bluuebunny/crossref_metadata_2025_split huggingface dataset:
A self‐preserving, partially biodegradable eDNA filter
Authors: Thomas Austen C. , Nguyen Phong L. , Howard Jesse , Goldberg Caren S. 
Published: June 2019

Abstract

eDNA studies often rely on water filtration in the field and immediate sample preservation to prevent DNA degradation during sample transport. However, filter membrane transfer steps for preservation can increase risk of sample contamination and the reliance on typical single‐use filter housings produces significant plastic waste.

We created a new eDNA filter housing (compatible with any suction pump) partially comprised of a biodegradable, hydrophilic material that functions to automatically preserve captured eDNA via desiccation—no filter membrane transfer steps, no chemical or cold storage required.

We tested the self‐preservation capabilities of the desiccating filter housings by filtering replicate samples in an eDNA mesocosm study and compared with ethanol preservation. Self‐preserving filters were placed back into original packaging for storage, and samples for both preservation methods were kept at room temperature until extraction at prescribed time points (11 days, 18 days, 25 days, 32 days, 60 days, 88 days, 172 days) post‐filtration. Paired field samples were also collected from six pond locations targeting an additional species to demonstrate field performance.

Quantitative PCR results from the mesocosm study indicated that both methods effectively preserved eDNA over a 6‐month storage period, with the self‐preserving filters yielding slightly more target DNA on average (SQ = 329 copies) than ethanol‐preserved samples (SQ = 288 copies) (F1,38 = 4.050, p = 0.051). Neither method showed signs of degradation after 172 days. Results from field sampling indicated a larger difference between preservation methods, with the self‐preserving filters containing approximately 2X the eDNA of ethanol‐preserved samples on average (paired t test, p = 0.020).

These data suggest that self‐preserving eDNA filter housings are a viable alternative to standard ethanol preservation methods and may provide higher detection sensitivity in some circumstances. The new filter housings should also help in reducing the risk of sample contamination, minimize protocol steps and result in less plastic waste. Such innovations are important to assure eDNA data quality and to help in facilitating the inclusion of non‐expert sample collectors (e.g. citizen scientists) in research programs.
Risk behaviours and alcohol in adolescence are negatively associated with testicular volume: results from the Amico‐Andrologo survey
Authors: Gianfrilli D. , Ferlin A. , Isidori A. M. , Garolla A. , Maggi M. , Pivonello R. , Santi D. , Sansone A. , Balercia G. , Granata A. R. M. , Sinisi A. , Lanfranco F. , Pasqualetti P. , Foresta C. , Lenzi A. ,   ‘Amico‐Andrologo’ Study Group
Published: June 2019

AbstractBackgroundRisk factors established during adolescence affect health outcomes in adulthood, although little is known about how adolescent health risk behaviours (HRBs) affect testicular development and reproductive health.ObjectivesTo assess prevalence of HRBs among last year high school students; to describe the most prevalent andrological disorders in this cohort; to explore HRBs associated with andrological disorders and investigate factors possibly associated with impaired testicular development in puberty.Materials and methodsThe Amico‐Andrologo Survey is a permanent nationwide surveillance programme conducted by the Italian Society of Andrology and Sexual Medicine and supported by the Ministry of Health. A nationally representative survey of final‐year male high school students was conducted using a validated structured interview (n = 10124) and medical examination (n = 3816).ResultsSmoking (32.6%), drinking (80.6%) and use of illegal drugs (46.5%) are common in adolescence. 16.6% of subjects were overweight, 3.1% were underweight and 2.3% were obese. Among sexually active students (60.3%), unprotected sex was very common (48.3%). Only 11.6% had been treated for andrological disorders, despite an abnormal clinical examination in 34.6%. Bilateral testicular hypotrophy (14.0%), varicocoele (27.1%) and phimosis (7.1%) were the most prevalent disorders; 5.1% complained of premature ejaculation and 4.7% had an STI. Underweight and heavy alcohol or drug use were associated with testicular hypotrophy. HRBs emerged as significant predictors of testicular hypotrophy, explaining up to 9.6% of its variance. Limitations include risk of selection bias for voluntary physical examination and recall bias for the self‐compiled questionnaire.DiscussionThere is an emerging global adverse trend of HRBs in male high school students. A significant proportion of adolescent males with unsuspected andrological disorders engage in behaviours that could impair testicular development.ConclusionGreater attention to the prevention of andrological health in adolescence is needed.
ECMO without anticoagulation in patients with disease‐related severe thrombocytopenia: Feasible but futile?
Authors: Hermann Alexander , Schellongowski Peter , Bojic Andja , Robak Oliver , Buchtele Nina , Staudinger Thomas 
Published: June 2019

