bluuebunny/crossref_metadata_2025_split huggingface dataset:
uS3/Rps3 controls fidelity of translation termination and programmed stop codon readthrough in co-operation with eIF3
Authors: Poncová Kristýna , Wagner Susan , Jansen Myrte Esmeralda , Beznosková Petra , Gunišová Stanislava , Herrmannová Anna , Zeman Jakub , Dong Jinsheng , Valášek Leoš Shivaya 
Published: October 2019

AbstractRibosome was long considered as a critical yet passive player in protein synthesis. Only recently the role of its basic components, ribosomal RNAs and proteins, in translational control has begun to emerge. Here we examined function of the small ribosomal protein uS3/Rps3, earlier shown to interact with eukaryotic translation initiation factor eIF3, in termination. We identified two residues in consecutive helices occurring in the mRNA entry pore, whose mutations to the opposite charge either reduced (K108E) or increased (R116D) stop codon readthrough. Whereas the latter increased overall levels of eIF3-containing terminating ribosomes in heavy polysomes in vivo indicating slower termination rates, the former specifically reduced eIF3 amounts in termination complexes. Combining these two mutations with the readthrough-reducing mutations at the extreme C-terminus of the a/Tif32 subunit of eIF3 either suppressed (R116D) or exacerbated (K108E) the readthrough phenotypes, and partially corrected or exacerbated the defects in the composition of termination complexes. In addition, we found that K108 affects efficiency of termination in the termination context-specific manner by promoting incorporation of readthrough-inducing tRNAs. Together with the multiple binding sites that we identified between these two proteins, we suggest that Rps3 and eIF3 closely co-operate to control translation termination and stop codon readthrough.
BacFITBase: a database to assess the relevance of bacterial genes during host infection
Authors: Rendón Javier Macho , Lang Benjamin , Tartaglia Gian Gaetano , Burgas Marc Torrent 
Published: October 2019

Abstract
Bacterial infections have been on the rise world-wide in recent years and have a considerable impact on human well-being in terms of attributable deaths and disability-adjusted life years. Yet many mechanisms underlying bacterial pathogenesis are still poorly understood. Here, we introduce the BacFITBase database for the systematic characterization of bacterial proteins relevant for host infection aimed to enable the identification of new antibiotic targets. BacFITBase is manually curated and contains more than 90 000 entries with information on the contribution of individual genes to bacterial fitness under in vivo infection conditions in a range of host species. The data were collected from 15 different studies in which transposon mutagenesis was performed, including top-priority pathogens such as Acinetobacter baumannii and Campylobacter jejuni, for both of which increasing antibiotic resistance has been reported. Overall, BacFITBase includes information on 15 pathogenic bacteria and 5 host vertebrates across 10 different tissues. It is freely available at www.tartaglialab.com/bacfitbase.
Prenatal Nicotine Exposure in Rodents: Why Are There So Many Variations in Behavioral Outcomes?
Authors: Polli Filip Souza , Kohlmeier Kristi Anne 
Published: October 2019

Abstract

Introduction
The World Health Organization (WHO) reported that smoking cessation rates among women have stagnated in the past decade and estimates that hundreds of millions of women will be smokers in the next decade. Social, environmental, and biological conditions render women more susceptible to nicotine addiction, imposing additional challenges to quit smoking during gestation, which is likely why more than 8% of pregnancies in Europe are associated with smoking. In epidemiological investigations, individuals born from gestational exposure to smoking exhibit a higher risk of development of attention-deficit/hyperactive disorder (ADHD) and liability to drug dependence. Among other teratogenic compounds present in tobacco smoke, nicotine actions during neuronal development could contribute to the observed outcomes as nicotine misleads signaling among progenitor cells during brain development. Several experimental approaches have been developed to address the consequences of prenatal nicotine exposure (PNE) to the brain and behavior but, after four decades of studies, inconsistent data have been reported and the lack of consensus in the field has compromised the hypothesis that gestational nicotine exposure participates in cognitive and emotional behavioral deficits.

Aims
In this review, we discuss the most commonly used PNE models with focus on their advantages and disadvantages, their relative validity, and how the different technical approaches could play a role in the disparate outcomes.

