bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-targeting strategy for precise, scarless gene editing with CRISPR/Cas9 and donor ssODNs in Chlamydomonas
Authors: Akella Soujanya , Ma Xinrong , Bacova Romana , Harmer Zachary P , Kolackova Martina , Wen Xiaoxue , Wright David A , Spalding Martin H , Weeks Donald P , Cerutti Heriberto 
Published: September 2021

Abstract
Programmable site-specific nucleases, such as the clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) ribonucleoproteins (RNPs), have allowed creation of valuable knockout mutations and targeted gene modifications in Chlamydomonas (Chlamydomonas reinhardtii). However, in walled strains, present methods for editing genes lacking a selectable phenotype involve co-transfection of RNPs and exogenous double-stranded DNA (dsDNA) encoding a selectable marker gene. Repair of the dsDNA breaks induced by the RNPs is usually accompanied by genomic insertion of exogenous dsDNA fragments, hindering the recovery of precise, scarless mutations in target genes of interest. Here, we tested whether co-targeting two genes by electroporation of pairs of CRISPR/Cas9 RNPs and single-stranded oligodeoxynucleotides (ssODNs) would facilitate the recovery of precise edits in a gene of interest (lacking a selectable phenotype) by selection for precise editing of another gene (creating a selectable marker)—in a process completely lacking exogenous dsDNA. We used PPX1 (encoding protoporphyrinogen IX oxidase) as the generated selectable marker, conferring resistance to oxyfluorfen, and identified precise edits in the homolog of bacterial ftsY or the WD and TetratriCopeptide repeats protein 1 genes in ∼1% of the oxyfluorfen resistant colonies. Analysis of the target site sequences in edited mutants suggested that ssODNs were used as templates for DNA synthesis during homology directed repair, a process prone to replicative errors. The Chlamydomonas acetolactate synthase gene could also be efficiently edited to serve as an alternative selectable marker. This transgene-free strategy may allow creation of individual strains containing precise mutations in multiple target genes, to study complex cellular processes, pathways, or structures.
R2R3-MYB genes coordinate conical cell development and cuticular wax biosynthesis in Phalaenopsis aphrodite
Authors: Lu Hsiang-Chia , Lam Sio-Hong , Zhang Diyang , Hsiao Yu-Yun , Li Bai-Jun , Niu Shan-Ce , Li Chia-Ying , Lan Siren , Tsai Wen-Chieh , Liu Zhong-Jian 
Published: September 2021

Abstract
Petals of the monocot Phalaenopsis aphrodite (Orchidaceae) possess conical epidermal cells on their adaxial surfaces, and a large amount of cuticular wax is deposited on them to serve as a primary barrier against biotic and abiotic stresses. It has been widely reported that subgroup 9A members of the R2R3-MYB gene family, MIXTA and MIXTA-like in eudicots, act to regulate the differentiation of conical epidermal cells. However, the molecular pathways underlying conical epidermal cell development and cuticular wax biosynthesis in monocot petals remain unclear. Here, we characterized two subgroup 9A R2R3-MYB genes, PaMYB9A1 and PaMYB9A2 (PaMYB9A1/2), from P. aphrodite through the transient overexpression of their coding sequences and corresponding chimeric repressors in developing petals. We showed that PaMYB9A1/2 function to coordinate conical epidermal cell development and cuticular wax biosynthesis. In addition, we identified putative targets of PaMYB9A1/2 through comparative transcriptome analyses, revealing that PaMYB9A1/2 acts to regulate the expression of cell wall-associated and wax biosynthetic genes. Furthermore, a chemical composition analysis of cuticular wax showed that even-chain n-alkanes and odd-chain primary alcohols are the main chemical constituents of cuticular wax deposited on petals, which is inconsistent with the well-known biosynthetic pathways of cuticular wax, implying a distinct biosynthetic pathway occurring in P. aphrodite flowers. These results reveal that the function of subgroup 9A R2R3-MYB family genes in regulating the differentiation of epidermal cells is largely conserved in monocots and dicots. Furthermore, both PaMYB9A1/2 have evolved additional functions controlling the biosynthesis of cuticular wax.
Morphology of the prefrontal cortex predicts body composition in early adolescence: cognitive mediators and environmental moderators in the ABCD Study
Authors: Hall Peter A , Best John R , Beaton Elliott A , Sakib Mohammad N , Danckert James 
Published: September 2021