AbstractSevere thrombocytopenia poses a high risk for bleeding thus representing a relative contraindication for anticoagulation and therefore extracorporeal membrane oxygenation (ECMO). We herein report on a series of immunocompromised patients with severe thrombocytopenia undergoing long‐term ECMO without systemic anticoagulation. We retrospectively identified seven adult patients with anticoagulation withdrawal for ≥3 days (range 5–317) during venovenous ECMO therapy due to thrombocytopenia < 50 G/L treated in a university‐affiliated hospital from January 2013 to April 2017. All ECMO systems used were heparin coated. Overall, 530 ECMO days were observed, 404 (76%) of them without systemic anticoagulation. Platelet count during ECMO treatment was 24 G/L (median, range 1‐138), ECMO duration was 35 days (5‐317), and ECMO was run without any anticoagulation for 20 days (5‐317). Altogether, five clotting events were seen leading to oxygenator exchanges. Bleeding was common including one fatal intracerebral hemorrhage. Altogether, 29 platelet concentrates per patient (7‐207) were administered, which correspond to 0.8 per day (0.6‐1.3). One patient survived ICU and hospital. In patients with thrombocytopenia, ECMO can be run without anticoagulation even for considerably long periods of time. Bleeding remains common, while clotting events seem to be rare. However, prognosis of this patient population undergoing ECMO support seems grim.
Interleukin‐6 production mediated by the IRE1‐XBP1 pathway confers radioresistance in human papillomavirus‐negative oropharyngeal carcinoma
Authors: Lyu Xintong , Zhang Miao , Li Guangqi , Cai Yiru , Li Guang , Qiao Qiao 
Published: June 2019

AbstractEndoplasmic reticulum stress (ERS) plays a key role in the pathogenesis and development of tumors and protects tumor cells from radiation damage and drug‐induced stress. We previously demonstrated that EGFR confers radioresistance in human papillomavirus (HPV)‐negative human oropharyngeal carcinoma by activating ERS signaling through PERK and IRE1α. In addition, PERK confers radioresistance by activating the inflammatory cytokine NF‐κB. However, the effect of IRE1 on radiosensitivity has not yet been fully elucidated. Here, we clarified that IRE1 overexpression was associated with poor outcome in HPV‐negative patients treated with radiotherapy (P = 0.0001). In addition, a significantly higher percentage of radioresistant HPV‐negative patients than radiosensitive HPV‐negative patients exhibited high IRE expression (66.7% vs 27.8%, respectively; P = 0.001). Silencing IRE1 and XBP1 increased DNA double‐strand break (DSB) and radiation‐induced apoptosis, thereby increasing the radiosensitivity of HPV‐negative oropharyngeal carcinoma cells. IRE1‐XBP1 silencing also inhibited radiation‐induced IL‐6 expression at both the RNA and protein levels. The regulatory effect of IRE1‐XBP1 silencing on DNA DSB‐induced and radiation‐induced apoptosis was inhibited by pretreatment with IL‐6. These data indicate that IRE1 regulates radioresistance in HPV‐negative oropharyngeal carcinoma through IL‐6 activation, enhancing X‐ray‐induced DNA DSB and cell apoptosis.
Pharmacometabolomics of Respiratory Phenotypic Response to Dexamethasone in Preterm Infants at Risk for Bronchopulmonary Dysplasia
Authors: Lewis Tamorah , Chalise Prabhakar , Gauldin Cheri , Truog William 
Published: June 2019