Results
We propose methodological considerations, which could improve the translational significance of the PNE models.

Conclusions
Such alterations might be helpful in reconciling experimental findings, as well as leading to development of treatment targets for maladaptive behaviors in those prenatally exposed.

Implications
In this article, we have reviewed the advantages and disadvantages of different variables of the commonly used experimental models of PNE. We discuss how variations in the nicotine administration methods, the timing of nicotine exposure, nicotine doses, and species employed could contribute to the disparate findings in outcomes for PNE offspring, both in behavior and neuronal changes. In addition, recent findings suggest consideration of epigenetic effects extending across generations. Finally, we have suggested improvements in the available PNE models that could contribute to the enhancement of their validity, which could assist in the reconciliation of experimental findings.
Genomic Epidemiology of Major Extraintestinal Pathogenic Escherichia coli Lineages Causing Urinary Tract Infections in Young Women Across Canada
Authors: Fibke Chad D , Croxen Matthew A , Geum Hyun Min , Glass Magdalena , Wong Eugenia , Avery Brent P , Daignault Danielle , Mulvey Michael R , Reid-Smith Richard J , Parmley E Jane , Portt Andrea , Boerlin Patrick , Manges Amee R 
Published: October 2019

Abstract

Background
A few extraintestinal pathogenic Escherichia coli (ExPEC) multilocus sequence types (STs) cause the majority of community-acquired urinary tract infections (UTIs). We examine the genomic epidemiology of major ExPEC lineages, specifically factors associated with intestinal acquisition.

Methods
A total of 385 women with UTI caused by E. coli across Canada were asked about their diet, travel, and other exposures. Genome sequencing was used to determine both ST and genomic similarity. Logistic regression was used to identify factors associated with the acquisition of and infection with major ExPEC STs relative to minor ExPEC STs.

Results
ST131, ST69, ST73, ST127, and ST95 were responsible for 54% of all UTIs. Seven UTI clusters were identified, but genomes from the ST95, ST127, and ST420 clusters exhibited as few as 3 single nucleotide variations across the entire genome, suggesting recent acquisition. Furthermore, we identified a cluster of UTIs caused by 6 genetically-related ST1193 isolates carrying mutations in gyrA and parC. The acquisition of and infection with ST69, ST95, ST127, and ST131 were all associated with increased travel. The consumption of high-risk foods such as raw meat or vegetables, undercooked eggs, and seafood was associated with acquisition of and infection with ST69, ST127, and ST131, respectively.

Conclusions
Reservoirs may aid in the dissemination of pandemic ExPEC lineages in the community. Identifying ExPEC reservoirs may help prevent future emergence and dissemination of high-risk lineages within the community setting.
The Mitochondrial Respiratory Chain Maintains the Photosynthetic Electron Flow in Arabidopsis thaliana Leaves under High-Light Stress
Authors: Yamada Shoya , Ozaki Hiroshi , Noguchi Ko 
Published: October 2019

Abstract
The plant respiratory chain includes the ATP-coupling cytochrome pathway (CP) and ATP-uncoupling alternative oxidase (AOX). Under high-light (HL) conditions, plants experience photoinhibition, leading to a damaged photosystem II (PSII). The respiratory chain is considered to affect PSII maintenance and photosynthetic electron transport under HL conditions. However, the underlying details remain unclear. In this study, we investigated the respiratory chain functions related to PSII maintenance and photosynthetic electron transport in plants exposed to HL stress. We measured the HL-induced decrease in the maximum quantum yield of PSII in the leaves of wild-type and AOX1a-knockout (aox1a) Arabidopsis thaliana plants in which CP was partially inhibited by a complex-III inhibitor. We also calculated PSII photodamage and repair rate constants. Both rate constants changed when CP was partially inhibited in aox1a plants, suggesting that the respiratory chain is related to both processes. Before HL stress, photosynthetic linear electron flow (LEF) decreased when CP was partially inhibited. After HL stress, aox1a in the presence of the CP inhibitor showed significantly decreased rates of LEF. The electron flow downstream from PSII and on the donor side of photosystem I may have been suppressed. The function of respiratory chain is required to maintain the optimal LEF as well as PSII maintenance especially under the HL stress.
Coverage of HIV testing among pregnant women in Nigeria: progress, challenges and opportunities
Authors: Ajayi Ai , Awopegba Oe , Owolabi Eo , Ajala A 
Published: October 2019

Abstract

Objective
This study assessed the progress, opportunities and challenges in scaling up of HIV testing for pregnant women in Nigeria.

