bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual Plasma Sampling Method to Determine the Hepatic and Renal Clearance of the 2 Diastereoisomers of Gd-EOB-DTPA
Authors: Yuan Xiaodong , Wang Su , Shi Wenwei , Cai Yu , Chen Yingxin , Chen Ming , Peng Yanghong , Ao Guokun 
Published: January 2020

Objectives
The aim of this study was to develop a method to determine hepatic and renal clearance of the 2 diastereoisomers (Gd-A, Gd-B) of Gd-EOB-DTPA separately.

Materials and Methods
Between July 2017 and February 2018, 41 patients with hepatic disease were prospectively included. For each patient, 1 mL of iopromide (to determine glomerular filtration rate [GFR]) was coadministered with Gd-EOB-DTPA (Gd-A and Gd-B; 65:35 wt/wt). The plasma clearances of Gd-A (PCL-GdA) and Gd-B (PCL-GdB) as well as the iopromide (GFR) were generated by using dual plasma sampling method. Meanwhile, the patient's urine was collected for measurement of renal clearance of Gd-A (RCL-GdA) and Gd-B (RCL-GdB) to confirm its agreement with GFR. Hepatic clearances of Gd-A (HCL-GdA) and Gd-B (HCL-GdB) were calculated by subtracting the GFR from PCL-GdA and PCL-GdB, respectively, and were correlated with indocyanine green (ICG) 15 minutes retention rate (ICG R15). Pharmacokinetic parameters were compared between the two isomers and between Child–Pugh classifications using student’s t test.

Results
Within the group of 41 patients evaluated, both RCL-GdA and RCL-GdB demonstrated a good correlation and agreement to GFR (statistics shown in the main body). HCL-GdA demonstrated a strong negative correlation (r = −0.86, P < 0.001) with ICG R15 and was much higher than HCL-GdB (116.18 ± 75.48 vs 19.74 ± 14.24 mL/min, P < 0.001). HCL-GdB demonstrated a weak correlation (r = −0.26, P = 0.102) with ICG R15. HCL-GdA of noncirrhosis and Child-Pugh class A (151.74 ± 68.28 mL/min, n = 26) was higher than that of Child-Pugh class B (54.54 ± 39.13 mL/min, n = 15; P = 0.001).

Conclusions
A practical method was established for the determination of hepatic and renal clearance of the 2 isomers of Gd-EOB-DTPA. The 2 isomers have equal renal clearance and different hepatic clearance. The HCL-GdA may serve as a novel marker to reflect liver function reserve.
Access to Multidisciplinary Care for Patients With 22q11.2 Deletion Syndrome: Identifying Breakdowns in the Screening Process
Authors: Abu-Ghname Amjed , Perdanasari Aurelia T. , Raj Sarth , Seema Jain , Wilson Kristina D. , Maricevich Renata S. 
Published: January 2020

Abstract
The 22q11.2 deletion syndrome affects approximately 1 in 4000 live births and involves cardiac defects, immunodeficiency, and endocrine disruption. The complexity of diagnosis and multifaceted care often leads to fragmented management in the short and long term. With the purpose of developing an effective multidisciplinary program, the authors aimed to identify the deficiencies in current screening and referral processes among the teams required in the care for patients with 22q11.2 deletion syndrome. A retrospective chart review was conducted at our institution between 2001 and 2016. Patients with confirmed 22q11.2 deletion diagnoses between the ages of 0 and 28 were included. A list of 15 relevant specialties that should evaluate patients with 22q11.2 deletion syndrome was created according to established guidelines. Patient medical and demographic information were collected and analyzed. A total of 270 patients were included. Mean age at diagnosis was 3.3 years. On average, patients visited 6 of 15 departments (1–14). Only 8.8% of patients visited >10 specialties. The majority were seen by Cardiology, Allergy and Immunology, Genetics, and Speech (57.4–87.8%). A minority were seen by Hematology and Oncology, Sleep Therapy, and Physical Therapy (13.3–16.3%). Only 34.1% encountered plastic surgery. Negative correlation (−0.128; P = 0.035) was demonstrated between patients’ age at diagnosis and number of specialty teams encountered. This study highlights the current underutilization of services required to manage patients with 22q11.2 deletion syndrome. While screening guidelines have been established, implementation can be challenging as it requires efficient care coordination between teams. Moving forward, the authors believe that a multidisciplinary clinical approach to streamline patient care is necessary.
Effect of light and darkness on the growth and development of downy mildew pathogenHyaloperonospora arabidopsidis
Authors: Telli Osman , Jimenez-Quiros Catherine , McDowell John M. , Tör Mahmut 
Published: January 2020

