bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-invasive assessment of ovarian activity in free-ranging eastern black rhinoceros (Diceros bicornis michaeli) in Kenya
Authors: Kamau Maureen W , Brown Janine L , Boisseau Nicole , Gaymer Jamie , Hassell James , Martins Dino J , Murray Suzan
Published: April 2023

Eastern black rhinos (Diceros bicornis michaeli) are a critically endangered species living in diverse habitats across Africa. In Kenya, once threatened with extinction due to massive poaching pressures, increased protection has resulted in losses being less than 1% annually today. Still, some populations have failed to achieve desired population growth targets. At Ol Jogi Wildlife Conservancy, some individuals are experiencing sub-optimal reproduction based on historical calving records and long inter-calving intervals (>3 years). Hormones drive the reproductive process, so non-invasive assessments of endocrine patterns can be useful indicators of individual reproductive health. In this study, we analysed longitudinal fecal progestagen metabolite (fPM) concentrations in all breeding female eastern black rhinos at Ol Jogi (n = 17) and compared the prevalence of irregular estrous cycles (longer or shorter than 20–40 days) and anestrous periods (interluteal period more than twice the length of a normal follicular phase, i.e. > 10 days) between optimal (inter-calving interval < 3 years) and sub-optimal (>3 years) reproducing individuals. Ten rhinos were pregnant during at least part of the study period. A total of 12 complete cycles were observed in seven females with an average length of 36 ± 3 days and equal numbers of regular and irregular cycles. Single anestrous periods averaging 67 ± 13 days were observed in five females. Surprisingly, a majority of cycles in optimal reproducing individuals were categorized as irregular based on fPM profiles. Overall, results suggest that irregular ovarian activity and isolated bouts of anestrus do not have negative impacts on reproductive performance in this subpopulation at Ol Jogi. A high priority is to continue using noninvasive hormone monitoring to evaluate how ecological or other variables influence reproductive success in this and other eastern black rhino subpopulations in Kenya.
Rapid identification of healthy Tegillarca granosa using laser-induced breakdown spectroscopy and fusion model
Authors: Chen Xiaojing , Chen Yanan , Chen Xi , Yuan Leiming , Jiang Chengxi , Huang Guangzao , Shi Wen
Published: April 2023

Objectives

This study presents a method combining a one-class classifier and laser-induced breakdown spectrometry (LIBS) to quickly identify healthy Tegillarca granosa (T. granosa).

Materials and Methods

The sum of ranking differences (SRD) was used to fuse multiple anomaly detection metrics to build the one-class classifier, which was only trained with healthy T. granosa. The one-class classifier can identify healthy T. granosa to exclude non-healthy T. granosa. The proposed method calculated multiple anomaly detection metrics and standardized them to obtain a fusion matrix. Based on the fusion matrix, the samples were ranked by SRD and those ranked lowest and below the threshold were considered to be unhealthy.

Results

Multiple anomaly detection metrics were fused by the SRD algorithm and tested on each band, and the final fusion model achieved an accuracy rate of 98.46%, a sensitivity of 100%, and a specificity of 80%. The remaining three single classification models obtained the following results: the SVDD model achieved an accuracy rate of 87.69%, a sensitivity of 90%, and a specificity of 60%; the OCSVM model achieved an accuracy rate of 80%, a sensitivity of 76.67%, and a specificity of 60%; and the DD-SIMCA model achieved an accuracy rate of 95.38%, a sensitivity of 98.33%, and a specificity of 60%.

Conclusions

The experimental results showed that the proposed method achieved better results than the traditional one-class classification methods with a single metric. Therefore, the fusion method effectively improves the performance of traditional one-class classifiers when using LIBS to quickly identify healthy substances (healthy T. granosa).
An updated de novo transcriptome for green ash (Fraxinus pennsylvanica)
Authors: Brungardt Jordan J , Bock Clive H
Published: April 2023

De novo transcriptome assembly of next-generation sequencing information has become a powerful tool for the study of non-model species. Transcriptomes generated by this method can have high variability due to endless combinations of user-defined variables and programs available for assembly. Many methods have been developed for evaluating the quality of these assemblies. Here, raw sequencing information for Green ash (Fraxinus pennsylvanica Marshall) that was previously published has been re-evaluated. An updated assembly has been developed by including additional sequencing information not used for the currently accepted transcriptome in combination with more stringent trimming parameters. Input reads were assembled with Trinity and Abyss assembly programs. The resulting Trinity assembly has a 7.3-fold increase in genomic breadth of coverage, a 2.4-fold increase in predicted complete open reading frames, an increased L50 value, and increased Benchmarking Universal Single-Copy Ortholog completeness compared to the earlier published transcriptome. This updated transcriptome can be leveraged to help fight the rapid decline of green ash due to pathogens.
Extension of the DNAJB2a isoform in a dominant neuromyopathy family
Authors: Sarparanta Jaakko , Jonson Per Harald , Reimann Jens , Vihola Anna , Luque Helena , Penttilä Sini , Johari Mridul , Savarese Marco , Hackman Peter , Kornblum Cornelia , Udd Bjarne
Published: April 2023

