bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exosomal miRNAs are potential diagnostic biomarkers between malignant and benign thyroid nodules based on next-generation sequencing
Authors: Pan Qunxiong , Zhao Jiangman , Li Mingzhu , Liu Xiaoyu , Xu Yaping , Li Wushuang , Wu Shouxin , Su Zijian 
Published: September 2019

Abstract
An accurate biomarker or method for diagnosis of thyroid nodule with indeterminate fine-needle aspiration result is essential for clinical treatment. Micro RNAs (miRNAs) of exosomes are advantageous in the diagnosis of tumors because they are highly stable, and be protected by a bilayer membrane structure. Exosomes were isolated from 13 papillary thyroid carcinoma (PTC) and 7 nodular goiter (NG) patients’ plasma. Small RNA sequencing was performed on exosomes’ RNA in next-generation sequencing (NGS) platform. Then, we performed comprehensive analysis on miRNA expression profile in exosome of two groups. One hundred and twenty-nine differentially expressed miRNAs were identified in plasma exosomes between PTC and NG patients. Forty-nine miRNAs were up-regulated, and 80 miRNAs were down-regulated in PTC patients. Receiver operating characteristic (ROC) curves of 129 miRNAs were plotted. Area under curve (AUC) of 129 miRNAs was 0.571–0.951, with distribution peak of 0.82–0.86. AUC of 11 miRNAs was above 0.9, miR-5189-3p had the most optimal performance for diagnosis between PTC and NG, with 0.951 of AUC. Target genes of 129 miRNAs were enriched into 7 cancer-related signaling pathways, including mitogen-activated protein kinase (MAPK), tumor necrosis factor (TNF), NF-kappa B signaling pathway and so on. This study profiled the miRNA signature of exosomes from PTC patients and NG patients. We proposed a group of miRNAs in plasma exosomes as candidate biomarkers for thyroid nodule diagnosis.
Viral Blips After Treatment Initiation During Acute Human Immunodeficiency Virus Infection
Authors: Crowell Trevor A , Pinyakorn Suteeraporn , Sacdalan Carlo , Kroon Eugène , Colby Donn J , Puttamaswin Suwanna , Ubolyam Sasiwimol , Trichavaroj Rapee , Butterworth Oratai , Turk Ellen , Mccullough Corinne , Chomont Nicolas , de Souza Mark , Robb Merlin L , Phanuphak Nittaya , Ananworanich Jintanat ,   RV254/SEARCH010 Study Group
Published: September 2019

Abstract
Transient viral blips ≥20 copies/mL were observed in 16.9% of acutely treated adults with HIV. Blip incidence increased from 0.0 (95% CI, 0.0–2.9)/100 person-years after ART in Fiebig I to 15.9 (7.6–29.2) in Fiebig V. Increasing viral load and Fiebig stage at ART initiation were independently predictive of blips.
PMBD: a Comprehensive Plastics Microbial Biodegradation Database
Authors: Gan Zhiqiang , Zhang Houjin 
Published: September 2019

Abstract
Since the invention over a hundred years ago, plastics have been used in many applications, and they are involved in every aspect of our lives. The extensive usage of plastics results in a tremendous amount of waste, which has become a severe burden on the environment. Several degradation approaches exist in nature to cope with ever-increasing plastic waste. Among these approaches, biodegradation by microorganisms has emerged as a natural way, which is favored by many environmentally conscious societies. To facilitate the study on biodegradation of plastics, we developed an online resource, Plastics Microbial Biodegradation Database (PMBD), to gather and present the information about microbial biodegradation of plastics. In this database, 949 microorganisms–plastics relationships and 79 genes involved in the biodegradation of plastics were manually collected and confirmed through literature searching. In addition, more than 8000 automatically annotated enzyme sequences, which were predicted to be involved in the plastics biodegradation, were extracted from the TrEMBL section of the UniProt database. The PMBD database is presented with a website at http://pmbd.genome-mining.cn/home. Data may be accessed through browsing or searching. Also included on the website are a sequence alignment tool and a function prediction tool.
Novel approaches and methods for quantifyingPhytophthora cinnamomiin avocado tree roots
Authors: Masikane Siyethemba , Jolliffe Jenna , Swart Laurika , McLeod Adele 
Published: September 2019