SummaryDisease development in plants requires a susceptible host, a virulent pathogen, and a favourable environment. Oomycete pathogens cause many important diseases and have evolved sophisticated molecular mechanisms to manipulate their hosts. Day length has been shown to impact plant-oomycete interactions but a need exists for a tractable reference system to understand the mechanistic interplay between light regulation, oomycete pathogen virulence, and plant host immunity. Here we present data demonstrating that light is a critical factor in the interaction betweenArabidopsis thalianaand its naturally occurring downy mildew pathogenHyaloperonospora arabidopsidis(Hpa). We investigated the role of light on spore germination, mycelium development, sporulation and oospore formation ofHpa, along with defence responses in the host. We observed abundantHpasporulation on compatible Arabidopsis under day lengths ranging from 10 to 14 hours. Contrastingly, exposure to constant light or constant dark suppressed sporulation. Exposure to constant dark suppressed spore germination, mycelial development and oospore formation. Interestingly, exposure to constant light stimulated spore germination, mycelial development and oospore formation. A biomarker of plant immune system activation was induced under both constant light and constant dark. Altogether, these findings demonstrate thatHpahas the molecular mechanisms to perceive and respond to light and that both the host and pathogen responses are influenced by the light regime. Therefore, this pathosystem can be used for investigations to understand the molecular mechanisms through which oomycete pathogens likeHpaperceive and integrate light signals, and how light influences pathogen virulence and host immunity during their interactions.
RECAS9: Recombining wild species introgression via mitotic gene editing in barley
Authors: Lazar Shelly , Prusty Manas Ranjan , Bishara Khaled , Sherman Amir , Fridman Eyal 
Published: January 2020

AbstractGenetic loci underlying variation in traits with agronomic importance or genetic risk factors in human diseases have been identified by linkage analysis and genome-wide association studies. However, narrowing down the mapping to the individual causal genes and variations within these is much more challenging, and so is the ability to break linkage drag between beneficial and unfavourable loci in crop breeding. We developed RECAS9 as a transgene-free approach for precisely targeting recombination events by delivering CRISPR/Cas9 ribonucleotide protein (RNP) complex into heterozygous mitotic cells for the barley (Hordeum vulgare)Heat3.1locus. A wild species (H. spontaneum) introgression in this region carries the agronomical unfavourable toughrachisphenotype (non-brittle) allele linked with a circadian clock accelerating QTL near GIGANTEA gene. We delivered RNP, which was targeted between two single nucleotide polymorphism (SNPs), to mitotic calli cells by particle bombardment. We estimated recombination events by next generation sequencing (NGS) and droplet digital PCR (ddPCR). While NGS analysis grieved from confounding effects of PCR recombination, ddPCR analysis allowed us to associate RNP treatment on heterozygous individuals with significant increase of homologous directed repair (HDR) between cultivated and wild alleles, with recombination rate ranging between zero to 57%. These results show for the first time in plants a directed and transgene free mitotic recombination driven by Cas9 RNP, and provide a starting point for precise breeding and fine scale mapping of beneficial alleles from crop wild relatives.
Macroevolutionary analysis of discrete character evolution using parsimony-informed likelihood
Authors: Grundler Michael C. , Rabosky Daniel L. 
Published: January 2020

AbstractRates of character evolution in macroevolutionary datasets are typically estimated by maximizing the likelihood function of a continuous-time Markov chain (CTMC) model of character evolution over all possible histories of character state change, a technique known as maximum average likelihood. An alternative approach is to estimate ancestral character states independently of rates using parsimony and to then condition likelihood-based estimates of transition rates on the resulting ancestor-descendant reconstructions. We use maximum parsimony reconstructions of possible pathways of evolution to implement this alternative approach for single-character datasets simulated on empirical phylogenies using a two-state CTMC. We find that transition rates estimated using parsimonious ancestor-descendant reconstructions have lower mean squared error than transition rates estimated by maximum average likelihood. Although we use a binary state character for exposition, the approach remains valid for an arbitrary number of states. Finally, we show how this method can be used to rapidly and easily detect phylogenetic variation in tempo and mode of character evolution with two empirical examples from squamates. These results highlight the mutually informative roles of parsimony and likelihood when testing hypotheses of character evolution in macroevolution.
Role of DNA Methylation in Persister Formation in UropathogenicE. coli
Authors: Xu Yuanyuan , Liu Shuang , Zhang Ying , Zhang Wenhong 
Published: January 2020