Recessive mutations in the DNAJB2 gene, encoding the J-domain co-chaperones DNAJB2a and DNAJB2b, have previously been reported as the genetic cause of progressive peripheral neuropathies, rarely involving pyramidal signs, parkinsonism and myopathy. We describe here a family with the first dominantly acting DNAJB2 mutation resulting in a late-onset neuromyopathy phenotype. The c.832 T > G p.(*278Glyext*83) mutation abolishes the stop codon of the DNAJB2a isoform resulting in a C-terminal extension of the protein, with no direct effect predicted on the DNAJB2b isoform of the protein. Analysis of the muscle biopsy showed reduction of both protein isoforms. In functional studies, the mutant protein mislocalized to the endoplasmic reticulum due to a transmembrane helix in the C-terminal extension. The mutant protein underwent rapid proteasomal degradation and also increased the turnover of co-expressed wild-type DNAJB2a, potentially explaining the reduced protein amount in the patient muscle tissue. In line with this dominant negative effect, both wild-type and mutant DNAJB2a were shown to form polydisperse oligomers.
Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio
Authors: Bhattarai Gehendra , Shi Ainong , Mou Beiquan , Correll James C
Published: April 2023

Commercial production of spinach (Spinacia oleracea L.) is centered in California and Arizona in the US, where downy mildew caused by Peronospora effusa is the most destructive disease. Nineteen typical races of P. effusa have been reported to infect spinach, with 16 identified after 1990. The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach. We attempted to map and delineate the RPF2 locus at a finer resolution, identify linked single nucleotide polymorphism (SNP) markers, and report candidate downy mildew resistance (R) genes. Progeny populations segregating for RPF2 locus derived from resistant differential cultivar Lazio were infected using race 5 of P. effusa and were used to study for genetic transmission and mapping analysis in this study. Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb of chromosome 3 with peak SNP (Chr3_1, 221, 009) showing a LOD value of 61.6 in the GLM model in TASSEL, which was within 1.08 Kb from Spo12821, a gene that encodes CC-NBS-LRR plant disease resistance protein. In addition, a combined analysis of progeny panels of Lazio and Whale segregating for RPF2 and RPF3 loci delineated the resistance section in chromosome 3 between 1.18–1.23 and 1.75–1.76 Mb. This study provides valuable information on the RPF2 resistance region in the spinach cultivar Lazio compared to RPF3 loci in the cultivar Whale. The RPF2 and RPF3 specific SNP markers, plus the resistant genes reported here, could add value to breeding efforts to develop downy mildew resistant cultivars in the future.
Raising awareness of antimicrobial resistance: development of an ‘antibiotic footprint calculator’
Authors: Prapharsavat Ravikanya , Kittikongnapang Rattanasiri , Smithkittipol Chokdee , Udomrat Warute , Numsawat Sukanya , Hernandez-Koutoucheva Anastasia , Naemiratch Bhensri , Chomkatekaew Chalita , Amaratunga Chanaki , Bleho John , Mathee Kalai , Schneiders Mira Leonie , Khirikoekkong Napat , Kanthawang Nipaphan , Sumpradit Nithima , Suveeranont Rapee , Asarath Supa-at , Poomchaichote Tassawan , Schilling William , Chan Xin Hui S , Osterrieder Anne , Cheah Phaik Yeong , Limmathurotsakul Direk
Published: April 2023

Non-academic partners can be vital in successful public engagement activities on antimicrobial resistance. With collaboration between academic and non-academic partners, we developed and launched an open-access web-based application, the ‘antibiotic footprint calculator’, in both Thai and English. The application focused on a good user experience, addressing antibiotic overuse and its impact, and encouraging immediate action. The application was unveiled in joint public engagement activities. From 1 Nov 2021 to 31 July 2022 (9 month period), 2554 players estimated their personal antibiotic footprint by using the application.
Natural language processing-driven state machines to extract social factors from unstructured clinical documentation
Authors: Allen Katie S , Hood Dan R , Cummins Jonathan , Kasturi Suranga , Mendonca Eneida A , Vest Joshua R
Published: April 2023

Lay Summary

Social factors, such as an individual’s housing, food, employment, and income situations, affect their overall health and well-being. As a result, data on patients’ social factors aid in clinical decision making, planning by hospital administrators and policy-makers, and enrich research studies with data representative of more factors influencing the life of an individual. Data on social factors can be collected at the time of a healthcare visit through screening questionnaires or are often documented in the clinical text as part of the social narrative. This study examines the use of natural language processing—a machine method to identify certain text within a larger document—to identify housing instability, financial insecurity, and unemployment from within the clinical notes. Using a relatively unsophisticated methodology, this study demonstrates strong performance in identifying these social factors, which will enable stakeholders to utilize these details in support of improved clinical care.
The Genetic Architecture of Adaptation to Leaf and Root Bacterial Microbiota inArabidopsis thaliana
Authors: Roux Fabrice , Frachon Léa , Bartoli Claudia
Published: April 2023

