bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-existing Antineuraminidase Antibodies Are Associated With Shortened Duration of Influenza A(H1N1)pdm Virus Shedding and Illness in Naturally Infected Adults
Authors: Maier Hannah E , Nachbagauer Raffael , Kuan Guillermina , Ng Sophia , Lopez Roger , Sanchez Nery , Stadlbauer Daniel , Gresh Lionel , Schiller Amy , Rajabhathor Arvind , Ojeda Sergio , Guglia Andrea F , Amanat Fatima , Balmaseda Angel , Krammer Florian , Gordon Aubree 
Published: July 2019

Abstract

Background
Influenza causes a substantial burden worldwide, and current seasonal influenza vaccine has suboptimal effectiveness. To develop better, more broadly protective vaccines, a more thorough understanding is needed of how antibodies that target the influenza virus surface antigens, hemagglutinin (HA) (including head and stalk regions) and neuraminidase (NA), impact influenza illness and virus transmission.

Methods
We used a case-ascertained, community-based study of household influenza virus transmission set in Managua, Nicaragua. Using data from 170 reverse transcriptase–polymerase chain reaction (RT-PCR)–confirmed influenza virus A(H1N1)pdm infections and 45 household members with serologically confirmed infection, we examined the association of pre-existing NA, hemagglutination inhibiting, and HA stalk antibody levels and influenza viral shedding and disease duration using accelerated failure time models.

Results
Among RT-PCR–confirmed infections in adults, pre-existing anti-NA antibody levels ≥40 were associated with a 69% (95% confidence interval [CI], 34–85%) shortened shedding duration (mean, 1.0 vs 3.2 days). Neuraminidase antibody levels ≥80 were associated with further shortened shedding and significantly shortened symptom duration (influenza-like illness, 82%; 95% CI, 39–95%). Among RT-PCR–confirmed infections in children, hemagglutination inhibition titers ≥1:20 were associated with a 32% (95% CI, 13–47%) shortened shedding duration (mean, 3.9 vs 6.0 days).

Conclusions
Our results suggest that anti-NA antibodies play a large role in reducing influenza illness duration in adults and may impact transmission, most clearly among adults. Neuraminidase should be considered as an additional target in next-generation influenza virus vaccine development.
We found that antibodies against neuraminidase were associated with significantly shortened viral shedding, and among adults they were also associated with shortened symptom duration. These results support neuraminidase as a potential target of next-generation influenza virus vaccines.
National Safety Survey of Animal-use Commercial Probiotics and Their Spillover Effects From Farm to Humans: An Emerging Threat to Public Health
Authors: Fu Songzhe , Yang Qian , He Fenglan , Lan Ruiting , Hao Jingwei , Ni Ping , Liu Ying , Li Ruijun 
Published: July 2019

Abstract

Background
Human-use probiotics have recently been associated with clinical infections and antibiotic resistance transfer, raising public concern over their safety. However, despite their extensive application in aquaculture and animal husbandry, the safety of animal-use probiotics remains poorly described.

Methods
We evaluated the safety of 92 animal-use probiotics from China. The pattern of spread of pathogens from probiotics and the consequent public health implications were also examined by conducting in-field genomic surveillance at 2 farms.

Results
A total of 123 probiotic Bacillus species isolates were obtained from 92 brands of probiotics, of which 45 isolates were resistant to antibiotics. Notably, 33.7% of probiotic products were contaminated with life-threatening pathogens such as Klebsiella pneumoniae. Genomic surveillance at a chicken farm identified an anthrax toxin–positive Bacillus cereus strain in a probiotic product used as a feed supplement, which was transferred into the groundwater and to a nearby fish farm. Following up retrospective analysis of the surveillance data during 2015–2018 in 3 provinces retrieved 2 B. cereus strains from human with intestinal anthrax symptoms and confirmed the transmission of B. cereus from farm to human. Surveillance of anthrax toxin revealed that cya was detected in 8 of 31 farms.