AbstractMorphological features of the lateral prefrontal cortex (PFC) in late childhood and early adolescence may provide important clues as to the developmental etiology of clinical conditions such as obesity. Body composition measurements and structural brain imaging were performed on 11 226 youth at baseline (age 9 or 10 years) and follow-up (age 11 or 12 years). Baseline morphological features of the lateral PFC were examined as predictors of body composition. Findings revealed reliable associations between middle frontal gyrus volume, thickness and surface area and multiple indices of body composition. These findings were consistent across both time points and remained significant after covariate adjustment. Cortical thicknesses of the inferior frontal gyrus and lateral orbitofrontal cortex were also reliable predictors. Morphology effects on body composition were mediated by performance on a non-verbal reasoning task. Modest but reliable moderation effects were observed with respect to environmental self-regulatory demand after controlling for sex, race/ethnicity, income and methodological variables. Overall findings suggest that PFC morphology is a reliable predictor of body composition in early adolescence, as mediated through select cognitive functions and partially moderated by environmental characteristics.
The Diversification of Downy Mildew Species Was Not Driven by the Loss of Mycorrhizal Associations or the Evolution of C4 Photosynthesis
Authors: Davis William J. , Crouch Jo Anne 
Published: September 2021

There are approximately 700 obligate biotrophic species grouped into 20 genera (Oomycota, Peronosporaceae) that cause downy mildew diseases. In 2001, Dick hypothesized that diversification of downy mildew species was driven in part by host plant secondary metabolites. Dick further speculated that this was driven by the transition of host plants away from mycorrhizal associations or the evolution of C4 photosynthesis. Specifically, loss of mycorrhizal associations or the use of C4 photosynthesis would result in more free carbon that the plants could then use to produce more secondary metabolites. If true, then there should be more downy mildew species that infect hosts from plant lineages that lack mycorrhizal associations or use C4 photosynthesis. However, analysis of 677 downy mildew species for host plant mycorrhizal associations and host plant photosynthetic pathway type shows that this is not what occurred. Seventy percent of downy mildew species parasitize hosts that form mycorrhizal associations, and 94% of downy mildew species parasitize hosts that use C3 photosynthesis. From this, it is concluded that the diversification of downy mildew species was not driven by the loss of mycorrhizal associations or the evolution of C4 photosynthesis. However, 85% of downy mildew species that parasitize Poaceae (grasses) parasitize C4 hosts. Thus, it is possible that C4 photosynthesis plays a role in the diversification of these genera. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
Netrin1 and reelin signaling are required for the migration of anterolateral system neurons in the embryonic spinal cord
Authors: Roome R. Brian , Rastegar-Pouyani Shima , Ker Amy , Dumouchel Annie , Kmita Marie , Kania Artur 
Published: September 2021

Abstract
Projection neurons of the spinal cord dorsal horn which transmit pain, itch, and temperature information to the brain comprise the anterolateral system (AS). A recent molecular and genetic study showed that many developing AS neurons express the transcription factor Phox2a and provided insights into the mechanisms of their ontogeny and wiring of nociceptive neuronal circuits. Here, we show that the loss of the axonal guidance and neuronal migration signal netrin1 results in impaired migration of mouse Phox2a+ AS neurons into the spinal lamina I. Furthermore, we show that in the absence of Dab1, an intracellular transducer of the neuronal migration signal reelin, the migration of spinal lamina V and lateral spinal nucleus Phox2a+ AS neurons is impaired, in line with deficits in nociception seen in mice with a loss of reelin signaling. Together, these results provide evidence that netrin1 and reelin control the development of spinal nociceptive projection neurons, suggesting a mechanistic explanation for studies that link sequence variations in human genes encoding these neurodevelopmental signals and abnormal pain sensation.
Sex differences in medical cannabis-related adverse effects
Authors: Aviram Joshua , Lewitus Gil M. , Vysotski Yelena , Berman Paula , Shapira Anna , Procaccia Shiri , Meiri David 
Published: September 2021