Understanding the role of the host genome in modulating microbiota variation is a need to shed light on the holobiont theory and overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. In addition, most association genetic studies on microbiota are often carried out outside the native habitats where the host evolves and the identification of signatures of local adaptation on the candidate genes has been overlooked. To fill these gaps and dissect the genetic architecture driving adaptive plant-microbiota interactions, we adopted a genome-environment association (GEA) analysis on 141 whole-genome sequenced natural populations of Arabidopsis thaliana characterized in situ for their leaf and root bacterial communities in fall and spring, and a large range of nonmicrobial ecological factors (i.e., climate, soil, and plant communities). A much higher fraction of among-population microbiota variance was explained by the host genetics than by nonmicrobial ecological factors. Importantly, the relative importance of host genetics and nonmicrobial ecological factors in explaining the presence of particular operational taxonomic units (OTUs) differs between bacterial families and genera. In addition, the polygenic architecture of adaptation to bacterial communities was highly flexible between plant compartments and seasons. Relatedly, signatures of local adaptation were stronger on quantitative trait loci (QTLs) of the root microbiota in spring. Finally, plant immunity appears as a major source of adaptive genetic variation structuring bacterial assemblages in A. thaliana.
LncRNAEPRregulates intestinal mucus production and protects against inflammation and tumorigenesis
Authors: Briata Paola , Mastracci Luca , Zapparoli Ettore , Caputo Luca , Ferracci Elisa , Silvestri Alessandra , Garuti Anna , Hamadou Meriem Hadjer , Inga Alberto , Marcaccini Elisa , Grillo Federica , Bucci Gabriele , Puri Pier Lorenzo , Beznoussenko Galina , Mironov Alexander , Chiacchiera Fulvio , Gherzi Roberto
Published: April 2023

The long non-coding RNA EPR is expressed in epithelial tissues, binds to chromatin and controls distinct biological activities in mouse mammary gland cells. Because of its high expression in the intestine, in this study we have generated a colon-specific conditional targeted deletion (EPR cKO) to evaluate EPR in vivo functions in mice. EPR cKO mice display epithelium hyperproliferation, impaired mucus production and secretion, as well as inflammatory infiltration in the proximal portion of the large intestine. RNA sequencing analysis reveals a rearrangement of the colon crypt transcriptome with strong reduction of goblet cell-specific factors including those involved in the synthesis, assembly, transport and control of mucus proteins. Further, colon mucosa integrity and permeability are impaired in EPR cKO mice, and this results in higher susceptibility to dextran sodium sulfate (DSS)-induced colitis and tumor formation. Human EPR is down-regulated in human cancer cell lines as well as in human cancers, and overexpression of EPR in a colon cancer cell line results in enhanced expression of pro-apoptotic genes. Mechanistically, we show that EPR directly interacts with select genes involved in mucus metabolism whose expression is reduced in EPR cKO mice and that EPR deletion causes tridimensional chromatin organization changes.
Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology
Authors: McCarthy Erika , Ekesan Şölen , Giese Timothy J , Wilson Timothy J , Deng Jie , Huang Lin , Lilley David M J , York Darrin M
Published: April 2023

A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4  kcal·mol−1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity–pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.
Impact of stereopure chimeric backbone chemistries on the potency and durability of gene silencing by RNA interference
Authors: Liu Wei , Iwamoto Naoki , Marappan Subramanian , Luu Khoa , Tripathi Snehlata , Purcell-Estabrook Erin , Shelke Juili Dilip , Shah Himali , Lamattina Anthony , Pan Qianli , Schrand Brett , Favaloro Frank , Bedekar Mugdha , Chatterjee Arindom , Desai Jigar , Kawamoto Tomomi , Lu Genliang , Metterville Jake , Samaraweera Milinda , Prakasha Priyanka Shiva , Yang Hailin , Yin Yuan , Yu Hui , Giangrande Paloma H , Byrne Michael , Kandasamy Pachamuthu , Vargeese Chandra
Published: April 2023

Herein, we report the systematic investigation of stereopure phosphorothioate (PS) and phosphoryl guanidine (PN) linkages on siRNA-mediated silencing. The incorporation of appropriately positioned and configured stereopure PS and PN linkages to N-acetylgalactosamine (GalNAc)-conjugated siRNAs based on multiple targets (Ttr and HSD17B13) increased potency and durability of mRNA silencing in mouse hepatocytes in vivo compared with reference molecules based on clinically proven formats. The observation that the same modification pattern had beneficial effects on unrelated transcripts suggests that it may be generalizable. The effect of stereopure PN modification on silencing is modulated by 2′-ribose modifications in the vicinity, particularly on the nucleoside 3′ to the linkage. These benefits corresponded with both an increase in thermal instability at the 5′-end of the antisense strand and improved Argonaute 2 (Ago2) loading. Application of one of our most effective designs to generate a GalNAc-siRNA targeting human HSD17B13 led to ∼80% silencing that persisted for at least 14 weeks after administration of a single 3 mg/kg subcutaneous dose in transgenic mice. The judicious use of stereopure PN linkages improved the silencing profile of GalNAc-siRNAs without disrupting endogenous RNA interference pathways and without elevating serum biomarkers for liver dysfunction, suggesting they may be suitable for therapeutic application.
Requirements for mammalian promoters to decode transcription factor dynamics
Authors: Antwi Enoch B , Marrakchi Yassine , Çiçek Özgün , Brox Thomas , Di Ventura Barbara
Published: April 2023

