bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twenty-five-year research progress in hookworm excretory/secretory products
Authors: Abuzeid Asmaa M. I. , Zhou Xue , Huang Yue , Li Guoqing 
Published: March 2020

AbstractHookworm infection is a major public health problem that threatens about 500 million people throughout tropical areas of the world. Adult hookworms survive for many years in the host intestine, where they suck blood, causing iron deficiency anemia and malnutrition. Numerous molecules, named excretory/secretory (ES) products, are secreted by hookworm adults and/or larvae to aid in parasite survival and pathobiology. Although the molecular cloning and characterization of hookworm ES products began 25 years ago, the biological role and molecular nature of many of them are still unclear. Hookworm ES products, with distinct structures and functions, have been linked to many essential events in the disease pathogenesis. These events include host invasion and tissue migration, parasite nourishment and reproduction, and immune modulation. Several of these products represent promising vaccine targets for controlling hookworm disease and therapeutic targets for many inflammatory diseases. This review aims to summarize our present knowledge about hookworm ES products, including their role in parasite biology, host-parasite interactions, and as vaccine and pharmaceutical targets and to identify research gaps and future research directions in this field.
Genetic validation of Leishmania genes essential for amastigote survival in vivo using N-myristoyltransferase as a model
Authors: Paape Daniel , Prendergast Catriona T. , Price Helen P. , Doehl Johannes S. P. , Smith Deborah F. 
Published: March 2020

AbstractBackgroundProving that specific genes are essential for the intracellular viability ofLeishmaniaparasites within macrophages remains a challenge for the identification of suitable targets for drug development. This is especially evident in the absence of a robust inducible expression system or functioning RNAi machinery that works in allLeishmaniaspecies. Currently, if a target gene of interest in extracellular parasites can only be deleted from its genomic locus in the presence of ectopic expression from a wild type copy, it is assumed that this gene will also be essential for viability in disease-promoting intracellular parasites. However, functional essentiality must be proven independently in both life-cycle stages for robust validation of the gene of interest as a putative target for chemical intervention.MethodsHere, we have used plasmid shuffle methodsin vivoto provide supportive genetic evidence thatN-myristoyltransferase (NMT) is essential forLeishmaniaviability throughout the parasite life-cycle. Following confirmation of NMT essentiality in vector-transmitted promastigotes, a range of mutant parasites were used to infect mice prior to negative selection pressure to test the hypothesis that NMT is also essential for parasite viability in an established infection.ResultsEctopically-expressedNMTwas only dispensable under negative selection in the presence of another copy. Total parasite burdens in animals subjected to negative selection were comparable to control groups only if an additionalNMTcopy, not affected by the negative selection, was expressed.ConclusionsNMTis an essential gene in all parasite life-cycle stages, confirming its role as a genetically-validated target for drug development.
One-step RT-qPCR assay for ZIKV RNA detection in Aedes aegypti samples: a protocol to study infection and gene expression during ZIKV infection
Authors: Araujo Ricardo Vieira , Feitosa-Suntheimer Fabiana , Gold Alexander S. , Londono-Renteria Berlin , Colpitts Tonya M. 
Published: March 2020

Abstract
Background
Zika virus (ZIKV) is transmitted to humans during the bite of an infected mosquito. In a scenario of globalization and climate change, the frequency of outbreaks has and will increase in areas with competent vectors, revealing a need for continuous improvement of ZIKV detection tools in vector populations. A simple, rapid and sensitive assay for viral detection is quantitative reverse transcription polymerase chain reaction (qRT-PCR), yet oligos optimized for ZIKV detection in mammalian cells and samples have repeatedly shown high background when used on mosquito ribonucleic acid (RNA). In this paper, we present a one-step qRT-PCR protocol that allows for the detection of ZIKV in mosquitoes and for the evaluation of gene expression from the same mosquito sample and RNA. This assay is a less expensive qRT-PCR approach than that most frequently used in the literature and has a much lower background, allowing confident detection.

Methods
Our new oligo design to detect ZIKV RNA included in silico analysis of both viral and mosquito (Ae. aegypti and Ae. albopictus) genomes, targeting sequences conserved between Asian and African ZIKV lineages, but not matching Aedes genomes. This assay will allow researchers to avoid nonspecific amplification in insect samples due to viral integration into the mosquito genome, a phenomenon known to happen in wild and colonized populations of mosquitoes. Standard curves constructed with in vitro transcribed ZIKV RNA were used to optimize the sensitivity, efficiency and reproducibility of the assay.

