bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Significance of Early Hospital Readmission in Continuous-Flow Left Ventricular Assist Device Patients
Authors: Kutyifa Valentina , Naqvi Syed Y. , Vidula Himabindu , Thomas Sabu , Sherazi Saadia , McNitt Scott , Alexis Jeffrey D.
Published: August 2019

Data on the clinical significance of early hospital readmission within 90 days following left ventricular assist device (LVAD) implantation in patients with continuous-flow LVAD are limited. We aimed to assess the incidence, predictors, and outcomes of 90-day readmission in LVAD patients. Hospital readmission or death was assessed within 90 days after hospital discharge in 177 patients with HeartMate II LVADs implanted between May 2008 and June 2014. Predictors of early readmission and risk of death were evaluated using multivariable Cox models following adjustment for clinical covariates. Hospital readmission or death rate was 37% within 90 days. Age at implantation (hazard ratio [HR] = 1.03 per 1 year increase, p = 0.016), diabetes (HR = 2.19, p = 0.031) and smoking at baseline (HR = 2.06, p = 0.034) predicted early hospital readmission, while a higher baseline body mass index was found to be protective (HR = 0.92 per each unit increase in body mass index, p = 0.003). One-year all-cause mortality was 19% in patients with early hospital readmission as compared to 1% with no early hospital readmission (HR 15.50, p = 0.01). One-year mortality was 35% in patients with 2 or more readmissions compared to 10% mortality in patients with one readmission and 1% mortality in patients with no readmissions (p < 0.001). In LVAD patients, there is a high incidence of hospital readmission within 90 days, which is associated with an increased mortality. Targeted interventions, such as closer follow-up to prevent early and recurrent hospital readmissions in LVAD recipients, are warranted to improve outcomes.
Volume Guaranteed Ventilation During Neonatal Transport*
Authors: Belteki Gusztav , Szell Andras , Lantos Lajos , Kovacs Gabor , Szanto Gyula , Berenyi Aniko , Szilagyi Monika , Liszkay Gabor , Kohalmi Ferenc , Morley Colin , Somogyvari Zsolt
Published: August 2019

Objectives:

To compare tidal volumes, inflating pressures and other ventilator variables of infants receiving synchronized intermitted mandatory ventilation with volume guarantee during emergency neonatal transport with those of infants receiving synchronized intermitted mandatory ventilation without volume guarantee.

Design:

Retrospective observational study.

Setting:

A regional neonatal emergency transport service.

Patients:

We enrolled 77 infants undergoing emergency neonatal transfer. Forty-five infants were ventilated with synchronized intermittent mandatory ventilation with volume guarantee and 32 with synchronized intermitted mandatory ventilation without volume guarantee.

Interventions:

Infants received synchronized intermitted mandatory ventilation with or without volume guarantee during interhospital emergency neonatal transport using a Fabian + nCPAP evolution neonatal ventilator (Software Version: 4.0.1; Acutronic Medical Instruments, Hirzel, Switzerland).

Measurements and Main Results:

We downloaded detailed ventilator data with 0.5 Hz sampling rate. We analyzed data with the Python computer language and its data science packages. The mean expiratory tidal volume of inflations was lower and less variable in infants ventilated with volume guarantee than in babies ventilated without volume guarantee (group median 4.8 vs 6.0 mL/kg; p = 0.001). Babies ventilated with synchronized intermittent mandatory ventilation with volume guarantee had on average lower and more variable peak inflating pressures than babies ventilated without volume guarantee (group median 15.5 vs 19.5 cm H2O;p = 0.0004). With volume guarantee, a lower proportion of the total minute ventilation was attributed to ventilator inflations rather than to spontaneous breaths between inflations (group median 66% vs 83%; p = 0.02). With volume guarantee, babies had fewer inflations with tidal volumes greater than 6 mL/kg and greater than 8 mL/kg (group medians 3% vs 44% and 0% vs 7%, respectively; p = 0.0001). The larger tidal volumes in the non-volume guarantee group were not associated with significant hypocapnia except in one case.

Conclusions:

During neonatal transport, synchronized intermittent mandatory ventilation with volume guarantee ventilation reduced the occurrence of excessive tidal volumes, but it was associated with larger contribution of spontaneous breaths to minute ventilation compared with synchronized intermitted mandatory ventilation without volume guarantee.
Interstitial Lung Disease: Update on the Role of Computed Tomography in the Diagnosis of Idiopathic Pulmonary Fibrosis
Authors: Chen Lucia , Halai Varsha , Leandru Andreea , Wallis Adam
Published: August 2019

Idiopathic pulmonary fibrosis is the commonest interstitial lung disease. Radiologists play an essential role in making an accurate diagnosis, and this is necessary given its prognostic implications and potential use of antifibrotic therapies. This review highlights the radiologic features and imaging classification of fibrosis with reference to recently updated international guidelines and emphasizing the importance of the multidisciplinary team in idiopathic pulmonary fibrosis diagnosis and, in particular, when pathological sampling is required.
Safety Profile of the New Harmonic Focus: Different Emissivity and Temperature Behavior Between the Active and the Inactive Blade
Authors: Latteri Saverio , Stella Giuseppe , Gueli Anna M. , Mazzaglia Stefania , Palumbo Valentina , Guastella Tommaso
Published: August 2019

