2020

Background

The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, there is no hitherto a comprehensive survey of genome-wide CTCF binding patterns across different human cancers.

Results

To dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions in patient samples, but not always with DNA methylation changes or sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events are induced by oncogenic transcription factors and exhibit enhancer activities. We validate these findings in T-cell acute lymphoblastic leukemia and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena.

Conclusions

Cancer-specific CTCF binding events are not always associated with DNA methylation changes or mutations, but can be induced by other transcription factors to regulate oncogenic gene expression. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.
Kctd15 regulates nephron segment development by repressing Tfap2a activity
Authors: Chambers Brooke E. , Clark Eleanor G. , Gatz Allison E. , Wingert Rebecca A.
Published: January 2020

A functional vertebrate kidney relies on structural units called nephrons, which are epithelial tubules that contain a sequence of segments each expressing a distinct repertoire of solute transporters. To date, the transcriptional codes driving regional specification, solute transporter program activation, and terminal differentiation of segment populations remain poorly understood. We demonstrate for the first time that the KCTD15 paralogs,kctd15aandkctd15b, function in concert to restrict distal early (DE)/thick ascending limb (TAL) segment lineage assignment in the developing zebrafish pronephros by repressing Tfap2a activity. During renal ontogeny, expression of these factors co-localized withtfap2ain distal tubule precursors.kctd15loss primed nephron cells to adopt distal fates by driving expansions inslc12a1,kcnj1a.1, andstc1marker expression. These phenotypes were resultant of Tfap2a hyperactivity, wherekctd15a/b-deficient embryos exhibited increased abundance of this transcription factor. Interestingly,tfap2areciprocally promotedkctd15transcription, unveiling a circuit of autoregulation operating in nephron progenitors. Concomitantkctd15bknockdown withtfap2aoverexpression produced genetic synergy and further expanded the DE population. Our study provides strong evidence that a transcription factor-repressor feedback module employs tight regulation of Tfap2a and Kctd15 kinetics to control nephron segment fate choice and differentiation during kidney development.
A role for reward valuation in the serotonergic modulation of impulsivity
Authors: Desrochers Stephanie S. , Lesko Emma , Magalong Valerie M. , Balsam Peter D. , Nautiyal Katherine M.
Published: January 2020

Impulsive behavior is a deleterious component of a number of mental health disorders but has few targeted pharmacotherapies. One contributing factor to the difficulty in understanding the neural substrates of disordered impulsivity is the diverse presentations of impulsive behavior. Defining the behavioral and cognitive processes which contribute to different subtypes of impulsivity is integral to understanding and treating disorders with dysregulated impulsive behavior. Our approach was to first determine what behavioral and cognitive phenotypes are associated with increased impulsive behavior, and then probe if they could causally contribute to increasing impulsivity. We used a mouse model for disordered impulsivity - mice lacking the serotonin 1B receptor (5-HT1BR) which have deficits specific to impulsive action, and not other components of impulsive behavior. Here we report, that in addition to increased impulsive action, mice lacking expression of 5-HT1BR also have increased goal-directed responding and motivation, with no differences in extinction, development of habitual behavior, delay discounting, or effort-based discounting. Interestingly, mice lacking 5-HT1BR expression did show an overall increase in the choice of higher value rewards, increased hedonic responses to sweet rewards, and responded more to cues that predict reward, compared to controls. We developed a novel paradigm to demonstrate that increasing anticipated reward value could directly increase impulsive action. Furthermore, we found that 5-HT1BR KO-induced impulsivity could be ameliorated by decreasing the reward value relative to controls, suggesting that the increased 5-HT1BR-associated impulsive action is a result of increased reward valuation. Taken together, these data show that the effects of serotonin on impulsive action are mediated through the modulation of hedonic value, which may alter the reward representations that motivate action. Additionally this work supports a role for reward valuation as an important substrate in impulsive action which may drive clinically-relevant increases in impulsivity.
ChronicStaphylococcus aureusinfection is cured by theory-driven therapy
Authors: Papaxenopoulou Lito A. , Zhao Gang , Khailaie Sahamoddin , Katsoulis-Dimitriou Konstantinos , Schmitz Ingo , Medina Eva , Hatzikirou Haralampos , Meyer-Hermann Michael
Published: January 2020