Results
Finally, the assay was used with success to detect both ZIKV RNA in infected mosquitoes and to detect expression of the Defensin A gene, an antimicrobial peptide (AMP) involved in Aedes aegypti immune response to virus infection.

Conclusions
The experimental approach to detect ZIKV RNA in Aedes aegypti presented here has demonstrated to be specific, sensitive and reliable, and additionally it allows for the analysis of mosquito gene expression during ZIKV infection.
Targeted deep amplicon sequencing of kelch 13 and cytochrome b in Plasmodium falciparum isolates from an endemic African country using the Malaria Resistance Surveillance (MaRS) protocol
Authors: L’Episcopia Mariangela , Kelley Julia , Patel Dhruviben , Schmedes Sarah , Ravishankar Shashidahar , Menegon Michela , Perrotti Edvige , Nurahmed Abduselam M. , Talha Albadawi A. , Nour Bakri Y. , Lucchi Naomi , Severini Carlo , Talundzic Eldin 
Published: March 2020

Abstract
Background
Routine molecular surveillance for imported drug-resistant malaria parasites to the USA and European Union is an important public health activity. The obtained molecular data are used to help keep chemoprophylaxis and treatment guidelines up to date for persons traveling to malaria endemic countries. Recent advances in next-generation sequencing (NGS) technologies provide a new and effective way of tracking malaria drug-resistant parasites.

Methods
As part of a technology transfer arrangement between the CDC Malaria Branch and the Istituto Superiore di Sanità (ISS), Rome, Italy, the recently described Malaria Resistance Surveillance (MaRS) protocol was used to genotype 148 Plasmodium falciparum isolates from Eritrea for kelch 13 (k13) and cytochrome b (cytb) genes, molecular markers associated with resistance to artemisinin (ART) and atovaquone/proguanil (AP), respectively.

Results
Spanning the full-length k13 gene, seven non-synonymous single nucleotide polymorphisms (SNPs) were found (K189N, K189T, E208K, D281V, E401Q, R622I and T535M), of which none have been associated with artemisinin resistance. No mutations were found in cytochrome b.

Conclusion
All patients successfully genotyped carried parasites susceptible to ART and AP treatment. Future studies between CDC Malaria Branch and ISS are planned to expand the MaRS system, including data sharing, in an effort to maintain up to date treatment guidelines for travelers to malaria endemic countries.
Dynamic of resistance alleles of two major insecticide targets in Anopheles gambiae (s.l.) populations from Benin, West Africa
Authors: Assogba Benoît S. , Pasteur Nicole , Makoundou Patrick , Unal Sandra , Baba-Moussa Lamine , Labbé Pierrick , Weill Mylène 
Published: March 2020

Abstract
Background
Insecticide resistance is a growing concern for malaria control and vector control effectiveness relies on assessing it distribution and understanding its evolution.

Methods
We assessed resistance levels and the frequencies of two major target-site mutations, L1014F-VGSC and G119S-ace-1, conferring resistance to pyrethroids (PYRs) and carbamates/organophosphates (CXs/OPs) insecticides. These data were compared to those acquired between 2006 and 2010 to follow resistance evolutionary trends over ten years.

Results
We report the results of a 3-year survey (2013–2015) of insecticide resistance in 13 localities across the whole country of Benin. Permethrin (PYR) resistance was found in all populations tested, L1014F-VGSC being almost fixed everywhere, while bendiocarb resistance was limited to a few localities, G119S-ace-1 remaining rare, with very limited variations during surveyed period. Interestingly, we found no effect of the type of insecticide pressure on the dynamics of these mutations.

Conclusions
These results confirm both the high prevalence of PYR resistance and the potential of CXs/OPs as short- to medium-term alternatives in Benin. They also underline the need for regular resistance monitoring and informed management in their usage, as the G119S-ace-1 mutation is already present in Benin and surrounding countries. Their unwise usage would rapidly lead to its spread, which would jeopardize PYR-resistant Anopheles control.
Alu retrotransposons modulate Nanog expression through dynamic changes in regional chromatin conformation via aryl hydrocarbon receptor
Authors: González-Rico Francisco J. , Vicente-García Cristina , Fernández Almudena , Muñoz-Santos Diego , Montoliu Lluís , Morales-Hernández Antonio , Merino Jaime M. , Román Angel-Carlos , Fernández-Salguero Pedro M. 
Published: March 2020