Ultrasonic devices disperse less energy in the tissues. The new Harmonic Focus+ (HF+) seems to be more efficient but thermal damages have been reported. This study examined the temperature and the emissivity profile of the active and passive blades of the HF+, on a pig tissue model at different power settings. The FLIR System B series thermal imaging camera has been used on various biological pig tissues to evaluate the emissivity of the ultrasonic device. The active blade heats up faster than the passive one and the increase in power increases the speed of the temperature raising only on the active blade. Increasing the power setting reduces the dissection time and the temperature of both blades. Active blade temperatures of <60°C are obtained with cutting times close to 5 seconds; with these cutting times, the inactive blade does not exceed 30°C. The HF+ emissivity profiles demonstrate that the behavior of the inactive blade is significantly different from the active one. To prevent thermal damages, keep the active blade toward the operator, do not exceed 5 seconds of activation, use the maximum power, and avoid the use of the instrument as a dissector immediately after its activation.
Transcranial Magnetic Stimulation in Adults With Amblyopia
Authors: Tuna Ana Rita , Pinto Nuno , Brardo Francisco Miguel , Fernandes Andresa , Nunes Amélia Fernandes , Pato Maria Vaz
Published: August 2019

Background:

Through transcranial magnetic stimulation (TMS) it is possible to change cortical excitability of the visual cortex, and to influence binocular balance. The main goal of our study is to assess the effect of transcranial magnetic stimulation, specifically theta burst stimulation (TBS), in a group of amblyopic volunteers measuring several visual parameters: visual acuity, suppressive imbalance, and stereoacuity.

Methods:

Thirteen volunteers aged 19 to 24 years, randomly split in 2 groups, underwent 1 session of continuous TBS, stimulating the right occipital lobe. The first group with 8 volunteers was exposed to active stimulation with cTBS, and the other group with 5 volunteers was exposed to placebo stimulation.

Results:

Significant improvements in visual acuity, suppressive imbalance, and stereoacuity were found in the amblyopic eye after cTBS. The average value of amblyopia in visual acuity before stimulation was 0.32 ± 0.20 logMar and after cTBS was 0.19 ± 0.17 logMar. The mean value for the control group before placebo stimulation was 0.28 ± 0.17 and after placebo stimulation was 0.28 ± 0.16. The suppressive imbalance in the group of amblyope subjects stimulated before cTBS was 0.26 ± 0.18 and after was 0.12 ± 0.12; the suppressive imbalance of the control group before the placebo stimulation was 0.34 ± 0.37 and after was 0.32 ± 0.40.

Conclusions:

Visual acuity, suppressive imbalance, and stereoacuity had significant enhancements compared with baseline after cTBS over the right occipital lobe in an ambliopic population.
Distinct psychopathology profiles in patients with epileptic seizures compared to non-epileptic psychogenic seizures
Authors: Wang Albert D , Leong Michelle , Johnstone Benjamin , Rayner Genevieve , Kalincik Tomas , Roos Izanne , Kwan Patrick , O’Brien Terence J , Velakoulis Dennis , Malpas Charles B
Published: August 2019

Objective

Similarities in clinical presentations between epileptic seizures (ES) and psychogenic non-epileptic seizures (PNES) produces a risk of misdiagnosis. Video-EEG monitoring (VEM) is the diagnostic gold standard, but involves significant cost and time commitment, suggesting a need for efficient screening tools.

Methods

628 patients were recruited from an inpatient VEM unit; 293 patients with ES, 158 with PNES, 31 both ES and PNES, and 146 non-diagnostic. Patients completed the SCL-90-R, a standardised 90-item psychopathology instrument. Bayesian linear models were computed to investigate whether SCL-90-R domain scores or the overall psychopathology factorpdiffered between groups. Receiver operating characteristic (ROC) curves were computed to investigate the PNES classification accuracy of each domain score andp. A machine learning algorithm was also used to determine which subset of SCL-90-R items produced the greatest classification accuracy.

Results

Evidence was found for elevated scores in PNES compared to ES groups in the symptom domains of anxiety (b= 0.47, 95%HDI = [0.10, 0.80]), phobic anxiety (b= 1.32, 95%HDI = [0.98, 1.69]), somatisation (b= 0.84, 95%HDI = [0.49, 1.20]), and the general psychopathology factorp(b= 1.35, 95%HDI = [0.86, 1.82]). Of the SCL-90-R domain scores, somatisation produced the highest classification accuracy (AUC = 0.74, 95%CI = [0.69, 0.79]). The genetic algorithm produced a 6-item subset from the SCL-90-R, which produced comparable classification accuracy to the somatisation scores (AUC = 0.73, 95%CI = [0.64, 0.82]).