Methods
Data were retrieved from the 2016–2017 fifth multiple cluster survey. Adjusted and unadjusted logistic regression models were used to examine demographic factors associated with HIV testing while controlling for geopolitical zones.

Results
At the population level, the coverage of HIV testing among pregnant women increased by 10% points from 32.8 to 42.7% between 2013 and 2017. Also, the coverage of antenatal HIV testing grew by 20 points, from 50.1 to 70.5% over the period. However, women were still more likely to be tested for HIV during pregnancy if they were older than 24 years [adjusted odds ratio (AOR) 1.33, 95% CI 1.04–1.69], had higher education [AOR 6.94, 95% CI 5.07–9.49], resided in urban areas [AOR 1.26, 95% CI 1.07, 1.50] and belong to richest wealth quintile [AOR 7.43, 95% CI 5.72–9.66].

Conclusion
Our findings suggest that progress has been made in scaling up of antenatal coverage of HIV testing. However, the level of HIV testing during pregnancy remains low and far below the 95% national target. Appropriate interventions are needed in resource-poor communities where antenatal care utilization is very low.
Association of telomere length with risk of rheumatoid arthritis: a meta-analysis and Mendelian randomization
Authors: Zeng Zhen , Zhang Wanting , Qian Yu , Huang Huijun , Wu David J H , He Zhixing , Ye Ding , Mao Yingying , Wen Chengping 
Published: October 2019

Abstract

Objective
To evaluate the telomere length (TL) in patients with RA relative to that in controls and to test whether TL is causally associated with risk of RA.

Methods
Systematic review and meta-analysis of relevant literature was conducted to evaluate the association between TL and RA. Standardized mean differences with 95% CIs of TL in RA patients relative to controls were pooled using fixed or random-effects models. TL-related single-nucleotide polymorphisms were selected from a genome-wide association study of 37 684 individuals, and summary statistics of RA were obtained from a genome-wide association study meta-analysis including 14 361 RA patients and 43 923 controls. Mendelian randomization was performed using the inverse-variance weighted, weighted-median and likelihood-based methods. Sensitivity analyses were performed to test the robustness of the association.

Results
In the meta-analysis of 911 RA patients and 2498 controls, we found that patients with RA had a significantly shorter TL compared with controls (standardized mean differences = −0.50; 95% CI −0.88, −0.11; P = 0.012). In the Mendelian randomization analysis, we found that genetically predicted longer TL was associated with a reduced risk of RA [odds ratio = 0.68; 95% CI 0.54, 0.86; P = 0.002 using the inverse-variance weighted method]. Sensitivity analyses using alternative Mendelian randomization approaches yielded similar findings, suggesting the robustness of the causal association.

Conclusion
Our study provides evidence for a negative causal association of TL with risk of RA. Further studies are warranted to elucidate the underlying mechanism for the role of telomeres in the development of RA.
Far away, so close! Integrative taxonomy reveals a new genus and species of land flatworm (Platyhelminthes: Geoplanidae) from southern South America
Authors: Negrete Lisandro , Do Amaral Silvana Vargas , Ribeiro Giovana Gamino , Wolmann Gonçalves Juliana , Valiati Victor Hugo , Damborenea Cristina , Brusa Francisco , Leal-Zanchet Ana Maria 
Published: October 2019