Conclusions
This study provides the first national safety survey of animal-use probiotics in China and confirms the spillover effects of probiotics from the farms to human. These results suggest that the large-scale application of pathogen-containing probiotics leads to the transfer of pathogens, with worrisome implications for public health. Good Manufacturing Practice should be implemented during the production of all probiotics.
Animal-use probiotic products are frequently contaminated with viable pathogenic bacteria. This study revealed that virulent probiotic organisms and contaminating pathogens were colonized with farm animals and shed into the environment, which facilitated the transfer of pathogens to humans.
Community-acquired Bacterial Meningitis in Adults With Cerebrospinal Fluid Leakage
Authors: ter Horst Liora , Brouwer Matthijs C , van der Ende Arie , van de Beek Diederik 
Published: July 2019

Abstract

Background
Cerebrospinal fluid (CSF) leakage is a risk factor for developing bacterial meningitis.

Methods
We analyzed episodes of community-acquired bacterial meningitis associated with CSF leakage from a prospective nationwide cohort study.

Results
CSF leakage was identified in 65 episodes of 2022 episodes (3%) in 53 patients. The cause of CSF leakage was identified in 49 of 65 episodes (75%), which most commonly consisted of ear-nose-throat surgery (19 of 49 episodes [29%]) and remote head trauma (15 of 49 episodes [23%]). The episode was a recurrent meningitis episode in 38 patients (59%). Of the recurrent episodes, 27 had known CSF leakage (71%) of whom 20 (53%) had previous surgery aiming to close the leak. Nine patients (38%) with known CSF leakage had been vaccinated (23-valent pneumococcal vaccine in 9 patients, meningococcal serogroup C vaccine in 2, meningococcal serogroup A and Haemophilus influenzae type b vaccine each in 1 patient). Streptococcus pneumoniae was cultured in 33 episodes (51%) and H. influenzae in 11 episodes (17%). The most common pneumococcal serotypes were 3 (4 episodes), 35B, 9N, 38, and 15C (each 2 episodes). Haemophilus influenzae was unencapsulated in all 10 episodes with known capsule type. The outcome was unfavorable in 8 episodes (12%) and no patient died.

Conclusions
Bacterial meningitis in patients with CSF leakage has a high recurrence rate, despite surgical repair or vaccination, and outcome is generally favorable. CSF leakage should be suspected in patients with bacterial meningitis presenting with liquorrhea, recurrent meningitis, or with disease caused by H. influenzae.
Multiple factors drive the abundance and diversity of the diazotrophic community in typical farmland soils of China
Authors: Han Li-Li , Wang Qing , Shen Ju-Pei , Di Hong J , Wang Jun-Tao , Wei Wen-Xue , Fang Yun-Ting , Zhang Li-Mei , He Ji-Zheng 
Published: July 2019

ABSTRACTBiological nitrogen fixation plays an important role in nitrogen cycling by transferring atmospheric N2 to plant-available N in the soil. However, the diazotrophic activity and distribution in different types of soils remain to be further explored. In this study, 152 upland soils were sampled to examine the diazotrophic abundance, nitrogenase activity, diversity and community composition by quantitative polymerase chain reaction, acetylene reduction assay and the MiSeq sequencing of nifH genes, respectively. The results showed that diazotrophic abundance and nitrogenase activity varied among the three soil types. The diazotrophic community was mainly dominated by Bradyrhizobium, Azospirillum, Myxobacter, Desulfovibrio and Methylobacterium. The symbiotic diazotroph Bradyrhizobium was widely distributed among soils, while the distribution of free-living diazotrophs showed large variation and was greatly affected by multiple factors. Crop type and soil properties directly affected the diazotrophic ɑ-diversity, while soil properties, climatic factors and spatial distance together influenced the diazotrophic community. Network structures were completely different among all three types of soils, with most complex interactions observed in the Red soil. These findings suggest that diazotrophs have various activities and distributions in the three soil types, which played different roles in nitrogen input in agricultural soil in China, being driven by multiple environmental factors.
Primed to be strong, primed to be fast: modeling benefits of microbial stress responses
Authors: Wesener Felix , Tietjen Britta 
Published: July 2019