AbstractTranscriptional repression of Nanog is an important hallmark of stem cell differentiation. Chromatin modifications have been linked to the epigenetic profile of the Nanog gene, but whether chromatin organization actually plays a causal role in Nanog regulation is still unclear. Here, we report that the formation of a chromatin loop in the Nanog locus is concomitant to its transcriptional downregulation during human NTERA-2 cell differentiation. We found that two Alu elements flanking the Nanog gene were bound by the aryl hydrocarbon receptor (AhR) and the insulator protein CTCF during cell differentiation. Such binding altered the profile of repressive histone modifications near Nanog likely leading to gene insulation through the formation of a chromatin loop between the two Alu elements. Using a dCAS9-guided proteomic screening, we found that interaction of the histone methyltransferase PRMT1 and the chromatin assembly factor CHAF1B with the Alu elements flanking Nanog was required for chromatin loop formation and Nanog repression. Therefore, our results uncover a chromatin-driven, retrotransposon-regulated mechanism for the control of Nanog expression during cell differentiation.
High-throughput quantitative histology in systemic sclerosis skin disease using computer vision
Authors: Correia Chase , Mawe Seamus , Lofgren Shane , Marangoni Roberta G. , Lee Jungwha , Saber Rana , Aren Kathleen , Cheng Michelle , Teaw Shannon , Hoffmann Aileen , Goldberg Isaac , Cowper Shawn E. , Khatri Purvesh , Hinchcliff Monique , Mahoney J. Matthew 
Published: March 2020

Abstract
Background
Skin fibrosis is the clinical hallmark of systemic sclerosis (SSc), where collagen deposition and remodeling of the dermis occur over time. The most widely used outcome measure in SSc clinical trials is the modified Rodnan skin score (mRSS), which is a semi-quantitative assessment of skin stiffness at seventeen body sites. However, the mRSS is confounded by obesity, edema, and high inter-rater variability. In order to develop a new histopathological outcome measure for SSc, we applied a computer vision technology called a deep neural network (DNN) to stained sections of SSc skin. We tested the hypotheses that DNN analysis could reliably assess mRSS and discriminate SSc from normal skin.

Methods
We analyzed biopsies from two independent (primary and secondary) cohorts. One investigator performed mRSS assessments and forearm biopsies, and trichrome-stained biopsy sections were photomicrographed. We used the AlexNet DNN to generate a numerical signature of 4096 quantitative image features (QIFs) for 100 randomly selected dermal image patches/biopsy. In the primary cohort, we used principal components analysis (PCA) to summarize the QIFs into a Biopsy Score for comparison with mRSS. In the secondary cohort, using QIF signatures as the input, we fit a logistic regression model to discriminate between SSc vs. control biopsy, and a linear regression model to estimate mRSS, yielding Diagnostic Scores and Fibrosis Scores, respectively. We determined the correlation between Fibrosis Scores and the published Scleroderma Skin Severity Score (4S) and between Fibrosis Scores and longitudinal changes in mRSS on a per patient basis.

Results
In the primary cohort (n = 6, 26 SSc biopsies), Biopsy Scores significantly correlated with mRSS (R = 0.55, p = 0.01). In the secondary cohort (n = 60 SSc and 16 controls, 164 biopsies; divided into 70% training and 30% test sets), the Diagnostic Score was significantly associated with SSc-status (misclassification rate = 1.9% [training], 6.6% [test]), and the Fibrosis Score significantly correlated with mRSS (R = 0.70 [training], 0.55 [test]). The DNN-derived Fibrosis Score significantly correlated with 4S (R = 0.69, p = 3 × 10− 17).

Conclusions
DNN analysis of SSc biopsies is an unbiased, quantitative, and reproducible outcome that is associated with validated SSc outcomes.
Draft genome sequence of Bacillus sp. EE-W1 isolated from a biogas reactor
Authors: Mohammed Waleed S. , Ziganshina Elvira E. , Akhmetova Ramilya F. , Ziganshin Ayrat M. 
Published: March 2020

Abstract
Objectives
The genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data may be useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics.