ABSTRACTPhytophthora cinnamomi Rands is a devastating root rot pathogen of avocado. Robust and sensitive root quantification methods are required for determining seasonal P. cinnamomi root colonization patterns and evaluating management strategies. Our study investigated four P. cinnamomi root quantification methods using a newly developed P. cinnamomi-avocado-seedling bioassay system and a P. cinnamomi-specific probe-based qPCR assay. Phytophthora cinnamomi quantification through plating of roots (root plating) or lemon leaf disks obtained from root baitings (root-baiting-plating) onto semi-selective media were the best methods. Root plating consistently yielded significant differences in P. cinnamomi quantities obtained from seedling roots inoculated with five zoospore concentrations (10–1 × 105 zoospores/ml), whereas root-baiting-plating did so less often. The two methods were comparable in yielding root quantities that were significantly correlated with the inoculated zoospore concentrations, rarely yielding false negatives and having the lowest variability between replicates of the same treatment. qPCR quantification from roots was also an effective method; however, treatment replicates were highly variable and false negatives occurred more frequently. The least effective quantification method was qPCR quantification from lemon leaf disks obtained from root baitings.
Be prepared – Learning for the future
Authors: Fahnert Beatrix 
Published: September 2019

ABSTRACT
Forward-looking papers from around the globe, addressing themes of current educational practice, were published in the FEMS Microbiology Letters virtual Thematic Issue ‘Learning for the future' in October 2019. Its dynamic content is reviewed here to facilitate discussions within the professional community. The focus is on preparing generations of 21st century professionals as lifelong learners for yet unknown working environments and demands. Active and authentic learning is covered in various contexts from interactive lectures, via innovative tasks exploring the scientific method to conducting research over a distance. Naturally, authentic assessment features. Moreover, authentic learning is taken out of the classroom into the community as service learning for students to develop skills and see unexpected Science, Technology, Engineering and Maths career opportunities. Approaches to public engagement with science are presented including through art. Art is also brought into the classroom, as well as educational games, to foster creativity. Additionally, sharing science with large audiences on social media is discussed. Future-proofing education requires being innovative and imaginative. This comes with challenges and risks, but being prepared is worth it.
Genome of the Parasitoid Wasp Diachasma alloeum, an Emerging Model for Ecological Speciation and Transitions to Asexual Reproduction
Authors: Tvedte Eric S , Walden Kimberly K O , McElroy Kyle E , Werren John H , Forbes Andrew A , Hood Glen R , Logsdon John M , Feder Jeffrey L , Robertson Hugh M 
Published: September 2019

Abstract
Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model for understanding how ecological speciation can “cascade” across trophic levels. Identification of gene content confirmed the overall quality of the draft genome, and we manually annotated ∼400 genes as part of this study, including those involved in oxidative phosphorylation, chemosensation, and reproduction. Through comparisons to model hymenopterans such as the European honeybee Apis mellifera and parasitoid wasp Nasonia vitripennis, as well as a more closely related braconid parasitoid Microplitis demolitor, we identified a proliferation of transposable elements in the genome, an expansion of chemosensory genes in parasitoid wasps, and the maintenance of several key genes with known roles in sexual reproduction and sex determination. The D. alloeum genome will provide a valuable resource for comparative genomics studies in Hymenoptera as well as specific investigations into the genomic changes associated with ecological speciation and transitions to asexuality.
Increasing HIV treatment access, uptake and use among men who have sex with men in urban Indonesia: evidence from a qualitative study in three cities
Authors: Lazuardi Elan , Newman Christy E , Anintya Irma , Rowe Emily , Wirawan Dewa N , Wisaksana Rudi , Subronto Yanri W , Kusmayanti Nur Aini , Iskandar Shelly , Kaldor John , Bell Stephen 
Published: September 2019