Staphylococcus aureusis considered a dangerous pathogen due to its ability to evade the immune system and resist multiple antibiotics. These evasive strategies lead to difficult-to-treat chronic infections and abscesses in internal organs including kidneys, which are associated with the expansion of myeloid-derived suppressor cells (MDSCs) and their suppressive effect on T cells. Here, we developed a mathematical model of chronicS. aureusinfection that incorporates the T-cell suppression by MDSCs and suggests therapeutic strategies to eradicateS. aureus. We quantifiedin silicoa therapeutic protocol with heat-killedS. aureus(HKSA), which we testedin vivo. Contrary to conventional administration of heat-killed bacteria as vaccination prior to infection, we administered HKSA as treatment, when the hosts were already chronically infected. Our treatment cured all chronicallyS. aureus-infected mice, reduced MDSCs, and reversed T-cell dysfunction by inducing acute inflammation during ongoing, chronic infection without any use of standard treatments that involve antibiotics, MDSC-targeting drugs (chemotherapy), or procedures such as abscess drainage. This study is a proof-of-principle for a treatment protocol against chronicS. aureusinfection and renal abscesses by repurposing heat-killed treatments, guided and quantified by mathematical modelling. Our mathematical model further explains why previous treatment with inactivatedS. aureusadministered to long-term infected human patients has not led to cure. Overall, our results can have direct relevance to the design of human therapeutics against chronicS. aureusinfections.

In brief

A theory-driven treatment protocol with heat-killedS. aureuseradicatesS. aureus, reduces MDSCs, and reverses T-cell dysfunctionin vivo.

Graphical abstract
ER-Anchored Transcription Factors bZIP17 and bZIP60 Regulate Triterpene Saponin Biosynthesis inMedicago truncatula1[OPEN]
Authors: Ribeiro Bianca , Erffelinck Marie-Laure , Colinas Maite , Williams Clara , Van Hamme Evelien , Lacchini Elia , De Clercq Rebecca , Perassolo Maria , Goossens Alain
Published: January 2020

Triterpene saponins (TS) are a structurally diverse group of metabolites that are widely distributed in plants. They primarily serve as defense compounds and their production is often triggered by biotic stresses through signaling cascades that are modulated by phytohormones such as the jasmonates (JA). Two JA-modulated basic helix-loop-helix (bHLH) transcription factors (TFs), TRITERPENE SAPONIN BIOSYNTHESIS ACTIVATING REGULATOR 1 (TSAR1) and TSAR2, have been previously identified as direct activators of TS biosynthesis in the model legumeMedicago truncatula. Here, we report on the involvement of the core endoplasmic reticulum (ER) stress basic leucine zipper (bZIP) TFs bZIP17 and bZIP60 in the regulation of TS biosynthesis. Expression and processing ofM. truncatulabZIP17 and bZIP60 proteins was altered in roots with perturbed TS biosynthesis or treated with JA. Accordingly, such roots displayed an altered ER network structure.M. truncatulabZIP17 and bZIP60 proteins were shown to be capable of interfering with the TSAR-mediated transactivation of TS biosynthesis genes, particularly under ER stress conditions, when they translocate from the ER to the nucleus. Furthermore, the inhibitory role of ER stress bZIP TFs in the regulation of JA-dependent terpene biosynthetic pathways appears to be widespread in the plant kingdom, as we demonstrate that it also occurs in the regulation of monoterpene indole alkaloid biosynthesis in the medicinal plantCatharanthus roseus. We postulate that activation of ER stress bZIP TFs provides the plant with a mechanism to balance metabolic activities and thereby adequately govern modulation of growth, development and defense processes in defined stress situations.