AbstractUropathogenicEscherichia coli(UPEC) persister bacteria play crucial roles in clinical treatment failure and relapse. DNA methylation is known to regulate gene expression in bacteria, but its role in persister formation has not been investigated. Here, we created adenine methylation deletion mutant (Δdam) and cytosine methylation mutant (Δdcm) from UPEC strain UTI89 and found that theΔdammutant but notΔdcmmutant had significant defect in persister formation during exposure to various antibiotics (gentamicin, fluroquinolones and cephalosporin) and stresses (acid pH and hyperosmosis), and that complementation of thedammutant restored its persister defect phenotype. PacBio sequencing of epigenetic genomewide methylation signature and RNA sequencing of theΔdammutant were performed to define, for the first time, the role of adenine methylation in persister formation. Methylome data analysis showed that 99.73% of m6A modifications on GATC were demethylated in theΔdammutant, and demethylation nucleotide site related genes suggested an overwhelming effect on transcription and metabolic processes. Transcriptome analysis of theΔdammutant in comparison to wild type showed that flagella biosynthesis, galactitol transport/utilization, and signaling related genes were upregulated while pilus, fimbriae, virulence, glycerol, nitrogen metabolism pathways and transcriptional regulators were downregulated. The comparative COG analysis of methylome and transcriptome enriched pathways identified translation, ribosomal structure and biogenesis, and cell motility were upregulated, whereas DNA repair, secondary metabolite biosynthesis and diverse transport systems, some of which are known to be involved in persister formation, were downregulated in theΔdammutant. These findings provide new insights about the molecular basis of how DNA adenine methylation may be involved in persister formation and offer novel therapeutic targets for combating persister bacteria.
Development and validation of a potent and specific inhibitor for the CLC-2 chloride channel
Authors: Koster Anna K. , Reese Austin L. , Kuryshev Yuri , Wen Xianlan , McKiernan Keri A. , Gray Erin E. , Wu Caiyun , Huguenard John R. , Maduke Merritt , Bois J. Du 
Published: January 2020

AbstractCLC-2 is a voltage-gated chloride channel that is widely expressed in many mammalian tissues. In the central nervous system (CNS), CLC-2 is expressed in neurons and glia. Studies to define how this channel contributes to normal and pathophysiological function in the CNS have been controversial, in part due to the absence of precise pharmacological tools for modulating CLC-2 activity. Herein, we describe the development and optimization of AK-42, a specific small-molecule inhibitor of CLC-2 with nanomolar potency (IC50 = 17 ± 1 nM). AK-42 displays unprecedented selectivity (>1000-fold) over CLC-1, the closest CLC-2 homolog, and exhibits no off-target engagement against a panel of 58 common channels, receptors, and transporters expressed in brain tissue. Computational docking, validated by mutagenesis and kinetic studies, indicates that AK-42 binds to an extracellular vestibule above the channel pore. In electrophysiological recordings of mouse CA1 hippocampal pyramidal neurons, AK-42 acutely and reversibly inhibits CLC-2 currents; no effect on current is observed on brain slices taken from CLC-2 knockout mice. These results establish AK-42 as a powerful new tool for investigating CLC-2 neurophysiology.Significance StatementThe CLC-2 ion channel facilitates selective passage of Cl− ions across cell membranes. In the central nervous system (CNS), CLC-2 is expressed in both neurons and glia and is proposed to regulate electrical excitability and ion homeostasis. CLC-2 has been implicated in various CNS disorders, including certain types of epilepsy and leukodystrophy. Establishing a causative role for CLC-2 in neuropathologies, however, has been limited by the absence of selective reagents that enable acute and specific channel modulation. Our studies have resulted in the identification of a highly potent, small-molecule inhibitor that enables specific block of CLC-2 Cl− currents in hippocampal brain slices. This precise molecular tool should enable future efforts to identify and treat CLC-2-related disease.
Receptor compaction and GTPase movements drive cotranslational protein translocation
Authors: Lee Jae Ho , Chung SangYoon , Fu Yu-Hsien Hwang , Qian Ruilin , Sun Xuemeng , Weiss Shimon , Shan Shu-ou 
Published: January 2020