Significance

Compared to patients with ES, patients with PNES report greater symptoms of somatisation, general anxiety, and phobic anxiety against a background of generally elevated psychopathology. While self-reported psychopathology scores are not accurate enough for diagnosis in isolation, elevated psychopathology in these domains should raise the suspicion of PNES in clinical settings.
Evaluation of Patient-Level Retrieval from Electronic Health Record Data for a Cohort Discovery Task
Authors: Bedrick Steven D. , Cohen Aaron M. , Wang Yanshan , Wen Andrew , Liu Sijia , Liu Hongfang , Hersh William R.
Published: August 2019

Objective

Growing numbers of academic medical centers offer patient cohort discovery tools to their researchers, yet the performance of systems for this use case is not well-understood. The objective of this research was to assess patient-level information retrieval (IR) methods using electronic health records (EHR) for different types of cohort definition retrieval.

Materials and Methods

We developed a test collection consisting of about 100,000 patient records and 56 test topics that characterized patient cohort requests for various clinical studies. Automated IR tasks using word-based approaches were performed, varying four different parameters for a total of 48 permutations, with performance measured using B-Pref. We subsequently created structured Boolean queries for the 56 topics for performance comparisons. In addition, we performed a more detailed analysis of 10 topics.

Results

The best-performing word-based automated query parameter settings achieved a mean B-Pref of 0.167 across all 56 topics. The way a topic was structured (topic representation) had the largest impact on performance. Performance not only varied widely across topics, but there was also a large variance in sensitivity to parameter settings across the topics. Structured queries generally performed better than automated queries on measures of recall and precision, but were still not able to recall all relevant patients found by the automated queries.

Conclusion

While word-based automated methods of cohort retrieval offer an attractive solution to the labor-intensive nature of this task currently used at many medical centers, we generally found suboptimal performance in those approaches, with better performance obtained from structured Boolean queries. Insights gained in this preliminary analysis will help guide future work to develop new methods for patient-level cohort discovery with EHR data.
A modular neural network model of grasp movement generation
Authors: Michaels Jonathan A. , Schaffelhofer Stefan , Agudelo-Toro Andres , Scherberger Hansjörg
Published: August 2019

One of the primary ways we interact with the world is using our hands. In macaques, the circuit spanning the anterior intraparietal area, the hand area of the ventral premotor cortex, and the primary motor cortex is necessary for transforming visual information into grasping movements. We hypothesized that a recurrent neural network mimicking the multi-area structure of the anatomical circuit and using visual features to generate the required muscle dynamics to grasp objects would explain the neural and computational basis of the grasping circuit. Modular networks with object feature input and sparse inter-module connectivity outperformed other models at explaining neural data and the inter-area relationships present in the biological circuit, despite the absence of neural data during network training. Network dynamics were governed by simple rules, and targeted lesioning of modules produced deficits similar to those observed in lesion studies, providing a potential explanation for how grasping movements are generated.
A molecular cell atlas of the human lung from single cell RNA sequencing
Authors: Travaglini Kyle J. , Nabhan Ahmad N. , Penland Lolita , Sinha Rahul , Gillich Astrid , Sit Rene V. , Chang Stephen , Conley Stephanie D. , Mori Yasuo , Seita Jun , Berry Gerald J. , Shrager Joseph B. , Metzger Ross J. , Kuo Christin S. , Neff Norma , Weissman Irving L. , Quake Stephen R. , Krasnow Mark A.
Published: August 2019

Although single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing applied to ∼75,000 human lung and blood cells, combined with a multi-pronged cell annotation approach, which have allowed us to define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 of 45 previously known cell types or subtypes and 14 new ones. This comprehensive molecular atlas elucidates the biochemical functions of lung cell types and the cell-selective transcription factors and optimal markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signaling interactions including sources and targets of chemokines in immune cell trafficking and expression changes on lung homing; and identifies the cell types directly affected by lung disease genes and respiratory viruses. Comparison to mouse identified 17 molecular types that appear to have been gained or lost during lung evolution and others whose expression profiles have been substantially altered, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution.
Preparation of DPPC liposomes using probe-tip sonication: investigating intrinsic factors affecting temperature phase transitions
Authors: Rieth Monica D. , Lozano Andrew
Published: August 2019

Liposomes are an important tool and have gained much attention for their promise as an effective means of delivering small therapeutic compounds to targeted sites. In an effort to establish an effective method to produce liposomes from the lipid, dipalmitoyl-phosphatidylcholine or DPPC, we have found important aspects that must be taken into consideration. Here, we used probe-tip sonication to prepare liposomes on a batch scale. During this process we uncovered interesting steps in their preparation that altered the thermodynamic properties and phase transitions of the resulting liposome mixtures. Using differential scanning calorimetry to assess this we found that increasing the sonication time had the most dramatic effect on our sample, producing almost an entirely separate phase transition relative to the main phase transition. This result is consistent with reports from the current literature. We also highlight a smaller transition, which we attribute to traces of unincorporated lipid that seems to gradually disappear as the total lipid concentration decreases. Overall, sonication is an effective means of producing liposomes, but we cannot assert this method is optimal in producing them with precise physical properties. Here we highlight the physical effects at play during this process.
Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of matched stool and colon biopsy samples
Authors: Mas-Lloret Joan , Obón-Santacana Mireia , Ibáñez-Sanz Gemma , Guinó Elisabet , Pato Miguel L , Rodriguez-Moranta Francisco , Mata Alfredo , García-Rodríguez Ana , Moreno Victor , Pimenoff Ville Nikolai
Published: August 2019