In response to different stimuli many transcription factors (TFs) display different activation dynamics that trigger the expression of specific sets of target genes, suggesting that promoters have a way to decode dynamics. Here, we use optogenetics to directly manipulate the nuclear localization of a synthetic TF in mammalian cells without affecting other processes. We generate pulsatile or sustained TF dynamics and employ live cell microscopy and mathematical modelling to analyse the behaviour of a library of reporter constructs. We find decoding of TF dynamics occurs only when the coupling between TF binding and transcription pre-initiation complex formation is inefficient and that the ability of a promoter to decode TF dynamics gets amplified by inefficient translation initiation. Using the knowledge acquired, we build a synthetic circuit that allows obtaining two gene expression programs depending solely on TF dynamics. Finally, we show that some of the promoter features identified in our study can be used to distinguish natural promoters that have previously been experimentally characterized as responsive to either sustained or pulsatile p53 and NF-κB signals. These results help elucidate how gene expression is regulated in mammalian cells and open up the possibility to build complex synthetic circuits steered by TF dynamics.
A Belgian Population-Based Study Reveals Subgroups of Right-sided Colorectal Cancer with a Better Prognosis Compared to Left-sided Cancer
Authors: Janssens Katleen , Fransen Erik , Van Camp Guy , Prenen Hans , Op de Beeck Ken , Van Damme Nancy , Peeters Marc
Published: April 2023

Background

Patients with left-sided colorectal cancer (L-CRC) are known to have a significantly better prognosis than those with right-sided CRC (R-CRC). It has been hypothesized that RAS, BRAF mutations, or deficient mismatch repair status (MMR) might be responsible for the prognostic effect of primary tumor location (PTL). This study aims to evaluate the prognostic effect of PTL in the Belgian population and to determine the role of biomarkers (MMR, BRAF, and RAS status) in this effect.

Patients and Methods

We performed a retrospective analysis of Belgian Cancer Registry data. First, we studied the prognostic effect of PTL on 5-year relative survival of 91,946 patients diagnosed with CRC (all stages) from 2004-2015. Second, we investigated the interaction between biomarkers and the prognostic effect of PTL in 1818 patients diagnosed with stage IV CRC in 2014-2015.

Results

L-CRC was associated with a significantly better 5-year relative survival compared to R-CRC in all stages and ages combined (68.4%, 95% CI, 67.7-69.1% vs 65.6%, 95% CI, 64.7-66.4%). Also, when stratified by age, sex, and stage, the prognosis of L-CRC was better compared to R-CRC in most subgroups. Only in stage II and certain subgroups of elderly patients, the opposite was observed. Furthermore, our data showed that none of the biomarkers had a significant interaction with the effect of PTL on survival.

Conclusion

This population-based study confirms that L-CRC is associated with significantly better relative survival compared to R-CRC, in all stages and ages combined. Furthermore, in stage IV L-CRC is associated with a longer survival than R-CRC, regardless of MMR, RAS, and BRAF status.
2021 superoutburst of the WZ Sge-type dwarf nova V627 Pegasi lacks an early superhump phase
Authors: Tampo Yusuke , Kato Taichi , Kojiguchi Naoto , Shugarov Sergey Yu , Itoh Hiroshi , Matsumoto Katsura , Nakagawa Momoka , Nishida Yukitaka , Richmond Michael , Shibata Masaaki , Ito Junpei , Kokhirova Gulchehra , Rakhmatullaeva Firuza , Tordai Tamás , Kiyota Seiichiro , Ruiz Javier , Dubovsky Pavol A , Medulka Tomáš , Pavlenko Elena P , Antonyuk Oksana I , Sosnovskij Aleksei A , Baklanov Aleksei V , Krushevska Viktoriia , Vanmunster Tonny , Brincat Stephen M , Petrik Karol , Galdies Charles , Hambsch Franz-Josef , Maeda Yutaka , Nogami Daisaku
Published: April 2023

Superoutbursts in WZ Sge-type dwarf novae (DNe) are characterized by both early superhumps and ordinary superhumps originating from the 2 : 1 and 3 : 1 resonances, respectively. However, some WZ Sge-type DNe show a superoutburst lacking early superhumps; it is not well established how these differ from superoutbursts with an early superhump phase. We report time-resolved photometric observations of the WZ Sge-type DN V627 Peg during its 2021 superoutburst. The detection of ordinary superhumps before the superoutburst peak highlights that this 2021 superoutburst of V627 Peg, like that in 2014, did not feature an early superhump phase. The duration of stage B superhumps was slightly longer in the 2010 superoutburst accompanied by early superhumps than that in the 2014 and 2021 superoutbursts, which lacked early superhumps. This result suggests that an accretion disk experiencing the 2 : 1 resonance may have a larger mass at the inner part of the disk and hence needs more time for the inner disk to become eccentric. The presence of a precursor outburst in the 2021 superoutburst suggests that the maximum disk radius should be smaller than that of the 2014 superoutburst, even though the duration of quiescence was longer than that before the 2021 superoutburst. This could be accomplished if the 2021 superoutburst was triggered as an inside-out outburst or if the mass transfer rate in quiescence changes by a factor of two, suggesting that the outburst mechanism and quiescence state of WZ Sge-type DNe may have more variety than ever thought.
Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome
Authors: Yin Xiaochang , Romero-Campero Francisco J , Yang Minqi , Baile Fernando , Cao Yuxin , Shu Jiayue , Luo Lingxiao , Wang Dingyue , Sun Shang , Yan Peng , Gong Zhiyun , Mo Xiaorong , Qin Genji , Calonje Myriam , Zhou Yue
Published: April 2023