ABSTRACTOrganisms are prone to different stressors and have evolved various defense mechanisms. One such defense mechanism is priming, where a mild preceding stress prepares the organism toward an improved stress response. This improved response can strongly vary, and primed organisms have been found to respond with one of three response strategies: a shorter delay to stress, a faster buildup of their response or a more intense response. However, a universal comparative assessment, which response is superior under a given environmental setting, is missing. We investigate the benefits of the three improved responses for microorganisms with an ordinary differential equation model, simulating the impact of an external stress on a microbial population that is either naïve or primed. We systematically assess the resulting population performance for different costs associated with priming and stress conditions. Our results show that independent of stress type and priming costs, the stronger primed response is most beneficial for longer stress phases, while the faster and earlier responses increase population performance and survival probability under short stresses. Competition increases priming benefits and promotes the early stress response. This dependence on the ecological context highlights the importance of including primed response strategies into microbial stress ecology.
Synbiotics impact on dominant faecal microbiota and short-chain fatty acids production in sows
Authors: Śliżewska Katarzyna , Chlebicz Agnieszka 
Published: July 2019

ABSTRACT
The aim of this study was to estimate the influence of synbiotics on intestinal microbiota and its metabolism in sows. Three different synbiotics were administered with feed to animals from three experimental groups. Two groups of sows were given commercially available probiotics (BioPlus 2B®, Cylactin® LBC) as forage additives for comparison. The control group of sows was given unmodified fodder. The study was conducted for 48 days (10 days before farrowing, and continued 38 days after) and faeces samples were collected four times. The scope of this work was to designate the dominant microbiota in sows’ faeces. Therefore, the total number of anaerobic bacteria, Bifidobacterium sp., Lactobacillus sp., Bacteroides sp., Clostridium sp., Enterococcus sp., Enterobacteriaceae, Escherichia coli and yeast was determined, using the plate method. Changes in the concentration of lactic acid, short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were also determined in correlation with the feed additives administered to the sows using high-performance liquid chromatography analysis (HPLC). Our results allowed us to conclude that synbiotics have a beneficial effect on intestinal microbiota of sows and its metabolism. We observed that the impact of the synbiotics on the microbiota was more significant than the one induced by probiotics.
Survivors of Ebola Virus Disease Develop Polyfunctional Antibody Responses
Authors: Gunn Bronwyn M , Roy Vicky , Karim Marcus M , Hartnett Jessica N , Suscovich Todd J , Goba Augustine , Momoh Mambu , Sandi John Demby , Kanneh Lansana , Andersen Kristian G , Shaffer Jeffrey G , Schieffelin John S , Garry Robert F , Grant Donald S , Alter Galit 
Published: July 2019

Abstract
Monoclonal antibodies can mediate protection against Ebola virus (EBOV) infection through direct neutralization as well as through the recruitment of innate immune effector functions. However, the antibody functional response following survival of acute EBOV disease has not been well characterized. In this study, serum antibodies from Ebola virus disease (EVD) survivors from Sierra Leone were profiled to capture variation in overall subclass/isotype abundance, neutralizing activity, and innate immune effector functions. Antibodies from EVD survivors exhibited robust innate immune effector functions, mediated primarily by IgG1 and IgA1. In conclusion, development of functional antibodies follows survival of acute EVD.
Development of a Humanized Murine Model for the Study of Oxalobacter formigenes Intestinal Colonization
Authors: Pebenito Amanda M , Liu Menghan , Nazzal Lama , Blaser Martin J 
Published: July 2019

Abstract

Background
Oxalobacter formigenes are bacteria that colonize the human gut and degrade oxalate, a component of most kidney stones. Findings of clinical and epidemiological studies suggest that O. formigenes colonization reduces the risk for kidney stones. We sought to develop murine models to allow investigating O. formigenes in the context of its native human microbiome.

Methods
For humanization, we transplanted pooled feces from healthy, noncolonized human donors supplemented with a human O. formigenes strain into recipient mice. We transplanted microbiota into mice that were treated with broad-spectrum antibiotics to suppress their native microbiome, were germ free, or received humanization without pretreatment or received sham gavage (controls).

Results
All humanized mice were stably colonized with O. formigenes through 8 weeks after gavage, whereas mice receiving sham gavage remained uncolonized (P < .001). Humanization significantly changed the murine intestinal microbial community structure (P < .001), with humanized germ-free and antibiotic-treated groups overlapping in β-diversity. Both germ-free and antibiotic-treated mice had significantly increased numbers of human species compared with sham-gavaged mice (P < .001).