Abstract
Studies have shown that women are more susceptible to adverse effects (AEs) from conventional drugs. This study aimed to investigate the differences of medical cannabis (MC)-related AEs between women and men in patients with chronic noncancer pain (CNCP). This is a cross-sectional study of adult patients licensed for MC treatment who were also diagnosed as patients with CNCP by a physician. Data included self-reported questionnaires and comprehensive MC treatment information. Simultaneously, identification and quantification of phytocannabinoids and terpenoids from the MC cultivars were performed. Comparative statistics were used to evaluate differences between men and women. Four hundred twenty-nine patients with CNCP (64% males) reported fully on their MC treatment. Subgrouping by sex demonstrated that the weight-adjusted doses were similar between men and women (0.48 [0.33-0.6] gr for men and 0.47 [0.34-0.66] gr for women). Nonetheless, women reported more than men on MC-related AEs. Further analysis revealed that women consumed different MC cultivar combinations than men, with significantly higher monthly doses of the phytocannabinoids CBD and CBC and significantly lower monthly doses of the phytocannabinoid 373-15c and the terpenoid linalool. Our findings demonstrate sex differences in MC-related AEs among patients with CNCP. Women are more susceptible to MC-related AEs, presumably because of both the inherent sex effect and the consumption of specific phytocannabinoid compositions in the MC cultivar(s). The understanding of these differences may be crucial for planning MC treatments with safer phytocannabinoid and terpenoid compositions and to better inform patients of expected AEs.
Voltage-gated calcium currents in human dorsal root ganglion neurons
Authors: Hartung Jane E. , Moy Jamie K. , Loeza-Alcocer Emanuel , Nagarajan Vidhya , Jostock Ruth , Christoph Thomas , Schroeder Wolfgang , Gold Michael S. 
Published: September 2021

Abstract
Voltage-gated calcium channels in sensory neurons underlie processes ranging from neurotransmitter release to gene expression and remain a therapeutic target for the treatment of pain. Yet virtually all we know about voltage-gated calcium channels has been obtained through the study of rodent sensory neurons and heterologously expressed channels. To address this, high voltage–activated (HVA) Ca2+ currents in dissociated human and rat dorsal root ganglion neurons were characterized with whole-cell patch clamp techniques. The HVA currents from both species shared basic biophysical and pharmacological properties. However, HVA currents in human neurons differed from those in the rat in at least 3 potentially important ways: (1) Ca2+ current density was significantly smaller, (2) the proportion of nifedipine-sensitive currents was far greater, and (3) a subpopulation of human neurons displayed relatively large constitutive current inhibition. These results highlight the need to for the study of native proteins in their native environment before initiating costly clinical trials.
Greater baseline pain inclusion criteria in clinical trials increase regression to the mean effect: a modelling study
Authors: Kamerman Peter R. , Vollert Jan 
Published: September 2021

Abstract
We modelled the effects of pain intensity inclusion thresholds (3/10, 4/10, and 5/10 on a 0- to 10-point numerical pain rating scale) on the magnitude of the regression to the mean effect under conditions that were consistent with the sample mean and variance, and intermeasurement correlation observed in clinical trials for the management of chronic pain. All data were modelled on a hypothetical placebo control group. We found a progressive increase in the mean pain intensity as the pain inclusion threshold increased, but this increase was not uniform, having an increasing effect on baseline measurements compared with study endpoint measurements as the threshold was increased. That is, the regression to the mean effect was magnified by increasing inclusion thresholds. Furthermore, the effect increasing pain inclusion thresholds had on the regression to the mean effect was increased by decreasing sample mean values at baseline and intermeasurement correlations, and increasing sample variance. At its smallest, the regression to the mean effect was 0.13/10 (95% confidence interval: 0.03/10-0.24/10; threshold: 3/10, baseline mean pain: 6.5/10, SD: 1.6/10, and correlation: 0.44), and at its greatest, it was 0.78/10 (95% confidence interval: 0.63/10-0.94/10; threshold: 5/10, baseline mean pain: 6/10, SD: 1.8/10, and correlation: 0.19). We have shown that using pain inclusion thresholds in clinical trials drives progressively larger regression to the mean effects. We believe that a threshold of 3/10 offers the best compromise between maintaining assay sensitivity (the goal of thresholds) and the size of the regression to the mean effect.
Biopsy in interstitial lung disease: specific diagnosis and the identification of the progressive fibrotic phenotype
Authors: Ravaglia Claudia , Nicholson Andrew G. 
Published: September 2021

Purpose of review
The evaluation of progression in fibrotic interstitial lung diseases (ILDs) may require a multidimensional approach. This review will cover the role and usefulness of lung biopsy in diagnosis and assessment of the progressive fibrotic phenotype.