Three-dimensional (3D) chromatin organization is highly dynamic during development and seems to play a crucial role in regulating gene expression. Self-interacting domains, commonly called topologically associating domains (TADs) or compartment domains (CDs), have been proposed as the basic structural units of chromatin organization. Surprisingly, although these units have been found in several plant species, they escaped detection in Arabidopsis (Arabidopsis thaliana). Here, we show that the Arabidopsis genome is partitioned into contiguous CDs with different epigenetic features, which are required to maintain appropriate intra-CD and long-range interactions. Consistent with this notion, the histone-modifying Polycomb group machinery is involved in 3D chromatin organization. Yet, while it is clear that Polycomb repressive complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) helps establish local and long-range chromatin interactions in plants, the implications of PRC1-mediated histone H2A monoubiquitination on lysine 121 (H2AK121ub) are unclear. We found that PRC1, together with PRC2, maintains intra-CD interactions, but it also hinders the formation of H3K4me3-enriched local chromatin loops when acting independently of PRC2. Moreover, the loss of PRC1 or PRC2 activity differentially affects long-range chromatin interactions, and these 3D changes differentially affect gene expression. Our results suggest that H2AK121ub helps prevent the formation of transposable element/H3K27me1-rich long loops and serves as a docking point for H3K27me3 incorporation.
Accelerating synergistic effects of preconditioned mesenchymal stem cells with Crocin and dexamethasone in pulmonary epithelial cells injury
Authors: Jamshidi Vahid , Halabian Raheleh , Saeedi Pardis , Bagheri Hasan , Nobakht Motlagh Ghoochani Bibi Fatemeh
Published: April 2023

Chemical warfare victims suffer from bronchiolitis and chronic pulmonary obstruction caused by sulfur mustard (SM) toxicity. Despite the mesenchymal stem cells capacity to alleviate inflammation, their low survival rate under oxidative stress severely limits their effectiveness. This study aimed to examine how natural (Crocin) and synthetic (Dexamethasone) antioxidants might affect MSC efficacy. MSCs were treated with the optimal doses of Crocin (Cr.), Dexamethasone (Dex.), and their combination. The A549 cells line was pretreated with the optimal dose of the CEES to mimic the lung disease. Then, the affected A549 cells were exposed to the preconditioned MSCs and conditioned media, and then their survival rates were estimated by MTTor2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Annexin-V PI apoptosis test was conducted for MSCs and A549 cells. Reactive Oxygen Species (ROS) assay and Enzyme-linked immunosorbent assay (ELISA) test demonstrated the percentage of production of ROS and the cytokines levels in A549/CEES, respectively. The results revealed significant increases in Cr. + Dex. treated MSCs (P < .01) and A549 cells treated with MSCs-CM/Cr/Dex (P < .01) groups’ survival. The apoptosis rate and ROS production were reduced in the MSCs-CM/Cr/Dex. Also, considerable decreases in IL-1β (P < .01) and IL-6 (P < .01) and a significant increase in IL-10 (P < .05) in treated A549/CEES by Cr/Dex and MSCs-CM/Cr/Dex supported the synergistic effects of Crocin and Dexamethasone.
Previsual and Early Detection of Myrtle Rust on Rose Apple Using Indices Derived from Thermal Imagery and Visible-to-Short-Infrared Spectroscopy
Authors: Watt Michael S. , Bartlett Michael , Soewarto Julia , de Silva Dilshan , Estarija Honey Jane C. , Massam Peter , Cajes David , Yorston Warren , Graevskaya Elizaveta , Dobbie Kiryn , Fraser Stuart , Dungey Heidi S. , Buddenbaum Henning
Published: April 2023

Myrtle rust, caused by the fungus Austropuccinia psidii, is a serious disease, which affects many Myrtaceae species. Commercial nurseries that propagate Myrtaceae species are prone to myrtle rust and require a reliable method that allows previsual and early detection of the disease. This study uses time-series thermal imagery and visible-to-short-infrared spectroscopy measurements acquired over 10 days from 81 rose apple plants ( Syzygium jambos) that were either inoculated with myrtle rust or maintained disease-free. Using these data, the objectives were to (i) quantify the accuracy of models using thermal indices and narrowband hyperspectral indices (NBHI) for previsual and early detection of myrtle rust using data from older resistant green leaves and young susceptible red leaves and (ii) identify the most important NBHI and thermal indices for disease detection. Using predictions made on a validation dataset, models using indices derived from thermal imagery were able to perfectly (F1 score = 1.0; accuracy = 100%) distinguish control from infected plants previsually one day before symptoms appeared (1 DBS) and for all stages after early symptoms appeared. Compared with control plants, plants with myrtle rust had lower and more variable normalized canopy temperature, which was associated with higher stomatal conductance and transpiration. Using NBHI derived from green leaves, excellent previsual classification was achieved 3 DBS, 2 DBS, and 1 DBS (F1 score range = 0.89 to 0.94). The accurate characterization of myrtle rust during previsual and early stages of disease development suggests that a robust detection methodology could be developed within a nursery setting.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Detection and Diagnosis of Bacterial Leaf Streak on Small Grain Cereals: From Laboratory to Field
Authors: Osdaghi Ebrahim , Taghavi S. Mohsen , Aliabadi Ali Alizadeh , Khojasteh Moein , Abachi Hamid , Moallem Mahsa , Mohammadikhah Sedighe , Shah Syed Mashab Ali , Chen Gongyou , Liu Zhaohui
Published: April 2023