Conclusions
Transplanting mice with human feces and O. formigenes introduced new microbial populations resembling the human microbiome, with stable O. formigenes colonization; such models can define optimal O. formigenes strains to facilitate clinical trials.
How Government Agencies React to Termination Threats
Authors: Askim Jostein , Blom-Hansen Jens , Houlberg Kurt , Serritzlew Søren 
Published: July 2019

AbstractMuch research following Kaufman’s classic study Are Government Organizations Immortal? has investigated the claim that government agencies enjoy great security and long life. Less attention has been paid to Kaufman’s thesis that government agencies facing a termination threat have strong incentives to react. In a study of the on-going Norwegian local government amalgamation reform, we demonstrate that this type of government agency reacts by hoarding (i.e., a last-minute flurry of spending) when faced with a termination threat. This finding shows that agencies facing termination threats are active players in the termination game. We discuss implications for research on agency termination and design implications for reformers of the public sector.
Alvesian Theopoetics, the Academy, and What May Come
Authors: Keefe-Perry L Callid 
Published: July 2019

Abstract
This article explores a significant stream of theopoetics largely informed by Rubem Alves and the work of ARC: Arts | Religion | Culture. It considers some of the features that differentiate theopoetic engagement from the scholarship of ‘Theology and The Arts’ and reflects on the relationship between theopoetics and the academy more broadly. It also grapples with the impact of coloniality on theopoetics and the ways in which this may have influenced the aversion to ideas like ‘rationalism’ and ‘objectivity’ in the Alvesian stream.
The migration decision process among returnees: Assessing the risks and benefits in contemporary Mexico–US migration
Authors: Chávez Sergio , Altman Claire E. , Gorman Bridget K. 
Published: July 2019

AbstractThis article investigates how return migrants assess the risks and benefits of migrating internationally by drawing on their previous migration experiences. We draw on data collected in a small city in Guanajuato, Mexico that contains in-depth interviews with 49 participants and 480 surveys on migration and health outcomes for return migrants and nonmigrants. This manuscript contributes to the literature by focusing on how return migrants, who previously worked in the USA without legal authorization, assess the risks and benefits in the migration decision process. Our article contributes to the substantive and theoretical migration literature by taking into consideration how the accumulation of migration and labor market experience may shape intentions and behaviors among returnees. Our findings highlight the broad array of factors that migrants consider including the dangers of crossing the border, hazardous working conditions, and prolonged family separation. Though the risks associated with unauthorized migration to the USA have escalated in recent years, some return migrants in our sample plan to migrate again to the USA. Respondents report wanting to return to the USA because of the perceived availability of jobs through social networks that provide access to higher wages and improvements to lifestyle and work experiences when compared to their current socioeconomic situation. Therefore, we argue that prior US experience provides migrants with a new frame of reference which they use to compare their lives upon returning to Mexico—and which likely informs their future desires to remigrate to the USA.
Risk factors for childhood and adult primary brain tumors
Authors: Ostrom Quinn T , Fahmideh Maral Adel , Cote David J , Muskens Ivo S , Schraw Jeremy M , Scheurer Michael E , Bondy Melissa L 
Published: July 2019

AbstractPrimary brain tumors account for ~1% of new cancer cases and ~2% of cancer deaths in the United States; however, they are the most commonly occurring solid tumors in children. These tumors are very heterogeneous and can be broadly classified into malignant and benign (or non-malignant), and specific histologies vary in frequency by age, sex, and race/ethnicity. Epidemiological studies have explored numerous potential risk factors, and thus far the only validated associations for brain tumors are ionizing radiation (which increases risk in both adults and children) and history of allergies (which decreases risk in adults). Studies of genetic risk factors have identified 32 germline variants associated with increased risk for these tumors in adults (25 in glioma, 2 in meningioma, 3 in pituitary adenoma, and 2 in primary CNS lymphoma), and further studies are currently under way for other histologic subtypes, as well as for various childhood brain tumors. While identifying risk factors for these tumors is difficult due to their rarity, many existing datasets can be leveraged for future discoveries in multi-institutional collaborations. Many institutions are continuing to develop large clinical databases including pre-diagnostic risk factor data, and developments in molecular characterization of tumor subtypes continue to allow for investigation of more refined phenotypes.Key Point1. Brain tumors are a heterogeneous group of tumors that vary significantly in incidence by age, sex, and race/ethnicity.2. The only well-validated risk factors for brain tumors are ionizing radiation (which increases risk in adults and children) and history of allergies (which decreases risk).3. Genome-wide association studies have identified 32 histology-specific inherited genetic variants associated with increased risk of these tumors.
CDKN2A homozygous deletion is a strong adverse prognosis factor in diffuse malignant IDH-mutant gliomas
Authors: Appay Romain , Dehais Caroline , Maurage Claude-Alain , Alentorn Agusti , Carpentier Catherine , Colin Carole , Ducray François , Escande Fabienne , Idbaih Ahmed , Kamoun Aurélie , Marie Yannick , Mokhtari Karima , Tabouret Emeline , Trabelsi Nesrine , Uro-Coste Emmanuelle , Delattre Jean-Yves , Figarella-Branger Dominique ,   POLA Network
Published: July 2019