Recent findings
The identification of specific findings and the balance between inflammation and fibrosis on lung biopsy may help distinguishing different disease entities and may likely determine the effect of treatment and possibly prognosis. The fibrotic morphological patterns potentially associated with a progressive phenotype include usual interstitial pneumonia (UIP), fibrotic nonspecific interstitial pneumonia, pleuroparenchymal fibroelastosis, desquamative interstitial pneumonia, fibrotic hypersensitivity pneumonitis and other less common fibrotic variants, with histopathological findings of UIP at the time of diagnosis being predictive of worse outcome compared with other patterns. The prognostic significance of lung biopsy findings has been assessed after both surgical lung biopsy (SLB) and transbronchial lung cryobiopsy (TBLC), the latter becoming a valid alternative to SLB, if performed in experienced centres, due to significantly lower morbidity and mortality.

Summary
Lung biopsy plays an important role in diagnosis and identification of the progressive fibrotic phenotype. The introduction of less invasive procedures could potentially expand the role of lung sampling, including for example patients with a known diagnosis of ILD or at an earlier stage of the disease.
Reduced Fractional Absorption of Zinc in Children With Environmental Enteropathy in Zambia
Authors: Zyambo Kanekwa , Hodges Phoebe , Chandwe Kanta , Mweetwa Monica , Westcott Jamie , Krebs Nancy F. , Amadi Beatrice , Kelly Paul 
Published: September 2021

ABSTRACTObjectives:We measured fractional absorption of zinc (FAZ) in children with environmental enteropathy (EE) and carried out transcriptomic analysis of biopsies from these children in order to compare FAZ to histology of intestinal biopsies, expression of zinc transporter genes, and biomarkers of enteropathy.Methods:Fractional absorption of a standardized aqueous dose of zinc was measured by a dual isotope ratio technique in a cohort of children ages between 9 and 24 months in Lusaka, Zambia, who all had non‐responsive stunting. Gene expression analysis was carried out on biopsies through RNA sequencing using an Illumina HiSeq2000 platform.Results:All 33 children had histological features of environmental enteropathy and plasma zinc concentrations below the lower limit of normal. Measured FAZ ranged from 0.18 to 0.93; all values >0.55 were observed in girls. FAZ was negatively correlated with faecal myeloperoxidase (MPO) (ρ = −0.51, n = 17; P = 0.04) and faecal calprotectin (ρ = −0.50, n = 16; P = 0.05), but not blood biomarkers. Of 41 genes with known roles in zinc metabolism, only three metallothionein genes were significantly correlated with FAZ.Conclusions:Zinc homeostasis is impaired in children with environmental enteropathy, and was inversely correlated with mucosal inflammation. Reduced FAZ without specific changes in expression of most zinc transporter genes could be explained by reduced absorptive surface area due to villus/microvillus atrophy.
Risk Factors for Syphilis at a Large Urban Emergency Department
Authors: Ford James S. , Shevchyk Ivan , Yoon Joseph , Chechi Tasleem , Voong Stephanie , Tran Nam , May Larissa 
Published: September 2021

Background
The prevalence of syphilis is increasing in the United States. The emergency department (ED) is an important setting to screen and treat underserved populations. To tailor testing protocols to the local population, we aimed to identify risk factors for syphilis positivity in ED patients.

Methods
We performed a retrospective analysis of ED patients who were screened for syphilis between November 2018 and August 2020. Patients were screened for Treponema pallidum antibody using a multiplex flow immunoassay, and positive results were confirmed by rapid plasma reagin or T. pallidum particle agglutination. Risk factors for new syphilis diagnoses were identified using multiple logistic regression.