Bacterial leaf streak of small-grain cereals is an economically important disease of wheat and barley crops. The disease occurs in many countries across the globe, with particular importance in regions characterized by high precipitation or areas in which sprinkler irrigation is used. Three genetically distinct lineages of the Gram-negative bacterium Xanthomonas translucens ( X. translucens pv. undulosa, X. translucens pv. translucens, and X. translucens pv. cerealis) are responsible for most of the bacterial leaf streak infections on wheat and barley crops. Considering the seedborne nature of the pathogens, they are included in the A2 (high-risk) list of quarantine organisms for some European countries; hence, they are under strict quarantine control and zero tolerance. Due to the taxonomic complexities within X. translucens, the exact geographic distribution of each pathovar has not yet been determined. In this mini review, we provide an updated overview of the detection and diagnosis of the bacterial leaf streak pathogens. First, a short history of the leaf streak pathogens is provided, followed by the symptomology and host range of the causal agents. Then, the utility of conventional methods and high-throughput molecular approaches in the precise detection and identification of the pathogens is explained. Finally, we highlight the role of quarantine inspections and early detection of the pathogen in combating the risk of bacterial leaf streak in the 21st century's small-grains cereals’ industry.
A Draft Genome Resource for Marasmius tenuissimus, an Emerging Causal Agent of Thread Blight Disease in Cacao
Authors: Leung Jason , Cohen Stephen P. , Baruah Indrani K. , Ali Shahin S. , Shao Jonathan , Bukari Yahaya , Amoako-Attah Ishmael , Meinhardt Lyndel W. , Bailey Bryan A.
Published: April 2023

Thread blight disease (TBD) is a serious emerging threat to global cacao production, causing leaf blight symptoms and necrosis in the canopy of infected trees. Though previously thought to be caused primarily by the fungus Marasmiellus scandens, recent work has revealed that a variety of pathogenic Marasmiaceae are responsible for TBD, with Marasmius tenuissimus identified as the dominant causal agent of TBD in Ghanaian cacao plantations. M. tenuissimus has also been reported in remote organic cacao plantations in the Amazonas Department of Peru, infecting 90 to 100% of the trees surveyed. Here, we have assembled and annotated the nuclear genome of M. tenuissimus isolate GH-37. This resource is a first attempt at a high-quality draft genome utilizing both second- and third-generation sequencing for M. tenuissimus and extends the current understanding of the evolution, ecology, and virulence of this pathogen.

[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Histological Comparative Analysis of Bowman Layer Grafts Procured Using 3 Different Techniques
Authors: Son Hyeck-Soo , Moon Loren , Wang Jiangxia , Eberhart Charles G. , Jun Albert S. , Srikumaran Divya , Soiberman Uri S.
Published: April 2023

Purpose:

The objective of this study is to perform a histological analysis of Bowman layer (BL) grafts.

Methods:

BL grafts were procured from 13 human cadaver corneal tissues using 3 different donor preparation techniques. Subsequently, the grafts were fixed in 10% buffered formalin phosphate and embedded in paraffin. Hematoxylin and eosin sections of BL grafts were obtained and analyzed under a light microscope. BL and full graft thickness were measured using an image-processing software.

Results:

All 13 BL grafts contained residual anterior stromal tissue. BL stripping using Kelman-McPherson and Moorfield forceps (technique 3) achieved the thinnest graft thickness with a mean full graft thickness of 18.7 μm (95% confidence interval [CI], −9.8 to 47.2) at the thinnest point of the graft, whereas BL procurement using the Melles lamellar dissector (technique 2) led to the highest mean full graft thickness of 279.9 μm (95% CI, 251.4–308.5) even at the thinnest area of the graft. By contrast, BL dissection using a blunt dissector (technique 1) provided a mean full graft thickness of 70.2 μm (95% CI, 40.4–100.1) at the graft's thinnest point. Although peripheral graft tears occurred in 50%, 50%, and 100% of techniques 1, 2, and 3, respectively, intact 6.25-mm diameter BL grafts could be secured in 50%, 100%, and 80% of techniques 1, 2, and 3, respectively.

Conclusions:

None of the techniques used led to the procurement of pure BL grafts devoid of the anterior stroma. Peripheral scoring with a thin needle and tissue manipulation with Kelman-McPherson and Moorfield forceps led to the thinnest grafts in this study.
Survival analysis of malignant peripheral nerve sheath tumor: Experience of a tertiary center in Taiwan
Authors: Chang Yu-Wei , Liao Wen-Chieh
Published: April 2023

Background:

This study aimed to analyze the demographic characteristics and prognostic factors of malignant peripheral nerve sheath tumor (MPNST) in a Taiwanese population. Single-center treatment outcomes were also presented.

Methods:

This retrospective cohort study analyzed the medical records of 54 patients with pathological diagnoses of MPNSTs from 2005 to 2021 at a single institution. The primary endpoint was the 5-year overall survival rate of MPNST, and the secondary endpoint was recurrence-free 5-year survival. Variables including patient characteristics, metastasis status at initial diagnosis, and surgical outcomes were analyzed with competing risk analysis.