Data description
Here, we present the draft genome sequence of Bacillus sp. strain EE-W1 isolated from a biogas reactor, Kazan, Russia. The assembled genome size was 5,769,164 bp, with a GC content 35.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession WIPE00000000.
An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci
Authors:   the Traumatic Stress Brain Study Group, Logue Mark W. , Miller Mark W. , Wolf Erika J. , Huber Bertrand Russ , Morrison Filomene G. , Zhou Zhenwei , Zheng Yuanchao , Smith Alicia K. , Daskalakis Nikolaos P. , Ratanatharathorn Andrew , Uddin Monica , Nievergelt Caroline M. , Ashley-Koch Allison E. , Baker Dewleen G. , Beckham Jean C. , Garrett Melanie E. , Boks Marco P. , Geuze Elbert , Grant Gerald A. , Hauser Michael A. , Kessler Ronald C. , Kimbrel Nathan A. , Maihofer Adam X. , Marx Christine E. , Qin Xue-Jun , Risbrough Victoria B. , Rutten Bart P. F. , Stein Murray B. , Ursano Robert J. , Vermetten Eric , Vinkers Christiaan H. , Ware Erin B. , Stone Annjanette , Schichman Steven A. , McGlinchey Regina E. , Milberg William P. , Hayes Jasmeet P. , Verfaellie Mieke 
Published: March 2020

AbstractBackgroundPrevious studies using candidate gene and genome-wide approaches have identified epigenetic changes in DNA methylation (DNAm) associated with posttraumatic stress disorder (PTSD).MethodsIn this study, we performed an EWAS of PTSD in a cohort of Veterans (n = 378 lifetime PTSD cases and 135 controls) from the Translational Research Center for TBI and Stress Disorders (TRACTS) cohort assessed using the Illumina EPIC Methylation BeadChip which assesses DNAm at more than 850,000 sites throughout the genome. Our model included covariates for ancestry, cell heterogeneity, sex, age, and a smoking score based on DNAm at 39 smoking-associated CpGs. We also examined in EPIC-based DNAm data generated from pre-frontal cortex (PFC) tissue from the National PTSD Brain Bank (n = 72).ResultsThe analysis of blood samples yielded one genome-wide significant association with PTSD at cg19534438 in the geneG0S2(p = 1.19 × 10-7,padj = 0.048). This association was replicated in an independent PGC-PTSD-EWAS consortium meta-analysis of military cohorts (p = 0.0024). We also observed association with the smoking-related locus cg05575921 inAHRRdespite inclusion of a methylation-based smoking score covariate (p = 9.16 × 10-6), which replicates a previously observed PGC-PTSD-EWAS association (Smith et al. 2019), and yields evidence consistent with a smoking-independent effect. The top 100 EWAS loci were then examined in the PFC data. One of the blood-based PTSD loci, cg04130728 inCHST11, which was in the top 10 loci in blood, but which was not genome-wide significant, was significantly associated with PTSD in brain tissue (in bloodp = 1.19 × 10-5,padj = 0.60, in brain,p = 0.00032 with the same direction of effect). Gene set enrichment analysis of the top 500 EWAS loci yielded several significant overlapping GO terms involved in pathogen response, including “Response to lipopolysaccharide” (p = 6.97 × 10-6,padj = 0.042).ConclusionsThe cross replication observed in independent cohorts is evidence that DNA methylation in peripheral tissue can yield consistent and replicable PTSD associations, and our results also suggest that that some PTSD associations observed in peripheral tissue may mirror associations in the brain.
Hooked epinephrine auto-injector devices in children: four case reports with three different proposed mechanisms
Authors: Goldman Ran D. , Long Katharine C. , Brown Julie C. 
Published: March 2020

Abstract
Background
The prevalence of epinephrine auto-injectors (EAI) use is on the rise. Our objective was to describes children with hooked EAI needles that were embedded in soft tissues.

Case presentation
Results: Two children self-injected in their shins. The embedded EAIs required removal in the Emergency Department. Both needles were hooked and splayed at the tip. A boy in anaphylaxis kicked his leg during EAI injection and the hooked needle embedded under his skin and was difficult to dislodge. The exposed needle was curved. A girl had an EAI administered for anaphylaxis, which was also difficult to dislodge. On removal, the distal needle tip was hooked approximately 160 degrees. Images of the device revealed that the needle fired off-center from the device and the device components were cracked. We propose three different explanations for these hooked EAI needles. The first is that the needle could hit bone during injection and curve rather than penetrates further. Secondly, the needle could bend when the patient moves during injection. Thirdly, if a needle fires sufficiently off-center to hit the cartridge carrier, this could hook the needle prior to injection.