AbstractMen who have sex with men make up one of four key populations identified as critical to a successful HIV response in Indonesia. Despite international policies supporting HIV treatment in low- and middle-income countries, Indonesia is one of the few countries experiencing low coverage of HIV treatment and little decrease in HIV incidence. There is poor retention in care and low viral suppression rates among key populations such as men who have sex with men. The national government has committed to increasing treatment access and uptake for people with HIV but little is known about how these men themselves view, use and experience these medications. Drawing on qualitative data collected in 2015–16 from 24 HIV-positive men who have sex with men living in three Indonesian cities, we observed multiple intersecting social and contextual factors that can influence effective HIV treatment use. Although shared stories of strong side effects and fear of unwanted disclosure inhibited treatment uptake, social support from ‘buddies’ helped to navigate healthcare systems and sharing medication among peers enabled adherence. In order to improve treatment uptake and adherence among Indonesian men who have sex with men living with HIV, these divergent effects of the social meanings and practices associated with HIV treatments in Indonesia must be better acknowledged. A more comprehensive understanding of social and community practices within key populations can strengthen national efforts to improve treatment access and increase adherence. Ongoing decentralization of healthcare in Indonesia, and differentiated care models that enable initiation of treatment in community settings and involve non-medical, community-based organizations in the provision of treatment services have the potential to address the needs of individuals who fall into a key population category such as men who have sex with men.
Successful bilateral lung transplantation and simultaneous Nuss technique correction of pectus excavatum post-allogeneic haematopoietic stem cell transplantation
Authors: Zhang Zhenrong , Ding Hao , Liu Feng , Chen Jingyu 
Published: September 2019

Abstract
Bronchiolitis obliterans syndrome after allogeneic haematopoietic stem cell transplantation has aroused clinical concern. We describe a case of a 39-year-old female patient diagnosed as bronchiolitis obliterans syndrome and concomitant pectus excavatum with a Haller index of 3.32. The patient received bilateral lung transplantation and simultaneously underwent Nuss surgery via bilateral anterolateral thoracotomies with veno-arterial extracorporeal membrane oxygenation support. The bar was removed 2 years after transplantation, and the patient has been stable in the past 4 years with haematological remission and satisfactory lung function.
Giant saccular aneurysm of the innominate artery
Authors: Robaldo Alessandro , Apostolou Dimitri , Peano Enrico , Novali Claudio 
Published: September 2019

Abstract
We report a rare case of a saccular aneurysm of innominate artery without any apparent causative history. Although the treatment choice remains debatable, due to the poor condition of the patient, the lesion was excluded by using a balloon-expandable covered stent with a satisfactory early-term outcome.
Metabolomic profiles associated with all-cause mortality in the Women’s Health Initiative
Authors: Balasubramanian Raji , Paynter Nina P , Giulianini Franco , Manson JoAnn E , Zhao Yibai , Chen Jiu-Chiuan , Vitolins Mara Z , Albert Christine A , Clish Clary , Rexrode Kathryn M 
Published: September 2019

Abstract

Background
Metabolomics profiling has shown promise in elucidating the biological pathways underpinning mortality, but there are limited data in female populations.

Methods
We applied a liquid chromatography-tandem mass spectrometry metabolomics platform to EDTA-plasma to measure 470 metabolites at baseline in a discovery set of 943 postmenopausal women (including 417 incident deaths, median time to death of 10.6 years) with validation in an independent set of 1355 postmenopausal women (including 685 deaths, median time to death of 9.1 years) in the Women’s Health Initiative.