AbstractLand flatworms usually show low ability to disperse and high endemicity, displaying many singletons in studies on land planarian assemblages. Thus, many species have been described based on specimens sampled in a single locality and/or on a few specimens. Based on phylogenetic analyses of concatenated COI and 18S rRNA genes and morphological analyses, a new genus and species of geoplaninid land planarian is described from central–east Argentina and southern Brazil. Winsoria gen. nov. shows, among its most outstanding features, a ventral cephalic retractor muscle and a subneural muscle layer that extends throughout the anterior region of the body. In addition, characters of the reproductive system and the phylogenetic analyses support the erection of this new genus. According to molecular phylogenies,Winsoria bipatria sp. nov. is closely related to species of Luteostriata, Supramontana and Issoca, taxa that also possess a cephalic retractor muscle. Despite its disjunct distribution, phylogenetic analyses, genetic divergence and morphological features show that the allopatric populations studied herein belong to a single species. We argue that the occurrence of W. bipatria in localities separated by hundreds of kilometres and a geographical barrier should be explained by passive dispersal.
Levamisole-induced vasculitis
Authors: George Tonya C. , Freet Daniel J. , Cross James M. , Huzar Todd F. 
Published: October 2019

ABSTRACT
Levamisole is a veterinary antihelminthic, chemotherapeutic agent, and immunomodulator that also is used as an adulterant and cutting agent in cocaine distribution. This drug may potentiate the sympathomimetic actions of cocaine and can cause neutropenia, agranulocytosis, purpuric retiform lesions, and skin necrosis. This article describes two cases of suspected levamisole-induced vasculitis. No standardized diagnostic or treatment algorithm exists for this challenging condition. Diagnosis and treatment require a multidisciplinary team approach.
T-Cell–Rich Recurrence of Primary Cutaneous Follicle Center Lymphoma After Systemic Rituximab: A Diagnostic Pitfall
Authors: Santonja Carlos , Prieto-Torres Lucía , Pérez-Sáenz María de los Ángeles , Requena Luis , Rodríguez-Pinilla Socorro-María 
Published: October 2019

Abstract:
We report on a 74-year-old man with a cutaneous B-cell follicle center lymphoma, which was treated upfront with systemic rituximab and suffered several local relapses. The first of the local recurrences, 10 months after completion of treatment, was characterized by a dense T-cell infiltrate that obscured a minor population of B-cell lymphoma cells, suggesting a second primary cutaneous T-cell lymphoma. This represents a previously not reported diagnostic pitfall and underscores the importance of performing sequential biopsies when dealing with lymphoma recurrences in this setting.
Maintaining Quality of Life: Electrochemotherapy for Palliative Periorbital Malignancy
Authors: Ullrich Katja , Bisase Brian , Kumar Siva , Malhotra Raman 
Published: October 2019

Electrochemotherapy has been used successfully for treatment of recurrent head and neck skin cancers and skin metastasis. It combines both electroporation and chemotherapy. The authors report 4 patients, who all had metastatic periorbital malignancy. These patients were palliative with widespread metastatic malignancy. All patients had either already had multiple procedures or declined surgical resection and preferred less involved measures. The authors report technique and outcomes. Patient 1: 83-year-old man with recurrent malignant melanoma (MM) nodules (BRAF negative) in the left medial orbit and medial canthal area after rhinectomy and previous resections. Patient 2: 72-year-old man with metastatic MM who developed painful and unsightly metastatic nodules on the right and left forehead and the left medial canthus. Patient 3: 93-year-old man with background of widespread multiple myeloma, considered palliative. He developed a left forehead SCC, apparent as a fungating ulcer, which caused significant pain due to perineural invasion. Patient 4: 91-year-old woman with recurrent metastatic sebaceous cell carcinoma of the left lower eyelid obstructing her vision. All patients experienced an improvement in their pain and quality of life. None of the patients developed any significant periorbital inflammation or adverse complications. Electrochemotherapy may be a useful palliative treatment for periorbital tumors. It improves pain and reduces tumor volume. It can be considered for tumors where palliative radiotherapy may be contraindicated.
Electrochemotherapy is a useful palliative treatment for metastases to the periorbital area, improving pain and size of the tumors.
Chronic, Symptomatic Orbital Inflammation Resulting From Retained Bone Wax
Authors: Thangamathesvaran Loka , Mirani Neena , Turbin Roger , Langer Paul D. 
Published: October 2019