The gut microbiome has a fundamental role in human health and disease. However, studying the complex structure and function of the gut microbiome using next generation sequencing is challenging and prone to reproducibility problems due to the heterogeneity of sample sets. Here, we obtained cross-sectional colon biopsies and faecal samples from nine participants in our COLSCREEN study and sequenced them in high coverage using Illumina pair-end shotgun (for faecal samples) and IonTorrent 16S (for paired feces and colon biopsies) technologies. The metagenomes consisted of between 47 and 92 million reads per sample and the targeted sequencing covered more than 300K reads per sample across seven hypervariable regions of the 16S gene. Our data is freely available and coupled with code for the presented metagenomic analysis using up-to-date bioinformatics algorithms. These results will add up to the informed insights into designing comprehensive microbiome analysis and also provide data for further testing for unambiguous gut microbiome analysis.
BiasDB: A Comprehensive Database for Biased GPCR Ligands
Authors: Omieczynski Christian , Nguyen Trung Ngoc , Sribar Dora , Deng Lihua , Stepanov Dmitri , Schaller David , Wolber Gerhard , Bermudez Marcel
Published: August 2019

G protein-coupled receptors transmit signals across membranes via interaction with intracellular binding partners. While there is an imprinted signaling profile for each receptor, biased ligands are able to shift intracellular pathways resulting in different recruitment profiles. We present the first comprehensive database of all literature-known biased ligands as a resource for medicinal chemistry and pharmacology. In addition to careful manual curation, we provide an analysis of the data. BiasDB is available at https://biasdb.drug-design.de/.
Wheat inositol pyrophosphate kinase TaVIH2-3B modulates cell-wall composition for drought tolerance in Arabidopsis
Authors: Shukla Anuj , Kaur Mandeep , Kanwar Swati , Kaur Gazaldeep , Sharma Shivani , Ganguli Shubhra , Kumari Vandana , Mazumder Koushik , Pandey Pratima , Rouached Hatem , Rishi Vikas , Bhandari Rashna , Pandey Ajay K
Published: August 2019

Background

Inositol pyrophosphates (PP-InsPs) are high-energy cellular molecules involved in different signalling and regulatory responses. Two distinct classes of inositol phosphate kinases responsible for the synthesis of PP-InsPs have been identified in Arabidopsis i.e. ITPKinase (inositol 1,3,4 trisphosphate 5/6 kinase) and PP-IP5Kinase (diphosphoinositol pentakisphosphate kinases). Plant PP-IP5Ks are capable of synthesizing InsP8 and were shown to control pathogenic defence and phosphate response signals. However, other roles offered by plant PP-IP5Ks, especially towards abiotic stress, remain poorly understood.

Results

Here, we characterized two Triticum aestivum L. (hexaploid wheat) PPIP5K homologs, TaVIH1 and TaVIH2, for their physiological functions. We demonstrated that wheat VIH proteins could utilize InsP7 as the substrate to produce InsP8, a process that requires the functional VIH-kinase domains. At the transcriptional level, both TaVIH1 and TaVIH2 are expressed in different wheat tissues, including developing grains, but show selective response to abiotic stresses during drought-mimic experiments. Overexpression of TaVIH2-3B homolog in Arabidopsis conferred tolerance to drought stress and rescued the sensitivity of Atvih2 mutants. RNAseq analysis of TaVIH2-3B transgenic lines of Arabidopsis showed a genome-wide reprogramming with remarkable effects on cell-wall biosynthesis genes with enhanced the accumulation of polysaccharides (arabinogalactan, cellulose and arabinoxylan).

Conclusions

Overall, this work identifies a novel function of VIH proteins, implying their roles in modulating cell-wall homeostasis genes and providing water-deficit stress tolerance. This work suggests that the plant VIH enzymes could be linked to drought tolerance and also opens up investigations to address the roles of plant VIH derived products in generating drought resistant plants.
Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations
Authors: Wang Jinan , Alekseenko Andrey , Kozakov Dima , Miao Yinglong
Published: August 2019

Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play a key role in cellular signaling, protein trafficking, immunology and oncology. However, it is challenging to predict peptide-protein binding with conventional computational modeling approaches, due to slow dynamics and high peptide flexibility. Here, we present a prototype of the approach which combines global peptide docking using ClusPro PeptiDock and all-atom enhanced simulations using Gaussian accelerated molecular dynamics (GaMD). For three distinct model peptides, the lowest backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures obtained from PeptiDock were 3.3 Å – 4.8 Å, being medium quality predictions according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. GaMD simulations refined the peptide-protein complex structures with significantly reduced peptide backbone RMSDs of 0.6 Å – 2.7 Å, yielding two high quality (sub-angstrom) and one medium quality models. Furthermore, the GaMD simulations identified important low-energy conformational states and revealed the mechanism of peptide binding to the target proteins. Therefore, PeptiDock+GaMD is a promising approach for exploring peptide-protein interactions.
MACF1 Facilitates SMAD7 Nuclear Translocation to Drive Bone Formation in Mice
Authors: Zhao Fan , Ma Xiaoli , Qiu Wuxia , Wang Pai , Zhang Ru , Chen Zhihao , Su Peihong , Zhang Yan , Li Dijie , Ma Jianhua , Yang Chaofei , Chen Lei , Yin Chong , Tian Ye , Hu Lifang , Li Yu , Zhang Ge , Wu Xiaoyang , Qian Airong
Published: August 2019

MACF1 is a large crosslinker that contributes to cytoskeleton integrity and cell differentiation. Loss of MACF1 impairs multiple cellular functions in neuron development and epidermal migration, and is the molecular basis for many diseases such as heart failure and Parkinson’s disease. MACF1 is highly abundant in bones, however, its involvements in osteogenic differentiation and bone formation are still unknown. In this study, by conditional gene targeting to delete the Macf1 gene specifically in MSCs, we observed ossification retardation and bone loss in MACF1 deficient mice in different developmental stages, which we traced to disorganized cytoskeleton and decreased osteogenic differentiation capability in MSCs. Further, we show that MACF1 interacts and facilitates SMAD7 nuclear translocation to initiate downstream transcription. These findings are hopefully to expand the biological scope of MACF1 in bones, and provide experimental basis for targeting MACF1 in degenerative bone diseases such as osteoporosis.
Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front
Authors: Schürch Christian M. , Bhate Salil S. , Barlow Graham L. , Phillips Darci J. , Noti Luca , Zlobec Inti , Chu Pauline , Black Sarah , Demeter Janos , McIlwain David R. , Samusik Nikolay , Goltsev Yury , Nolan Garry P.
Published: August 2019

Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this coordinated behavior in effective versus ineffective tumor control will advance immunotherapies. We optimized CO-Detection by indEXing (CODEX) for para ffin-em bedded tissue microarrays, enabling profiling of 140 tissue regions from 35 advanced-stage colorectal cancer (CRC) patients with 56 protein markers simultaneously. We identified nine conserved, distinct cellular neighborhoods (CNs)–a collection of components characteristic of the CRC iTME. Enrichment of PD-1+CD4+T cells only within a granulocyte CN positively correlated with survival in a high-risk patient subset. Coupling of tumor and immune CNs, fragmentation of T cell and macrophage CNs, and disruption of inter-CN communication was associated with inferior outcomes. This study provides a framework for interrogating complex biological processes, such as antitumoral immunity, demonstrating an example of how tumors can disrupt imm une functionality through interference in the concerted action of cells and spatial domains.
Cytokinin fluoroprobe and receptor CRE1/AHK4 localize to both plasma membrane and endoplasmic reticulum
Authors: Kubiasová Karolina , Montesinos Juan Carlos , Šamajová Olga , Nisler Jaroslav , Mik Václav , Plíhalová Lucie , Novák Ondřej , Marhavý Peter , Zalabák David , Berka Karel , Doležal Karel , Galuszka Petr , Šamaj Jozef , Strnad Miroslav , Benková Eva , Plíhal Ondřej , Spíchal Lukáš
Published: August 2019

The plant hormone cytokinin regulates various cell and developmental processes, including cell division and differentiation, embryogenesis, activity of shoot and root apical meristems, formation of shoot and root lateral organs and others 1. Cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Based on the subcellular localization of cytokinin receptors in various transient expression systems, such as tobacco leaf epidermal cells, and membrane fractionation experiments of Arabidopsis and maize, the endoplasmic reticulum (ER) membrane has been proposed as a principal hormone perception site 2–4. Intriguingly, recent study of the cytokinin transporter PUP14 has pointed out that the plasma membrane (PM)-mediated signalling might play an important role in establishment of cytokinin response gradients in various plant organs 5. However, localization of cytokinin HK receptors to the PM, although initially suggested 6, remains ambiguous. Here, by monitoring subcellular localizations of the fluorescently labelled natural cytokinin probe iP-NBD 7 and the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin fluoroprobes and receptors can enter the secretory pathway and reach the PM. We demonstrate that in cells of the root apical meristem, CRE1/AHK4 localizes to the PM and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. Our results provide a new perspective on cytokinin signalling and the possibility of multiple sites of perception at PM and ER, which may determine specific outputs of cytokinin signalling.
Winner(s)-take-all: nonlinear amplification of DNA-encoded library
Authors: Cui Meiying , Reddavide Francesco , Heiden Stephan , Mannocci Luca , Thompson Michael , Zhang Yixin
Published: August 2019