Results:

Among all 41 eligible patients diagnosed with MPNST, female predominance was noted, and the median age at diagnosis was 44 years. The most common site of lesion was found at the trunk (46.34%), and eight patients were diagnosed with notable metastasis. Twelve patients were diagnosed with type 1 neurofibromatosis (NF1). The 5-year overall survival rate was 36.84% and the 5-year recurrence-free survival was 28.95%. Metastasis diagnosed at presentation, large lesion sizes, and recurrence were identified as significant poor prognostic factors of survival. Metastasis diagnosed at presentation was identified as the only significant risk factor of recurrence.

Conclusion:

In our series, metastasis diagnosed at presentation, large lesion sizes, and recurrence were identified as significant poor prognostic factors of survival. Metastasis was also identified as the only significant risk factor of recurrence. NF1-associated MPNSTs presented with significantly larger tumor sizes and additional treatment postoperatively did not significantly improve survival. The limitations of this study include its retrospective nature and sample size.
Understanding renal phosphate handling: unfinished business
Authors: Lederer Eleanor
Published: April 2023

Purpose of review

The purpose of this review is to highlight the publications from the prior 12–18 months that have contributed significant advances in the field of renal phosphate handling.

Recent findings

The discoveries include new mechanisms for the trafficking and expression of the sodium phosphate cotransporters; direct link between phosphate uptake and intracellular metabolic pathways; interdependence between proximal tubule transporters; and the persistent renal expression of phosphate transporters in chronic kidney disease.

Discovery of new mechanisms for trafficking and regulation of expression of phosphate transporters suggest new targets for the therapy of disorders of phosphate homeostasis. Demonstration of stimulation of glycolysis by phosphate transported into a proximal tubule cell expands the scope of function for the type IIa sodium phosphate transporter from merely a mechanism to reclaim filtered phosphate to a regulator of cell metabolism. This observation opens the door to new therapies for preserving kidney function through alteration in transport. The evidence for persistence of active renal phosphate transport even with chronic kidney disease upends our assumptions of how expression of these transporters is regulated, suggests the possibility of alternative functions for the transporters, and raises the possibility of new therapies for phosphate retention.
Sagittal deformity of Garden type I and II geriatric femoral neck fractures is frequently misclassified by lateral radiographs
Authors: Tiee Madeline S. , Golz Andrew G. , Kim Andrew , Cohen Joseph B. , Summers Hobie D. , Alexander Anup J. , Lack William D.
Published: April 2023

Objectives:

The objective of this study was to determine the validity and inter-rater reliability of radiographic assessment of sagittal deformity of femoral neck fractures.

Design:

This is a retrospective cohort study.

Setting:

Level 1 trauma center.

Patients/Participants:

Thirty-one patients 65 years or older who sustained low-energy, Garden type I/II femoral neck fractures imaged with biplanar radiographs and either computed tomography or magnetic resonance imaging were included.

Main Outcome Measurements:

Preoperative sagittal tilt was measured on lateral radiographs and compared with the tilt identified on advanced imaging. Fractures were defined as “high-risk” if posterior tilt was ≥20 degrees or anterior tilt was >10 degrees.

Results:

Of 31 Garden type I/II femoral neck fractures, advanced imaging identified 10 high-risk fractures including 8 (25.8%) with posterior tilt ≥20 degrees and 2 (6.5%) with anterior tilt >10 degrees. Overall, there was no significant difference between sagittal tilt measured using lateral radiographs and advanced imaging (P = 0.84), and the 3 raters had good agreement between their measurements of sagittal tilt on lateral radiographs (interclass correlation coefficient 0.79, 95% confidence interval [0.65, 0.88], P < 0.01). However, for high-risk fractures, radiographic measurements from lateral radiographs alone resulted in greater variability and underestimation of tilt by 5.2 degrees (95% confidence interval [−18.68, 8.28]) when compared with computed tomography/magnetic resonance imaging. Owing to this underestimation of sagittal tilt, the raters misclassified high-risk fractures as “low-risk” in most cases (averaging 6.3 of 10, 63%, range 6 − 7) when using lateral radiographs while low-risk fractures were rarely misclassified as high-risk (averaging 1.7 of 21, 7.9%, range 1 − 3, P = 0.01).

Conclusions:

Lateral radiographs frequently lead surgeons to misclassify high-risk sagittal tilt of low-energy femoral neck fractures as low-risk. Further research is necessary to improve the assessment of sagittal plane deformity for these injuries.

Level of Evidence:

Level IV diagnostic study.
Historical, Diagnostic, and Chromatic Treatment in Visual Snow Syndrome: A Retrospective Analysis
Authors: Han M. H. Esther , Ciuffreda Kenneth J. , Rutner Daniella
Published: April 2023

SIGNIFICANCE

Visual snow syndrome is a relatively new medical condition, with presence of visual snow as the primary visual-perceptual symptom. Information from the present study will improve future clinical diagnostic and treatment aspects in this population.

PURPOSE

This study aimed to determine the historical, diagnostic, and treatment aspects in patients with documented visual snow syndrome/visual snow in an academic, optometric setting.

METHODS

A retrospective analysis was performed in patients (N = 40, aged 12 to 55 years) with documented visual snow syndrome/visual snow examined over a 4-year period. Information was collected by a detailed case history and the Visual Snow Syndrome Symptom Survey. Treatment assessment was performed using the Intuitive Colorimeter, and a wide selection of chromatic tints was assessed under the most provocative/exacerbating and other conditions.