One sentence summary

ER stress bZIP transcription factors can interfere with the activity of jasmonate-inducible bHLH transcription factors to modulate the elicitation of plant specialized metabolism in stress conditions.
Elucidating the complex organization of neural micro-domains in the locustSchistocerca gregariausing dMRI
Authors: Shahid S.S. , Kerskens C.M. , Burrows M. , Witney A.G.
Published: January 2020

To understand brain function it is necessary to characterize both the underlying structural connectivity between neurons and the physiological integrity of these connections. Previous research exploring insect brain connectivity has used microscopy techniques, but this methodology is time consuming and cannot be applied to living animals and so cannot be used to understand dynamic physiological processes. The relatively large brain of the desert locust,Schistercera gregaria(Forksȧl) is ideal for exploring a novel methodology; diffusion magnetic resonance imaging (dMRI) for the characterization of neuronal connectivity in an insect brain. The diffusion-weighted imaging (DWI) data were acquired on a preclinical system using a customised multi-shell diffusion MRI scheme. Endogenous imaging contrasts from the averaged DWIs and Diffusion Kurtosis Imaging (DKI) scheme were applied to classify various anatomical features and diffusion patterns in neuropils, respectively. The application of micro-MRI and dMRI modelling to the locust brain provides a novel means of identifying anatomical regions and connectivity in an insect brain. Furthermore, quantitative imaging indices derived from the kurtosis model that include fractional anisotropy (FA), mean diffusivity (MD) and kurtosis anisotropy (KA) could, in future, be used to quantify longitudinal structural changes in neuronal connectivity due to environmental stressors or ageing.
Hydroxyl carlactone derivatives are predominant strigolactones inArabidopsis
Authors: Yoneyama Kaori , Akiyama Kohki , Brewer Philip B. , Mori Narumi , Kawada Miyuki , Haruta Shinsuke , Nishiwaki Hisashi , Yamauchi Satoshi , Xie Xiaonan , Umehara Mikihisa , Beveridge Christine A. , Yoneyama Koichi , Nomura Takahito
Published: January 2020

Strigolactones (SLs) regulate important aspects of plant growth and stress responses. Many diverse types of SL occur in plants, but a complete picture of biosynthesis remains unclear. InArabidopsis thaliana, we have demonstrated that MAX1, a cytochrome P450 monooxygenase, converts carlactone (CL) into carlactonoic acid (CLA), and that LBO, a 2-oxoglutarate-dependent dioxygenase, converts methyl carlactonoate (MeCLA) into a metabolite called [MeCLA+16] Da. In the present study, feeding experiments with deuterated MeCLAs revealed that [MeCLA+16] Da is hydroxymethyl carlactonoate (1’-HO-MeCLA). Importantly, this LBO metabolite was detected in plants. Interestingly, other related compounds, methyl 4-hydroxycarlactonoate (4-HO-MeCLA) and methyl 16-hydroxycarlactonoate (16-HO-MeCLA) were also found to accumulate inlbomutants. 3-HO-, 4-HO- and 16-HO-CL were detected in plants, but their expected corresponding metabolites, HO-CLAs, were absent inmax1mutants. These results suggest that HO-CL derivatives are predominant SLs inArabidopsis, produced through MAX1 and LBO.
Intra-striatal AAV2.retro administration leads to extensive retrograde transport in the rhesus macaque brain: implications for disease modeling and therapeutic development
Authors: Weiss Alison R. , Liguore William A. , Domire Jacqueline S. , Button Dana , McBride Jodi L.
Published: January 2020

Recently, AAV2.retro, a new capsid variant capable of efficient retrograde transport in brain, was generated in mice using a directed evolution approach. However, it remains unclear to what degree transport will be recapitulated in the substantially larger and more complex nonhuman primate (NHP) brain. Here, we compared the biodistribution of AAV2.retro with its parent serotype, AAV2, in adult macaques following delivery into the caudate and putamen, brain regions which comprise the striatum. While AAV2 transduction was primarily limited to the injected brain regions, AAV2.retro transduced cells in the striatum and in dozens of cortical and subcortical regions with known striatal afferents. We then evaluated the capability of AAV2.retro to deliver disease-related gene cargo to biologically-relevant NHP brain circuits by packaging a fragment of human mutantHTT, the causative gene mutation in Huntington’s disease. Following intra-striatal delivery, pathological mHTT-positive protein aggregates were distributed widely among cognitive, motor, and limbic cortico-basal ganglia circuits. Together, these studies demonstrate strong retrograde transport of AAV2.retro in NHP brain, highlight its utility in developing novel NHP models of brain disease and suggest its potential for querying circuit function and delivering therapeutic genes in the brain, particularly where treating dysfunctional circuits, versus single brain regions, is warranted.