Information processing functions are essential for biological organisms to perceive and react to their complex enviornment, as well as for human to analyze and rationalize them. While our brain has an extraordinary power to process complex information, winner(s)-take-all computation is one of the simplest models of lateral inhibition and competition among biological neurons. It has been implemented as DNA-based neural networks, for example, to mimic pattern recognition. However, the utility of DNA-based computation in information processing for real biotechnological applications remains to be demonstrated. In this paper, we developed a winner(s)-take-all method for non-linear amplification of mixtures of DNA sequences. Unlike conventional biological experiments, selected species were not directly subjected to analysis. Instead, parallel computation among myriad of different DNA sequences was carried out with a neural network-inspired winner-take-all function, to reduce the information complexity. The method could be used for various oligonucleotide-encoded libraries, as we have demonstrated its application in decoding and data analysis for selection experiment with DNA-encoded chemical library against protein target.
Guanidine hydrochloride reactivates an ancient septin hetero-oligomer assembly pathway in budding yeast
Authors: Johnson Courtney R. , Steingesser Marc G. , Weems Andrew D. , Khan Anum , Gladfelter Amy , Bertin Aurélie , McMurray Michael A.
Published: August 2019

Septin proteins co-assemble into hetero-oligomers that polymerize into cytoskeletal filaments with a variety of cellular functions. InSaccharomyces cerevisiae, where septins were first discovered, five subunits comprise two species of septin hetero-octamers, Cdc11/Shs1–Cdc12–Cdc3–Cdc10– Cdc10–Cdc3–Cdc12–Cdc11/Shs1. Septins evolved from ancestral GTPases. We previously found evidence that slow GTPase activity by Cdc12 directs the choice of incorporation of Cdc11 vs Shs1 into septin complexes. It was unclear why many septins, including Cdc3, lack GTPase activity. We serendipitously discovered that the small molecule guanidine hydrochloride (GdnHCl) rescues septin function incdc10mutants by promoting assembly of non-native Cdc11/Shs1–Cdc12–Cdc3– Cdc3–Cdc12–Cdc11/Shs1 hexamers. We provide evidence that inS. cerevisiaeCdc3 guanidinium ion (Gdm) occupies the site of a “missing” Arg sidechain that is present in other fungal species in which (i) the Cdc3 subunit is an active GTPase and (ii) Cdc10-less hexamers co-exist with octamers in wild-type cells. These findings support a model in which Gdm reactivates a latent septin assembly pathway that was suppressed during fungal evolution in order to restrict assembly to hetero-octamers. Given that septin hexamers made natively in human cells also exclude Cdc10-like central subunits via homodimerization of an active GTPase, our results provide new mechanistic details that likely apply to septin assembly throughout phylogeny.
Succession of bacterial communities on carrion is independent of vertebrate scavengers
Authors: Dangerfield Cody R. , Frehner Ethan , Buechley Evan , Şekercioğlu Çağan H. , Brazelton William J.
Published: August 2019

The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by scavenging.
Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication
Authors: Pollak Bernardo , Matute Tamara , Nuñez Isaac , Cerda Ariel , Lopez Constanza , Vargas Valentina , Kan Anton , Bielinski Vincent , von Dassow Peter , Dupont Chris L. , Federici Fernán
Published: August 2019

Standardised Type IIS DNA assembly methods are becoming essential for biological engineering and research. Although a ‘common syntax’ has been proposed to enable higher interoperability between DNA libraries, Golden Gate (GG)-based assembly systems remain specific to target organisms. Furthermore, these GG assembly systems become laborious and unnecessarily complicated beyond the assembly of 4 transcriptional units. Here, we describe “universal Loop” (uLoop) assembly, a simple system based on Loop assembly that enables hierarchical fabrication of large DNA constructs (> 30 kb) for any organism of choice. uLoop comprises two sets of four plasmids that are iteratively used as odd and even levels to compile DNA elements in an exponential manner (4n-1). The elements required for transformation/maintenance in target organisms are also assembled as standardised parts, enabling customisation of host-specific plasmids. Thus, this species-agnostic method decouples efficiency of assembly from the stability of vectors in the target organism. As a proof-of-concept, we show the engineering of multi-gene expression vectors in diatoms, yeast, plants and bacteria. These resources will become available through the OpenMTA for unrestricted sharing and open-access.

Abstract Figure
PAG neurons encode a simplified action-selective signal during aggression
Authors: Falkner Annegret L. , Wei Dongyu , Song Anjeli , Watsek Li W. , Chen Irene , Feng James E. , Lin Dayu
Published: August 2019