A prospective cohort study was performed in preterm infants less than 32 weeks gestation at birth who were treated with dexamethasone for developing or established bronchopulmonary dysplasia (BPD). Respiratory phenotype (Respiratory Severity Score (RSS)), serum, and urine metabolomics were assessed before and after treatment. Ten infants provided nine matched serum and nine matched urine samples. There was a significant decrease in RSS with steroid treatment. Serum gluconic acid had the largest median fold change (140 times decreased, P = 0.008). In metabolite set enrichment analysis, in both serum and urine, the urea cycle, ammonia recycling, and malate‐aspartate shuttle pathways were most significantly enriched when comparing pretreatment and post‐treatment (P value < 0.05). In regression analyses, 6 serum and 28 urine metabolites were significantly associated with change in RSS. Urine gluconic acid lactone was the most significantly correlated with clinical response (correlational coefficient 0.915). Pharmacometabolomic discovery of drug response biomarkers in preterm infants may allow precision therapeutics in BPD treatment.
Racial differences in performance of HbA1c for the classification of diabetes and prediabetes among US adults of non‐Hispanic black and white race
Authors: Ford C. N. , Leet R. W. , Kipling L. M. , Rhee M. K. , Jackson S. L. , Wilson P. W. F. , Phillips L. S. , Staimez L. R. 
Published: June 2019

AbstractAimTo characterize differences between black and white people in optimal HbA1c thresholds for diagnoses of diabetes and prediabetes.MethodsData were included from the National Health and Nutrition Examination Survey, 2005–2014. Black and white adults (age 18–70 years) who underwent an oral glucose tolerance test and had available fasting plasma glucose, 2‐h plasma glucose and HbA1c measurements were eligible for inclusion. Diabetes or prediabetes status was defined by fasting plasma glucose and 2‐h plasma glucose using American Diabetes Association criteria. Classification of diabetes, prediabetes and dysglycaemia by HbA1c was evaluated for a range of HbA1c thresholds, with optimal thresholds defined as those values that maximized the sum of sensitivity and specificity (Youden's index).ResultsIn 5324 black (32.3%) and white (67.7%) individuals, Youden's index (optimal) thresholds for HbA1c were ≥42 mmol/mol (6.0%) and ≥39 mmol/mol (5.7%) for discriminating diabetes vs non‐diabetes, ≥ 44 mmol/mol (6.2%) and ≥39 mmol/mol (5.7%) for discriminating diabetes vs prediabetes (excluding normoglycaemia), ≥39 mmol/mol (5.7%) and ≥37 mmol/mol (5.5%) for discriminating dysglycaemia vs normoglycaemia, and ≥39 mmol/mol (5.7%) and ≥37 mmol/mol (5.5%) for discriminating prediabetes vs normoglycaemia (excluding diabetes), in black and white people, respectively.ConclusionsConsistently higher optimal HbA1c thresholds in black people than in white people suggest a need to individualize HbA1c relative to glucose levels if HbA1c is used to diagnose diabetes and prediabetes.
Hydraulic Tomography: 3D Hydraulic Conductivity, Fracture Network, and Connectivity in Mudstone
Authors: Tiedeman Claire R. , Barrash Warren 
Published: June 2019

AbstractWe present the first demonstration of hydraulic tomography (HT) to estimate the three‐dimensional (3D) hydraulic conductivity (K) distribution of a fractured aquifer at high‐resolution field scale (HRFS), including the fracture network and connectivity through it. We invert drawdown data collected from packer‐isolated borehole intervals during 42 pumping tests in a wellfield at the former Naval Air Warfare Center, West Trenton, New Jersey, in the Newark Basin. Five additional tests were reserved for a quality check of HT results. We used an equivalent porous medium forward model and geostatistical inversion to estimate 3D K at high resolution (K blocks <1 m3), using no strict assumptions about K variability or fracture statistics. The resulting 3D K estimate ranges from approximately 0.1 (highest‐K fractures) to approximately 10−13 m/s (unfractured mudstone). Important estimated features include: (1) a highly fractured zone (HFZ) consisting of a sequence of high‐K bedding‐plane fractures; (2) a low‐K zone that disrupts the HFZ; (3) several secondary fractures of limited extent; and (4) regions of very low‐K rock matrix. The 3D K estimate explains complex drawdown behavior observed in the field. Drawdown tracing and particle tracking simulations reveal a 3D fracture network within the estimated K distribution, and connectivity routes through the network. Model fit is best in the shallower part of the wellfield, with high density of observations and tests. The capabilities of HT demonstrated for 3D fractured aquifer characterization at HRFS may support improved in situ remediation for contaminant source zones, and applications in mining, repository assessment, or geotechnical engineering.
Quasi‐Saturated Layer: Implications for Estimating Recharge and Groundwater Modeling
Authors: Gonçalves Roger D. , Teramoto Elias H. , Engelbrecht Bruno Z. , Alfaro Soto Miguel A. , Chang Hung K. , van Genuchten Martinus Th. 
Published: June 2019