Abstract

Background
The 2016 WHO classification of the central nervous system tumors stratifies IDH-mutant gliomas into two major groups depending on the presence or absence of 1p/19q-codeletion. However, the grading system remains unchanged and it is now controversial whether it can be still applied to this updated molecular classification.

Methods
In a large cohort of 911 high grade IDH-mutant gliomas from the French national POLA network (including 428 IDH-mutant gliomas without 1p/19q-codeletion and 483 anaplastic oligodendrogliomas, IDH-mutant and 1p/19q-codeleted), we investigated the prognostic value of CDKN2A gene homozygous deletion as well as WHO grading criteria (mitoses, microvascular proliferation and necrosis). In addition, we also searched for other retinoblastoma pathway gene alterations (CDK4 amplification and RB1 homozygous deletion) in a subset of patients. CDKN2A homozygous deletion was also searched in an independent series of 40 grade II IDH-mutant gliomas.

Results
CDKN2A homozygous deletion was associated with dismal outcome among IDH-mutant gliomas lacking 1p/19q-codeletion (p<0.0001 for progression-free survival and p=0.004 for overall survival) as well as among anaplastic oligodendrogliomas, IDH-mutant and 1p/19q-codeleted (p=0.002 for progression-free survival and p<0.0001 for overall survival) in univariate and multivariate analysis including age, extend of surgery, adjuvant treatment, MVP and necrosis. In both groups, the presence of microvascular proliferation (MVP) and/or necrosis remained of prognostic value only in cases lacking CDKN2A homozygous deletion. CDKN2A homozygous deletion was not recorded in grade II gliomas.

Conclusions
Our study pointed out the utmost relevance of CDKN2A homozygous deletion as an adverse prognostic factor in the two broad categories of IDH-mutant gliomas stratified on 1p/19q-codeletion and suggest to refine the grading of these tumors.
Pattern recognition is a sequential process—accurate diagnosis and treatment 20 years after presentation
Authors: Merinopoulos Dimos , Saada Janak , Jones Colin , Mukhtyar Chetan 
Published: July 2019

Abstract
A 25-year-old woman presented with ophthalmic and neurological manifestations. Her ocular manifestations included bilateral uveitis, multifocal retinal phlebitis, vitreitis and multiple retinal haemorrhages. Her neurological manifestations included migrainous headaches with visual aura, transient sensory symptoms and posterior circulation Transient Ischemic Attack (TIA). Magnetic resonance imaging of the brain demonstrated lesions that involved the deep white matter lesions initially and progressed to also involve the juxta cortical white and deep grey matter and brain stem, but without further neurological manifestations. She was sequentially treated with intravenous and oral glucocorticoid, cyclophosphamide and mycophenolate mofetil, but she continued to suffer with persistent episodes of retinal haemorrhages. Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL), Susac syndrome and Behcet’s disease were considered in the differential diagnosis. Genetic workup and clinical picture were not suggestive of the former two. Further history of oro-genital ulceration in younger age emerged, which pointed strongly towards a diagnosis of Behcet’s disease with neurological involvement. She was treated with infliximab and methotrexate with complete resolution of her symptoms and withdrawal of corticosteroids for the first time in over two decades.