While the ventromedial hypothalamus, ventrolateral area (VMHvl) is now well established as a critical locus for the generation of conspecific aggression, its role is complex, with populations of neurons responding during the motivational, sensory, and action phases of aggression, and also during social interactions with the opposite sex. It has been previously unclear how the brain uses this complex multidimensional signal and generates a discrete action: the attack. Here we find that the largest posterior target of the VMHvl, the lateral periaqueductal gray (lPAG) encodes a simplified attack-selective signal during aggression. Single units in the lPAG exhibit greater selectivity for the attack action during aggression than VMHvl neurons and a subpopulation of neurons in the PAG exhibit short-latency, time-locked spiking relative to the activity of jaw muscles for biting during attack. In addition, channelrhodopsin assisted circuit mapping reveals a preferential projection from VMHvl glutamatergic cells to lPAG glutamatergic cells. Using projection-specific fiber photometry, we find that this excitatory projection conveys male-biased signals from the VMHvl to downstream glutamatergic PAG neurons that integrate ongoing male-related activity over several seconds, which suggests that action-selectivity is generated by a combination of both pre and postsynaptic filtering mechanisms.
Longitudinal bioluminescent imaging of HIV-1 infection during antiretroviral therapy and treatment interruption in humanized mice
Authors: Ventura John D. , Beloor Jagadish , Allen Edward , Zhang Tongyu , Haugh Kelsey A. , Uchil Pradeep D. , Ochsenbauer Christina , Kieffer Collin , Kumar Priti , Hope Thomas J. , Mothes Walther
Published: August 2019

Non-invasive bioluminescent imaging (NIBLI) of HIV-1 infection dynamics allows for real-time monitoring of viral spread and the localization of infected cell populations in living animals. In this report, we describe full-length replication-competent GFP and Nanoluciferase (Nluc) expressing HIV-1 reporter viruses from two clinical transmitted / founder (T/F) stains: TRJO.c and Q23.BG505. By infecting humanized mice with these HIV-1 T/F reporter viruses, we were able to directly monitor longitudinal viral spread at whole-animal resolution via NIBLI at a sensitivity of as few as 30-50 infected cells. Bioluminescent signal strongly correlated with HIV-1 infection and responded proportionally to virus suppression in vivo in animals treated daily with a combination antiretroviral therapy (cART) regimen. Longitudinal NIBLI following cART withdrawal visualized tissue-sites that harbored virus during infection recrudescence. Notably, we observed rebounding infection in the same lymphoid tissues where infection was first observed prior to ART treatment. Our work demonstrates the utility of our system for studying in vivo viral infection dynamics and identifying infected tissue regions for subsequent analyses.

Author Summary

Non-invasive bioluminescent imaging (NIBLI) in small animals allows for in vivo longitudinal imaging of infection spread and pathogenesis. We have taken advantage of the small luciferase reporter protein, Nanoluciferase (Nluc), to generate a replication-competent HIV-1 reporter virus to allow for NIBLI of viral infection in humanize mice. NIBLI via Nluc enabled us to directly visualize longitudinal spreading patterns before, during, and after interruption of daily doses of combined antiretroviral therapy (cART). We observed that rebounding infection often emerged in tissue regions originally associated with infected cells prior to cART treatment. Thus, Nluc-based NIBLI of HIV-1 infection can be used as an experimental tool to study early events involved in viral dissemination and spread from initial sites of infection to draining lymphoid tissues as well as locate infected tissues for subsequent cellular characterization of HIV-1 infected cells.
Spectroscopy and Machine Learning Based Rapid Point-of-Care Assessment of Core Needle Cancer Biopsies
Authors: Keshavamurthy Krishna Nand , Dylov Dmitry V. , Yazdanfar Siavash , Patel Dharam , Silk Tarik , Silk Mikhail , Jacques Frederick , Petre Elena N , Gonen Mithat , Rekhtman Natasha , Ostroverkhov Victor , Scher Howard I. , Solomon Stephen B. , Durack Jeremy C.
Published: August 2019

Solid tumor needle biopsies are essential to confirm malignancy and assess for actionable characteristics or genetic alterations to guide treatment selection. Ensuring that sufficient and suitable material is acquired for tumor profiling, while minimizing patient risk, remains a critical unmet need. Here, we evaluated the performance characteristics of transmission optical spectroscopy for rapid identification of malignant tissue in core needle biopsies (CNB). Human kidney biopsy specimens (545 CNB from 102 patients, 5583 spectra for analysis) were analyzed directly on core biopsy needles with a custom-built optical spectroscopy instrument. Machine learning classifiers were trained to differentiate malignant from normal tissue spectra. Classifiers were compared using receiver operating characteristics analysis and sensitivity and specificity were calculated relative to a histopathologic gold standard. The best performing algorithm was the random forest (sensitivity 96% and 93%, specificity 90% and 93% at the level of individual spectra and full CNB, respectively).Ex-vivospectroscopy paired with machine learning paves the way towards rapid and accurate characterization of CNB at the time of tissue acquisition and improving tumor biopsy quality.
Insight into the resistome and quorum sensing system of a divergent Acinetobacter pittii isolate from an untouched site of the Lechuguilla Cave
Authors: Gan Han Ming , Wengert Peter , Barton Hazel A. , Hudson André O. , Savka Michael A.
Published: August 2019