AbstractThis study presents an extension of the concept of “quasi‐saturation” to a quasi‐saturated layer, defined as the uppermost dynamic portion of the saturated zone subject to water table fluctuations. Entrapped air here may cause substantial reductions in the hydraulic conductivity (K) and fillable pore water. Air entrapment is caused by a rising water table, usually as a result of groundwater recharge. The most significant effects of entrapped air are recharge overestimation based on methods that use specific yield (Sy), such as the water table fluctuation method (WTF), and reductions in K values. These effects impact estimation of fluid flow velocities and contaminant migration rates in groundwater. In order to quantify actual groundwater recharge rates and the effects of entrapped air, numerical simulations with the FEFLOW (Version 7.0) groundwater flow model were carried out using a quasi‐saturated layer for a pilot area in Rio Claro, Brazil. The calculated recharge rate represented 16% of the average precipitation over an 8‐year period, approximately half of estimates using the WTF method. Air entrapment amounted to a fillable porosity of 0.07, significant lower that the value of 0.17 obtained experimentally for Sy. Numerical results showed that the entrapped air volume in the quasi‐saturated layer can be very significant (0.58 of the air fraction) and hence can significantly affect estimates of groundwater recharge and groundwater flow rates near the water table.
Bringing together coproduction and community participatory research approaches: Using first person reflective narrative to explore coproduction and community involvement in mental health research
Authors: King Colin , Gillard Steve 
Published: June 2019

AbstractBackgroundA growing literature explores the coproduction of research knowledge. Barriers to coproduction in mental health research have been identified, especially for the people from marginalized communities. There is an established body of participatory research that has potential to inform coproduction in mental health research.ObjectivesTo explore and articulate how learning from community participatory approaches to research enable barriers to knowledge coproduction to be overcome in mental health research.SettingAn evaluation of a primary care mental health service, led by an experienced survivor researcher, supported by a health service researcher and involving a team of community co‐researchers.DesignCycles of reflective writing (first‐person narrative) by the authors, and feedback from the co‐researcher team, on their experiences of undertaking the evaluation were used to explore the ways in which community actors, including those from marginalized communities, might be meaningfully involved in producing research knowledge about mental health services.ResultsA space was created where community co‐researchers, including those from traditionally marginalized communities, felt safe and empowered to move beyond essentialized “service user” identities and bring a range of skills and expertise to the evaluation. There was meaningful rebalancing of power between traditional university and community roles, although the issues around leadership remained complex and more could be done to explore how our different experiences of race and mental health shape the research we do.ConclusionsPotential was demonstrated for participatory research approaches to inform coproduction of knowledge in mental health research that fully reflects the diversity of identity and experience.
Necroptotic cell binding of β2‐glycoprotein I provides a potential autoantigenic stimulus in systemic lupus erythematosus
Authors: Salem David , Subang Rebecca , Pernet Erwan , Divangahi Maziar , Pineau Christian , Cayrol Romain , Levine Jerrold S , Rauch Joyce 
Published: June 2019