Results
Eight new metabolites were discovered to be associated with all-cause mortality. Findings included protective effects of increased levels of three amino acids (asparagine, homoarginine and tryptophan) and docosatrienoic acid; and detrimental effects of increased levels of C4-OH-carnitine, hexadecanedioate and two purine/pyrimidines (N2, N2-dimethylguanosine and N4-acetylcytidine). In addition, a set of nine previously published metabolite associations were replicated. A metabolite score comprising 17 metabolites was associated with mortality (P &lt; 10–8) after adjustment for risk factors, with a hazard ratio of 1.95 (95% CI: 1.46–2.62) for women in the highest quartile compared with the lowest quartile of metabolite score. The score was robust among younger women and older women, for both cardiovascular and non-cardiovascular mortality, and associated with both early deaths (within the first 10 years of baseline) and later deaths.

Conclusions
Our study fills a gap in the literature by identifying eight novel metabolite associations with all-cause mortality in women, using a robust study design involving independent discovery and validation datasets.
Recombinant Human Interleukin-15 and Anti-PD-L1 Combination Therapy Expands a CXCR3+PD1−/low CD8 T-Cell Subset in Simian Immunodeficiency Virus-Infected Rhesus Macaques
Authors: Chen Ping , Chen Hui , Moussa Maha , Cheng Jie , Li Tong , Qin Jing , Lifson Jeffrey D , Sneller Michael C , Krymskaya Ludmila , Godin Steven , Lane H Clifford , Catalfamo Marta 
Published: September 2019

Abstract

Background
The PD1/PD-L1 pathway contributes to the pathogenesis of human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection, and blockade of this pathway may have potential to restore immune function and promote viral control or elimination. In this study, we combined a checkpoint inhibitor anti-PD-L1 (Avelumab) and recombinant human interleukin-15 (rhIL-15) in SIV-infected rhesus macaques (RM).

Methods
The rhIL-15 was administered as continuous infusion in 2 cycles of 10 days in the context of weekly administration of anti-PD-L1 (Avelumab) in SIV-infected RM receiving combination antiretroviral therapy (cART). Safety, immunological parameters, and viral loads were monitored during the study.

Results
Administration of rhIL-15/anti-PD-L1 was safe and well tolerated. Treatment resulted in transient increases in proliferating (Ki67+) natural killer and CD8 T cells. In addition, treatment expanded a CXCR3+PD1−/low CD8 T-cell subset with the ability to secrete cytokines. Despite these effects, no changes in plasma viremia were observed after cART interruption.

Conclusions
Expansion of the CXCR3+PD1−/low CD8 T-cell subset with functional capacity and potential to traffic to sites of viral reservoirs in SIV-infected rhesus macaques had no demonstrable effect on plasma viremia after cART interruption.
Changing Motivations or Capabilities? Migration Deterrence in the Global Context
Authors: Kent Jonathan , Norman Kelsey P , Tennis Katherine H 
Published: September 2019

AbstractOver the last thirty-five years, Western liberal democracies have exerted more control over their borders through an array of innovative migration-control practices. Scholars have taken stock of these efforts and referred to them collectively as “deterrence” measures, ignoring the fact that deterrence is an established concept with a focused definition and meaning. We argue that in the context of migration governance, the concept of deterrence has been stretched beyond meaningful parameters. In order to restore conceptual clarity and develop a more useful framework, we build on the fourth wave of deterrence literature and apply its insights to these new migration-control practices. We construct a theoretically informed typology that differentiates between deterrence and defense policies. Deterrence aims to change the motivations of migrants, whereas defense policies change migrants’ capabilities. We also differentiate between the timing and location of the interventions. We elaborate on each category of policy with examples drawn from various geographic regions and propose a framework for expanding this analysis through a systematic exploration of global practices. We conclude with a discussion of the implications stemming from these insights with respect to normative and practical debates in this research area.
Biology, Predatory Potential, Life Table, and Field Evaluation of Propylea dissecta (Coleoptera: Coccinellidae), Against Lipaphis erysimi (Hemiptera: Aphididae) on Broccoli
Authors: Boopathi Thangavel , Singh Soibam Basanta , Dutta Sudip Kumar , Dayal Vishambhar , Singh Akoijam Ratankumar , Chowdhury Samik , Ramakrishna Yerraboina , Shakuntala Ingudam , Lalhruaipuii Khawlhring 
Published: September 2019