A 58-year-old man presented with a 9-month history of a chronically draining surgical wound and low-grade periorbital inflammation following a right lateral orbitotomy. Imaging of the right orbit revealed a peculiar lesion in the right lateral orbit that was hypointense on both T1- and T2-weighted MRI with peripheral enhancement. Exploratory orbitotomy and biopsy established the diagnosis of a chronic foreign body inflammatory reaction to bone wax; symptoms resolved following evacuation of the retained foreign material.
A 58-year-old man developed a chronic, symptomatic, inflammatory reaction to bone wax following a lateral orbitotomy; only once previously has symptomatic orbital inflammation following orbital surgery as a result of bone wax been reported.
The Programmed Death Pathway in Ocular Adnexal Sebaceous Carcinoma
Authors: Bowen Randy C. , Lawson Brendan M. , Jody Nicole M. , Potter Heather D. , Lucarelli Mark J. 
Published: October 2019

Sebaceous carcinoma of the ocular and periocular regions showed expression of immune checkpoint ligands PD-1, PD-L1, and PD-L2, which suggests PD blockade may provide benefit as an adjuvant therapy for patients with sebaceous carcinoma.

Purpose:
Sebaceous carcinoma can be highly malignant and difficult to treat. Surgical excision followed by periocular reconstruction is the primary method of treatment. In aggressive cases, radiation, topical chemotherapy, and systemic chemotherapy have been explored as adjuvant therapy. Immunotherapy, through immune checkpoint inhibitors, has proven to have significant antitumor effect in many cancer types, including melanoma, non-small cell lung cancer, renal cell carcinoma, and cutaneous squamous cell carcinoma. Little is known about endogenous immune response directed against sebaceous carcinoma. In this study, we aim to characterize the expression pattern of PD-1 and its ligands PD-L1 and PD-L2 in both sebaceous carcinoma and in infiltrating immune cells to explore the potential use of checkpoint blockade as therapy.

Methods:
We performed a retrospective chart and histology review of patients with sebaceous carcinoma between 1990 and 2017 at the University of Wisconsin. Tissue microarrays were made from paraffin blocks. Immunohistochemistry was performed for evaluation of tumor and immune cell infiltration for expression of PD-1, PD-L1, and PD-L2. Tumor or infiltrating immune cells were considered positive if ≥5% of cells had membranous (cell surface) expression.

Results:
Twenty-eight patients were included. PD-L1 and PD-1 were not significantly expressed on tumor cells; however, PD-L1 and PD-1 were expressed on infiltrating immune cells in 46% and 25% of patients, respectively. In contrast, PD-L2 demonstrated positive expression on tumor cells in 46% of the cases along with positive expression on infiltrating immune cells in 38% of the cases.

Conclusions:
Sebaceous carcinoma currently has few effective adjuvant treatment options. The expression of PD-1, PD-L1, and PD-L2 on infiltrating immune cells and PD-L2 on tumor cells restrains T-cells from full activation and proliferation, therefore limiting the antitumor effect of T-cells, tipping the balance toward unopposed tumor progression. Consequently, PD-1 or PD-L1 inhibitors may have a role in sebaceous carcinoma treatment. Given the prevalence of PD-L2 expression in sebaceous carcinoma and the lack of PD-L2 blockade therapy available, PD-1 blockade may provide benefit over PD-L1 inhibitors. PD-1 blockade in combination with current methods may be a viable therapeutic option for patients with sebaceous carcinoma and deserves further study.
Giant Bilateral Cysts of the Accessory Lacrimal Glands of Wolfring in a Child
Authors: Feijó Eduardo Damous , Alencastro Landim George , de Melo Dias Mirna , Alves de Souza Bruna Angelina , Murillo Limongi Roberto , Matayoshi Suzana 
Published: October 2019

Ductal cysts of the accessory lacrimal glands of Wolfring are rare clinical entities. They typically present as mobile and translucent lesions on the superior or inferior tarsal borders. Here, the authors describe a 7-year-old male child presenting with giant bilateral cysts of Wolfring. Management of such cysts is primarily surgical and the preferred route for excision is transconjunctival. To the best of the authors' knowledge, this is the first report of a bilateral Wolfring dacryops affecting a child.
Cysts of the accessory lacrimal glands of Wolfring are rare clinical entities. To the authors’ knowledge, here the authors describe the first report of a bilateral Wolfring dacryops affecting a child.