Acinetobacter are Gram-negative bacteria belonging to the sub-phyla Gammaproteobacteria, commonly associated with soils, animal feeds and water. Some members of the Acinetobacter have been implicated in hospital-acquired infections, with broad-spectrum antibiotic resistance. Here we report the whole genome sequence of LC510, an Acinetobacter species isolated from deep within a pristine location of the Lechuguilla Cave. Pairwise nucleotide comparison to three type strains within the genus Acinetobacter assigned LC510 as an Acinetobacter pittii isolate. Scanning of the LC510 genome identified two genes coding for β-lactamase resistance, despite the fact that LC510 was isolated from a portion of the cave not previously visited by humans and protected from anthropogenic input. The ability to produce acyl-homoserine lactone (AHL) signal in culture medium, an observation that is consistent with the identification of the luxI and luxR homologs in its genome, suggests that cell-to-cell communication remains important in an isolated cave ecosystem.
METTL2 forms a complex with the DALRD3 anticodon-domain binding protein to catalyze formation of 3-methylcytosine in specific arginine tRNA isoacceptors
Authors: Lentini Jenna M. , Fu Dragony
Published: August 2019

In mammals, a subset of arginine tRNA isoacceptors are methylated in the anticodon loop by the METTL2 methyltransferase to form the 3-methylcytosine (m3C) modification. However, the mechanism by which METTL2 identifies specific arginine tRNAs for m3C formation as well as the biological role of m3C in mammals is unknown. Here, we show that human METTL2 forms a complex with DALR anticodon binding domain containing 3 (DALRD3) protein in order to recognize particular arginine tRNAs destined for m3C modification. Using biochemical reconstitution, we find that METTL2-DALDR3 complexes catalyze m3C formationin vitrothat is dependent upon sequence elements specific to certain arginine tRNAs. Notably, DALRD3-deficient human cells exhibit nearly complete loss of the m3C modification in arginine tRNAs. These findings uncover an unexpected function for the DALRD3 protein in the targeting of distinct arginine tRNAs for m3C modification.
The loss of ATRX/DAXX complex disturbs rDNA heterochromatinization and promotes development of glioma
Authors: Cheng XiangRong , Jiang Qi , Hu XingLin , Huang XingWei , Hui Liu , Wei YanJun , Li Na , Wang Nan , Shen JingLing , Zhang Yan , Lei Lei
Published: August 2019

Background

Ribosomal DNA (rDNA) transcription by the RNA polymerase I (Pol I) is a rate-limited step for ribosome synthesis, which is critical for cell growth, cell differentiation, and tumorigenesis. Meanwhile rDNA transcription is modulated by DNA methylation and histone epigenetic modification. Though with great progress in epigenetic research recently, it still remains much uncertain about the relationship of histone variant epigenetic modification and rDNA transcription.

Results

In this study, epigenetic profiles of silent rDNA in next-generation sequencing datasets were examined. We found that the chaperone of histone variant H3.3, the alpha-thalassemia/mental retardation X-linked syndrome protein (ATRX)/death domain-associated protein (DAXX) complex, and methyltransferase SET domain bifurcated 1 (Setdb1, also known as ESET) help maintain H3.3K9me3 modifications among the promoter and coding regions of silent rDNA. Our experiments further confirmed that DAXX depletion leads to the conversion of silent rDNA into upstream binding factor-bound active rDNA and the release of rDNA transcriptional potency. Support for this model is provided by data from a low-grade glioma in which ATRX is lost and a higher level of ribosomal biosynthesis, nucleolus activity, and proliferation are observed.

Conclusions

We demonstrate a model of epigenetic regulation for rDNA with roles for the ATRX/DAXX complex and H3.3/H3K9me3 modifications identified. Thus, loss of ATRX/DAXX may represent a driving force for tumorigenesis due to its contribution to the release of rDNA transcriptional potency.
A machine learning approach to identifying objective biomarkers of anxiety and stress
Authors: Ramakrishnan Arjun , Pardes Adam , Lynch William , Molaro Christopher , Platt Michael Louis
Published: August 2019

Anxiety and stress-related disorders are highly prevalent and debilitating conditions that impose an enormous burden on society. Sensitive measurements that can enable early diagnosis could mitigate suffering and potentially prevent onset of these conditions. Self-reports, however, are intrusive and vulnerable to biases that can conceal the true internal state. Physiological responses, on the other hand, manifest spontaneously and can be monitored continuously, providing potential objective biomarkers for anxiety and stress. Recent studies have shown that algorithms trained on physiological measurements can predict stress states with high accuracy. Whether these predictive algorithms generalize to untested situations and participants, however, remains unclear. Further, whether biomarkers of momentary stress indicate trait anxiety – a vulnerability foreshadowing development of anxiety and mood disorders – remains unknown. To address these gaps, we monitored skin conductance, heart rate, heart rate variability and EEG in 39 participants experiencing physical and social stress and compared these measures to non-stressful periods of talking, rest, and playing a simple video game. Self-report measures were obtained periodically throughout the experiment. A support vector machine trained on physiological measurements identified stress conditions with ~96% accuracy. A decision tree that optimally combined physiological and self-report measures identified individuals with high trait anxiety with ~84% accuracy. Individuals with high trait anxiety also displayed high baseline state anxiety but a muted physiological response to acute stressors. Overall, these results demonstrate the potential for using machine learning tools to identify objective biomarkers useful for diagnosing and monitoring mental health conditions like anxiety and depression.