AbstractSystemic lupus erythematosus (SLE) is characterized by the development of autoantibodies against diverse self‐antigens with damage to multiple organs. Immunization with the SLE autoantigen β2‐glycoprotein I (β2GPI) and lipopolysaccharide (LPS), a known trigger of necroptosis, induces a murine model of SLE. We hypothesized that necroptotic cells, like apoptotic cells, provide a “scaffold” of cellular self‐antigens, but, unlike apoptotic cells, necroptotic cells do so in a proinflammatory and immunogenic context. We demonstrate that β2GPI indeed binds to necroptotic cells and serves as a target for anti‐β2GPI autoantibodies. We further demonstrate that necroptotic, but not apoptotic, cells promote antigenic presentation of β2GPI to CD4 T cells by dendritic cells. Finally, we show that β2GPI/LPS‐immunized mice deficient in RIPK3 (receptor‐interacting serine/threonine‐protein kinase 3) or MLKL (mixed lineage kinase domain like), and consequently unable to undergo necroptosis, have reduced SLE autoantibody production and pathology. RIPK3−/− mice had low levels of SLE autoantibodies and no renal pathology, while MLKL−/− mice produced low levels of SLE autoantibodies initially, but later developed levels comparable with wild type (WT) mice and pathology intermediate to that of WT and RIPK3−/− mice. Serum cytokine levels induced by LPS tended to be lower in RIPK3−/− and MLKL−/− mice than in WT mice, suggesting that impaired proinflammatory cytokine production may impact the initiation of autoantibody production in both strains. Our data suggest that self‐antigen (i.e. β2GPI) presented in the context of necroptosis and proinflammatory signals may be sufficient to overcome immune tolerance and induce SLE.
Emergence of waterfowl‐originated gene cassettes in HPAI H7N9 viruses caused severe human infection in Fujian, China
Authors: Yang Lei , Xie Jianfeng , Zhang Ye , Zhu Wenfei , Li Xiyan , Wei Hejiang , Li Zi , Zhao Lin , Bo Hong , Liu Jia , Dong Jie , Chen Tao , Shu Yuelong , Weng Yuwei , Wang Dayan 
Published: June 2019

AbstractBackgroundHighly pathogenic avian influenza (HPAI) A(H7N9) virus emerged and caused human infections during the 2016‐2017 epidemic wave of influenza A(H7N9) viruses in China. We report a human infection with HPAI H7N9 virus and six environmental isolates in Fujian Province, China.MethodsEnvironmental surveillance was conducted in live poultry markets and poultry farms in Fujian, China. Clinical and epidemiologic data and samples were collected. Real‐time RT‐PCRs were conducted for each sample, and H7‐positive samples were isolated using embryonated chicken eggs. Full genomes of the isolates were obtained by next‐generation sequencing. Phylogenetic analysis and antigenic analysis were conducted.ResultsA 59‐year‐old man who raised about 1000 ducks was identified as HPAI H7N9 infection. Six HPAI H7 viruses were isolated from environmental samples, including five H7N9 viruses and one H7N6 virus. Phylogenetic results showed the human and environmental viruses are highly genetically diverse and containing significantly different gene constellation from that of other HPAI H7N9 previously reported. The internal genes derived from H7N9/H9N2, H5N6, and the Eurasian wild‐bird gene pool, indicating waterfowl‐originated genotypes, have emerged in HPAI H7N9/N6 viruses and caused human infection.ConclusionThe new genotypes raise the concern that these HPAI H7 viruses might transmit back into migratory birds and spread to other countries as the HPAI H5Nx viruses. Considering their capability of causing severe infections in both human and poultry, the HPAI H7 viruses in this study pose a risk to public health and the poultry industry and highlight the importance of sustained surveillance of these viruses.
Detection of oseltamivir‐resistant zoonotic and animal influenza A viruses using the rapid influenza antiviral resistance test
Authors: Hodges Erin N. , Mishin Vasiliy P. , De la Cruz Juan , Guo Zhu , Nguyen Ha T. , Fallows Eric , Stevens James , Wentworth David E. , Davis Charles Todd , Gubareva Larisa V. 
Published: June 2019

AbstractMutations in the influenza virus neuraminidase (NA) that cause reduced susceptibility to the NA inhibitor (NAI) oseltamivir may occur naturally or following antiviral treatment. Currently, detection uses either a traditional NA inhibition assay or gene sequencing to identify known markers associated with reduced inhibition by oseltamivir. Both methods are laborious and require trained personnel. The influenza antiviral resistance test (iART), a prototype system developed by Becton, Dickinson and Company for research use only, offers a rapid and simple method to identify such viruses. This study investigated application of iART to influenza A viruses isolated from non‐human hosts with a variety of NA subtypes (N1‐N9).