RESULTS

Visual snow was typically constant and monochromatic, with it being present on average 6.43 years. Bright and dark surfaces were the most provocative/exacerbating/revealing conditions, along with the viewing of computer screens. The most common etiology was mild traumatic brain injury. The most common primary and secondary symptoms were photosensitivity and tinnitus, respectively. There was a high frequency of occurrence of oculomotor deficits, especially accommodative and vergence insufficiency (~40 to 50%). Eighty percent of the patients were prescribed a chromatic tint with subjective visual reduction of visual snow ranging from 15 to 100% (mean, 45%).

CONCLUSIONS

The present information will help in understanding this unusual medicoperceptual condition, especially with respect to simple treatment frequently using readily available chromatic tints.
Increases in IUD Provision at Alabama Department of Public Health Clinics From 2016 to 2019
Authors: Smith Michael G. , Beatty Kate E. , Khoury Amal J. , Gilliam Lynda , de Jong Jordan
Published: April 2023

The Alabama Department of Public Health (ADPH) began allocating Title X funding to intrauterine device (IUD) provision at family planning clinics in 2019, instated more training opportunities, and expanded nurse practitioner scope of practice to include IUD placements. We assessed IUD provision and protocols at ADPH Title X clinics in 2016 and 2019 before and after ADPH policy changes. Generalized binomial regression models assessed differences between years. The proportion of ADPH clinics reporting offering any IUD on-site increased by 61.6 percentage points (P < .001), stockpiling IUDs on-site increased by 85.9 percentage points (P < .001), IUD placement/removal training increased by 71.4 percentage points (P < .001), and same-visit IUD placement trainings increased by 64.1 percentage points (P < .001). Advanced practice nurses were significantly more likely to place IUDs in 2019 compared with 2016 (P < .001). These findings highlight the positive impact of policy changes related to Title X funding allocation and scope of practice on provision of a full range of contraceptive methods. These changes in policies and practices at the state and local levels within ADPH have expanded the availability of the full range of contraceptive options across the state of Alabama. This expanded access to contraceptive options is especially important given the rapid changes in reproductive health policies occurring in Alabama and across the United States.
Medical Cannabis in the Treatment of Parkinson’s Disease
Authors: Aladeen Traci S. , Mattle Anna G. , Zelen Kory , Mesha Moustafa , Rainka Michelle M. , Geist Tanya , Myers Bennett , Mechtler Laszlo
Published: April 2023

Objectives

Medical cannabis (MC) has recently garnered interest as a potential treatment for neurologic diseases, including Parkinson’s disease (PD). A retrospective chart review was conducted to explore the impact of MC on the symptomatic treatment of patients with PD.

Methods

Patients with PD treated with MC in the normal course of clinical practice were included (n = 69). Data collected from patient charts included MC ratio/formulation changes, PD symptom changes after initiation of MC, and adverse events (AEs) from MC use. Information regarding changes in concomitant medications after MC initiation, including opioids, benzodiazepines, muscle relaxants, and PD medications, was also collected.

Results

Most patients were initially certified for a 1:1 (∆9-tetrahydrocannabinol:cannabidiol) tincture. Eight-seven percent of patients (n = 60) were noted to exhibit an improvement in any PD symptom after starting MC. Symptoms with the highest incidence of improvement included cramping/dystonia, pain, spasticity, lack of appetite, dyskinesia, and tremor. After starting MC, 56% of opioid users (n = 14) were able to decrease or discontinue opioid use with an average daily morphine milligram equivalent change from 31 at baseline to 22 at the last follow-up visit. The MC was well-tolerated with no severe AEs reported and low rate of MC discontinuation due to AEs (n = 4).

Conclusions

The MC may improve motor and nonmotor symptoms in patients with PD and may allow for reduction of concomitant opioid medication use. Large, placebo-controlled, randomized studies of MC use in patients with PD are required.
John David Hunt. 12 December 1936—8 December 2012
Authors: Browne David J. , McCartney D. Graham
Published: April 2023

John Hunt was a scholar of the solidification of metallic alloys, and published seminal works that are of influence today in the design of alloy casting, welding and additive manufacturing processes. John was raised in the West Country of England, and following school did National Service in the Royal Air Force. He entered the University of Cambridge in 1957, being awarded an honours BA in metallurgy in 1960, and a PhD for studies of solidification of eutectic alloys in 1963. John met Ann Carroll during his Cambridge studies; they married in 1961 and later had three children. From 1963 to 1965 John carried out research with Ken Jackson at Bell Laboratories, New Jersey, USA. They published groundbreaking papers on solidification and pioneered the use of transparent organic analogues. John returned to England and, following a year working at the UK Atomic Energy Authority at Harwell, he joined the faculty at the University of Oxford in 1966. During a 36-year academic career at Oxford, John made significant contributions to the scientific understanding of solidification on many topics, including dendritic array growth, eutectic and peritectic solidification, the columnar-to-equiaxed transition and twin roll casting. As well as being a talented experimentalist, he published many groundbreaking theoretical analyses and also pioneered the use of numerical methods for the simulation of solidification phenomena. He was an accomplished educator of undergraduate and postgraduate students, and a fellow of St Edmund Hall, Oxford. John was a family man, and kept geese and pigs, grew apples and made legendary cider at his old farmhouse home north of Oxford.