Abstract
Propylea dissecta (Mulsant) (Coleoptera: Coccinellidae) is one of the most promising ladybird beetle against many sucking pests. Predation rates, developmental biology, life table, and field assessment of this ladybird were examined against mustard aphid, Lipaphis erysimi (Kalt.) (Hemiptera: Aphididae), on broccoli. Data on the life history were collected at 23 ± 1°C and 70 ± 1% RH and were evaluated using the two-sex, age-stage life table. Results showed that the two-sex, age-stage life table-based net reproductive rate (R0) was 11.264 ± 6.197 offspring. The adult females lived longer (33.8 ± 2.356 d) than the adult males (32.2 ± 0.841 d). The fourth instar consumed most of L. erysimi (113.97 ± 5.76) compared to the other larval stages of the predator. Male (1,821) and female (2,673) consumed more aphids than larvae. The net consumption rate was 741.78 ± 89.91 aphids. Other aphidophagous predators such as Coccinella septempunctata L., Micraspis discolor (F.), Coccinella transversalis (F.), and syrphid (Diptera: Syrphidae) were also noted in broccoli. Our research showed that inoculative release of 150 or 200 adults per 1,000 m2 for two times on broccoli achieved a significant decrease in aphids L. erysimi and Brevicoryne brassicae L. (Hemiptera: Aphididae) (&gt;95%). The release rate of 150 adults per 1,000 m2 for two times may, therefore, be recommended to manage the aphid population on broccoli.
Political Identity: Experimental Evidence on Anti-Americanism in Pakistan
Authors: Bursztyn Leonardo , Callen Michael , Ferman Bruno , Gulzar Saad , Hasanain Ali , Yuchtman Noam 
Published: September 2019

Abstract
We identify Pakistani men’s willingness to pay to preserve their anti-American identity using two experiments imposing clearly specified financial costs on anti-American expression, with minimal consequential or social considerations. In two distinct studies, one-quarter to one-third of subjects forgo payments from the U.S. government worth around one-fifth of a day’s wage to avoid an identity-threatening choice: anonymously checking a box indicating gratitude toward the U.S. government. We find sensitivity to both payment size and anticipated social context: when subjects anticipate that rejection will be observable by others, rejection falls suggesting that, for some, social image can outweigh self-image.
Behavioral and Morphological Studies of the Membranous Tergal Structure of Male Blattella germanica (Blattodea: Ectobiidae) During Courtship
Authors: Shimomura Kenji , Ishii Daisuke , Nojima Satoshi 
Published: September 2019

Abstract
The male German cockroach Blattella germanica (L.) exhibits a characteristic courtship display by raising its wings, turning around, and exposing its tergal glands on the seventh and eighth tergites to the female. The male secretes a courtship pheromone from the tergal glands which induces a strong feeding response in the female, facilitating copulation. Upon multiple, detailed microscopic observations of the courtship display, we found that the male markedly expanded the intersegmental area between the sixth and seventh tergites, but deflated this area as soon as it perceived a tactile stimulus on its back by the female, while continuing to raise its wings and exposing the tergal glands. The intersegmental area is composed of two parts: a membranous posterior part of the sixth tergite, and the regular intertergal membrane. The membranous posterior part was found to be crescentic in shape and clearly separated from the intertergal membrane by traverse tongue-shaped plates. Scanning electron microscopic observation revealed that there were many orifices or pores in the membranous crescentic zone, and its morphological structure was clearly different from that of the intertergal membrane. Our observations suggest that the crescentic zone is likely a secretory gland that may play an important role at the beginning of the male courtship display, different from the tergal glands.