Conclusions
Awareness of the reasons for needle hooking, damage observed, and challenges and successful approaches to their removal, can better prepare the provider for these uncommon events. Teaching parents, children and educators about safe EAI storage and appropriate restraint during use may prevent some of these accidental injuries. Reporting device failures may lead to improvements in device performance and design.
Umbilical cord-derived CD362+ mesenchymal stromal cells for E. coli pneumonia: impact of dose regimen, passage, cryopreservation, and antibiotic therapy
Authors: Horie Shahd , Masterson Claire , Brady Jack , Loftus Paul , Horan Emma , O’Flynn Lisa , Elliman Steve , Barry Frank , O’Brien Timothy , Laffey John G. , O’Toole Daniel 
Published: March 2020

Abstract
Background
Mesenchymal stromal cells (MSCs) demonstrate considerable promise for acute respiratory distress syndrome (ARDS) and sepsis. However, standard approaches to MSC isolation generate highly heterogeneous cell populations, while bone marrow (BM) constitutes a limited and difficult to access MSC source. Furthermore, a range of cell manufacturing considerations and clinical setting practicalities remain to be explored.

Methods
Adult male rats were subject to E. coli-induced pneumonia and administered CD362+ umbilical cord (UC)-hMSCs using a variety of cell production and clinical relevance considerations. In series 1, animals were instilled with E. coli and randomized to receive heterogeneous BM or UC-hMSCs or CD362+ UC-hMSCs. Subsequent series examined the impact of concomitant antibiotic therapy, MSC therapeutic cryopreservation (cryopreserved vs fresh CD362+ UC-hMSCs), impact of cell passage on efficacy (passages 3 vs 5 vs 7 vs 10), and delay of administration of cell therapy (0 h vs 6 h post-injury vs 6 h + 12 h) following E. coli installation.

Results
CD362+ UC-hMSCs were as effective as heterogonous MSCs in reducing E. coli-induced acute lung injury, improving oxygenation, decreasing bacterial load, reducing histologic injury, and ameliorating inflammatory marker levels. Cryopreserved CD362+ UC-hMSCs recapitulated this efficacy, attenuating E. coli-induced injury, but therapeutic relevance did not extend beyond passage 3 for all indices. CD362+ UC-hMSCs maintained efficacy in the presence of antibiotic therapy and rescued the animal from E. coli injury when delivered at 6 h + 12 h, following E. coli instillation.

Conclusions
These translational studies demonstrated the efficacy of CD362+ UC-hMSCs, where they decreased the severity of E. coli-induced pneumonia, maintained efficacy following cryopreservation, were more effective at early passage, were effective in the presence of antibiotic therapy, and could continue to provide benefit at later time points following E. coli injury.
MicroRNA-495 confers inhibitory effects on cancer stem cells in oral squamous cell carcinoma through the HOXC6-mediated TGF-β signaling pathway
Authors: You Xiaolong , Zhou Zhengyu , Chen Wen , Wei Xiaoyong , Zhou Heqiang , Luo Wenzheng 
Published: March 2020

Abstract
Background
Oral squamous cell carcinoma (OSCC) is associated with high morbidity and ranks sixth among malignancies worldwide. Increasing evidence suggests that microRNAs (miRNAs or miRs) play a critical role in regulating cancer stem cells (CSCs), which drive the proliferation and spread of OSCC. Therefore, based on the alteration of aberrantly expressed miR-495 and homeobox C6 (HOXC6) by Gene Expression Omnibus (GEO) analysis, we subsequently explore the potential effect of miR-495 on the progression of CSCs in OSCC.

Methods
After the isolation of CSCs from the clinical tissue samples of OSCC patients, the expression of miR-495 and HOXC6 was determined, followed by the validation of the relationship between miR-495 and HOXC6. Subsequently, gain- and loss-function approach was performed to detect the role of miR-495 and HOXC6 in cell proliferation, migration, invasion, cell cycle entry, apoptosis, and epithelial-mesenchymal transition (EMT) of CSCs in OSCC, as well as the tumor growth in vivo.

Results
HOXC6 was highly expressed while miR-495 was poorly expressed in OSCC. HOXC6 was verified to be a target gene of miR-495, and miR-495 could inhibit the activation of the TGF-β signaling pathway. CSCs with miR-495 overexpression or HOXC6 silencing exhibited reversed EMT process; reduced abilities of proliferation, migration, and invasion; and promoted cell apoptosis in vitro. Moreover, inhibited tumor growth was observed in vivo after injection with miR-495 agomir or sh-HOXC6. In contrast, the downregulation of miR-495 showed an induced role in the progression of OSCC.

Conclusion
These findings suggest that miR-495 may suppress HOXC6 to inhibit EMT, proliferation, migration, and invasion while promoting apoptosis of CSCs in OSCC by inhibiting the TGF-β signaling pathway.