AbstractSignal recognition particle (SRP) is a universally conserved targeting machine that couples the synthesis of ~30% of the proteome to their proper membrane localization1,2. In eukaryotic cells, SRP recognizes translating ribosomes bearing hydrophobic signal sequences and, through interaction with SRP receptor (SR), delivers them to the Sec61p translocase on the endoplasmic reticulum (ER) membrane1,2. How SRP ensures efficient and productive initiation of protein translocation at the ER is not well understood. Here, single molecule fluorescence spectroscopy demonstrates that cargo-loaded SRP induces a global compaction of SR, driving a >90 Å movement of the SRP•SR GTPase complex from the vicinity of the ribosome exit, where it initially assembles, to the distal site of SRP. These rearrangements bring translating ribosomes near the membrane, expose conserved Sec61p docking sites on the ribosome and weaken SRP’s interaction with the signal sequence on the nascent polypeptide, thus priming the translating ribosome for engaging the translocation machinery. Disruption of these rearrangements severely impairs cotranslational protein translocation and is the cause of failure in an SRP54 mutant linked to severe congenital neutropenia. Our results demonstrate that multiple largescale molecular motions in the SRP•SR complex are required to drive the transition from protein targeting to translocation; these post-targeting rearrangements provide potential new points for biological regulation as well as disease intervention.
Carbamazepine restores neuronal signaling, protein synthesis and cognitive function in a mouse model of fragile X syndrome
Authors: Ding Qi , Zhang Fan , Feng Yue , Wang Hongbing 
Published: January 2020

ABSTRACTFragile X syndrome (FXS) is a leading genetic disorder of intellectual disability caused by the loss of the functional fragile X mental retardation protein (FMRP). To date, there is no efficacious mechanism-based medication for FXS. With regard to potential disease mechanisms in FXS, it is widely accepted that the lack of FMRP causes elevated protein synthesis and deregulation of neuronal signaling. Abnormal enhancement of the ERK½ (extracellular signal-regulated kinase ½) and PI3K-Akt (Phosphoinositide 3 kinase-protein kinase B) signaling pathways has been identified in both FXS patients and FXS mouse models. In this study, we show that carbamazepine, which is an FDA-approved drug and has been mainly used to treat seizure and neuropathic pain, corrects cognitive deficits including passive avoidance and object location memory in FXS mice. Carbamazepine also rescues hyper locomotion and social deficits. At the cellular level, carbamazepine dampens the elevated level of ERK½ and Akt signaling as well as protein synthesis in FXS mouse neurons. Together, these results advocate repurposing carbamazepine for FXS treatment.
Post-transcriptional Regulation is the Major Driver of microRNA Expression Variation
Authors: Zhang Dingyao , Tian Jingru , Roden Christine , Lu Jun 
Published: January 2020

AbstractMicroRNA (miRNA) expression patterns are highly variable across human tissues and across cancer specimens. The intuitive assumption is that transcription is the main contributor to mature miRNA expression patterns, with post-transcriptional processes further modifying miRNA expression levels. Here we report the surprising model that, on the global level, post-transcriptional regulation dominates over transcriptional regulation in determining mature miRNA expression patterns in both normal tissues and cancer. Taking advantage of large genomic datasets in which the expression of both mature miRNAs and their host genes have been quantified, we establish and validate transcriptional and post-transcriptional metrics, with miRNA host gene expression estimating transcriptional regulation and mature miRNA to host gene ratio estimating post-transcriptional regulation. On average, the post-transcriptional metric contributes 2.8-fold more than the transcriptional metric to the variance of mature miRNA expression. The variation of the balance between the two mature miRNAs (5p and 3p miRNAs) produced from the same precursor hairpin is a non-negligible contributor to miRNA expression, explaining ∼27% of the variance of miRNAs’ post-transcriptional metric. Data of normal tissues yield similar results as cancer specimens. Additionally, the post-transcriptional metric is superior to the transcriptional metric in classifying cancer types. We further demonstrate that the post-transcriptional metric separates miRNAs into distinct groups, suggesting that there are groups of miRNAs that are co-regulated on the post-transcriptional level. Our data support a model in which the post-transcriptional regulation is the major driver of miRNA expression variation, and paves a way toward better mechanistic understanding of post-transcriptional regulation of mature miRNA expression.
cAMP-Fyn signaling in the dorsomedial striatum direct pathway drives excessive alcohol use
Authors: Ehinger Yann , Morisot Nadege , Phamluong Khanhky , Sakhai Samuel A. , Soneja Drishti , Adrover Martin F. , Alvarez Veronica A. , Ron Dorit 
Published: January 2020