Results
We screened 1974 patients for syphilis (mean age, 37 ± 16 years; 56% female). We identified 201 patients with new infections without previous treatment. Independent risk factors for a new diagnosis of syphilis included housing status (undomiciled, 23% [60 of 256]; domiciled, 9% [133 of 1559]; adjusted odds ratio [aOR], 1.9 [95% confidence interval {CI}, 1.2–3.0]), history of HIV (positive, 44% [28 of 63]; negative, 9% [173 of 1893]; aOR, 5.8 [95% CI, 3.0–11.2]), tobacco use (positive, 15% [117 of 797]; negative, 4% [29 of 665]; aOR, 2.4 [95% CI, 1.5–3.9]), and illicit drug use (positive, 14% [112 of 812]; negative, 8% [52 of 678]; aOR, 2.2 [95% CI, 1.0–2.5]).

Conclusions
Undomiciled housing status, history of HIV, history of tobacco use, and history of illicit drug use were independently associated with a new diagnosis of syphilis in the ED. Broadening targeted syphilis screening algorithms beyond sexually transmitted disease–related complaints could help identify new syphilis cases for treatment.
Quantifying Meibomian Gland Morphology Using Artificial Intelligence
Authors: Wang Jiayun , Li Shixuan , Yeh Thao N. , Chakraborty Rudrasis , Graham Andrew D. , Yu Stella X. , Lin Meng C. 
Published: September 2021

SIGNIFICANCE
Quantifying meibomian gland morphology from meibography images is used for the diagnosis, treatment, and management of meibomian gland dysfunction in clinics. A novel and automated method is described for quantifying meibomian gland morphology from meibography images.

PURPOSE
Meibomian gland morphological abnormality is a common clinical sign of meibomian gland dysfunction, yet there exist no automated methods that provide standard quantifications of morphological features for individual glands. This study introduces an automated artificial intelligence approach to segmenting individual meibomian gland regions in infrared meibography images and analyzing their morphological features.

METHODS
A total of 1443 meibography images were collected and annotated. The dataset was then divided into development and evaluation sets. The development set was used to train and tune deep learning models for segmenting glands and identifying ghost glands from images, whereas the evaluation set was used to evaluate the performance of the model. The gland segmentations were further used to analyze individual gland features, including gland local contrast, length, width, and tortuosity.

RESULTS
A total of 1039 meibography images (including 486 upper and 553 lower eyelids) were used for training and tuning the deep learning model, whereas the remaining 404 images (including 203 upper and 201 lower eyelids) were used for evaluations. The algorithm on average achieved 63% mean intersection over union in segmenting glands, and 84.4% sensitivity and 71.7% specificity in identifying ghost glands. Morphological features of each gland were also fed to a support vector machine for analyzing their associations with ghost glands. Analysis of model coefficients indicated that low gland local contrast was the primary indicator for ghost glands.

CONCLUSIONS
The proposed approach can automatically segment individual meibomian glands in infrared meibography images, identify ghost glands, and quantitatively analyze gland morphological features.
A physiatrist's understanding and application of the current literature on chronic pelvic pain: a narrative review
Authors: Shrikhande Allyson , Ullger Cory , Seko Kyle , Patil Soha , Natarajan Janaki , Tailor Yogita , Thompson-Chudy Carolyn 
Published: September 2021

Abstract
Chronic pelvic pain (CPP) is a highly prevalent condition which is underdiagnosed and poorly understood. The purpose of this review is to outline the various aspects of the nature of CPP, including its etiologies, clinical presentation, and nonoperative treatment options. For data collection, a PubMed search was conducted using indexing terms such as chronic pelvic pain and pelvic pain. Literature reviews and studies focusing on etiologies, clinical presentation, and/or the diagnosis of CPP were compiled for review by a team of 3 physiatrists. Studies investigating conservative treatments, medications, and interventional procedures for CPP and related conditions with comparable etiologies were also included. Of the 502 articles retrieved, 116 were deemed suitable by the team for this study. Although CPP is a complex, multifaceted condition, a particular susceptibility to nociceptive stimuli was demonstrated as an underlying theme in its evolution. There are many treatment options currently used; however, more robust evidence, such as randomized controlled trials, are needed before creating comprehensive guidelines for treating CPP.