ABSTRACTFyn kinase in the dorsomedial striatum (DMS) of rodents plays a central role in mechanisms underlying excessive alcohol intake. The DMS is comprised of medium spiny neurons (MSNs) that project directly (dMSNs) or indirectly (iMSNs) to the substantia nigra. Here, we examined the cell-type specificity of Fyn’s actions on alcohol use. First, we knocked down Fyn selectively in DMS dMSNs or iMSNs of mice and measured the level of alcohol consumption. We found that downregulation of Fyn in dMSNs, but not in iMSNs, reduces excessive alcohol but not saccharin intake. D1Rs are coupled to Gαs/olf, which activate cAMP signaling. To examine whether Fyn’s actions are mediated through cAMP signaling, DMS dMSNs were infected with GαsDREADD, and the activation of Fyn signaling was measured following CNO treatment. We found that remote stimulation of cAMP signaling in DMS dMSNs activates Fyn and promotes the phosphorylation of the Fyn substrate, GluN2B. In contract, remote activation of GαsDREADD in DLS dMSNs did not alter Fyn signaling. We then tested whether activation of GαsDREADD in DMS dMSNs or iMSNs alters alcohol intake and observed that CNO-dependent activation of GαsDREADD in DMS dMSNs but not iMSNs increases alcohol but not saccharin intake. Finally, we examined the contribution of Fyn to GαsDREADD-dependent increase in alcohol intake, and found that systemic administration of the Fyn inhibitor, AZD0503 blocks GαsDREADD-dependent increase in alcohol consumption. Our results suggest that the cAMP-Fyn axis in the DMS dMSNs is a molecular transducer of mechanisms underlying the development of excessive alcohol consumption.
Reconstruction of Gene Regulatory Networks by integrating biological model and a recommendation system
Authors: Wang Yijie , Fear Justin M , Berger Isabelle , Lee Hangnoh , Oliver Brian , Przytycka Teresa M 
Published: January 2020

AbstractGene Regulatory Networks (GRNs) control many aspects of cellular processes including cell differentiation, maintenance of cell type specific states, signal transduction, and response to stress. Since GRNs provide information that is essential for understanding cell function, the inference of these networks is one of the key challenges in systems biology. Leading algorithms to reconstruct GRN utilize, in addition to gene expression data, prior knowledge such as Transcription Factor (TF) DNA binding motifs or results of DNA binding experiments. However, such prior knowledge is typically incomplete hence resulting in missing values. Therefore, the integration of such incomplete prior knowledge with gene expression to elucidate the underlying GRNs remains difficult.To address this challenge we introduce NetREX-CF – RegulatoryNetworkReconstruction usingEXpression andCollaborativeFiltering – a GRN reconstruction approach that brings together a modern machine learning strategy (Collaborative Filtering model) and a biologically justified model of gene expression (sparse Network Component Analysis based model). The Collaborative Filtering (CF) model is able to overcome the incompleteness of the prior knowledge and make edge recommends for building the GRN. Complementing CF, the sparse Network Component Analysis (NCA) model can use gene expression data to validate the recommended edges. Here we combine these two approaches using a novel data integration method and show that the new approach outperforms the currently leading GRN reconstruction methods.Furthermore, our mathematical formalization of the model has lead to a complex optimization problem of a type that has not been attempted before. Specifically, the formulation containsℓ0norm that can not be separated from other variables. To fill this gap, we introduce here a new method Generalized PALM (GPALM) that allows us to solve a broad class of non-convex optimization problems and prove its convergence.