bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica
Authors: Coyne Kathryn J , Parker Alexander E , Lee Charles K , Sohm Jill A , Kalmbach Andrew , Gunderson Troy , León-Zayas Rosa , Capone Douglas G , Carpenter Edward J , Cary S Craig 
Published: January 2020

ABSTRACTThe McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
16S rRNA gene-based primer pair showed high specificity and quantification accuracy in detecting freshwater Brocadiales anammox bacteria
Authors: Ding Chang , Adrian Lorenz , Peng Yongzhen , He Jianzhong 
Published: January 2020

ABSTRACT
Anaerobic ammonium oxidizing (anammox) bacteria are widely distributed and contribute significantly to the global nitrogen cycle. Traditionally, identification and quantification based on the 16S rRNA gene were considered not reliable because of low 16S rRNA gene sequence identity within Brocadiales. Here we hypothesize that by using appropriate primers and methodology, 16S-based detection and quantification of anammox bacteria can be accurate. We modified an existing 16S rRNA gene-based primer pair (Amx694F–Amx960R) by changing one nucleotide (Amx694F position 18, G→C) (Amx694PF–Amx960R) so that they match the sequences of most Brocadiales anammox bacteria, and evaluated the modified primer pair with 29 freshwater samples from microcosms, anammox reactors and wastewater treatment plants of various geographical origins. The primer pair showed high specificity in detection and quantification of anammox populations in samples that contained &gt;0.1% anammox bacteria. Quantification of anammox abundance by quantitative real-time PCR and delineation of anammox species by denaturing gradient gel electrophoresis agreed well with amplicon sequencing results. A clear shift of anammox population towards ‘Candidatus Kuenenia’ was observed under laboratory cultivation conditions. With the help of amplicon sequencing, we demonstrated that 16S rRNA gene-based anammox-specific primers are able to achieve qualitative and quantitative monitoring of anammox communities in wastewater treatment plants and natural freshwater environments.2007;73:5261–7.
Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn’s Disease
Authors: Jones Casey M A , Connors Jessica , Dunn Katherine A , Bielawski Joseph P , Comeau André M , Langille Morgan G I , Van Limbergen Johan 
Published: January 2020

Abstract

Background
The gut microbiome is extensively involved in induction of remission in pediatric Crohn’s disease (CD) patients by exclusive enteral nutrition (EEN). In this follow-up study of pediatric CD patients undergoing treatment with EEN, we employ machine learning models trained on baseline gut microbiome data to distinguish patients who achieved and sustained remission (SR) from those who did not achieve remission nor relapse (non-SR) by 24 weeks.

Methods
A total of 139 fecal samples were obtained from 22 patients (8–15 years of age) for up to 96 weeks. Gut microbiome taxonomy was assessed by 16S rRNA gene sequencing, and functional capacity was assessed by metagenomic sequencing. We used standard metrics of diversity and taxonomy to quantify differences between SR and non-SR patients and to associate gut microbial shifts with fecal calprotectin (FCP), and disease severity as defined by weighted Pediatric Crohn’s Disease Activity Index. We used microbial data sets in addition to clinical metadata in random forests (RFs) models to classify treatment response and predict FCP levels.

Results
Microbial diversity did not change after EEN, but species richness was lower in low-FCP samples (&lt;250 µg/g). An RF model using microbial abundances, species richness, and Paris disease classification was the best at classifying treatment response (area under the curve [AUC] = 0.9). KEGG Pathways also significantly classified treatment response with the addition of the same clinical data (AUC = 0.8). Top features of the RF model are consistent with previously identified IBD taxa, such as Ruminococcaceae and Ruminococcus gnavus.

Conclusions
Our machine learning approach is able to distinguish SR and non-SR samples using baseline microbiome and clinical data.
Using parent-reported experience measures as quality improvement tools in paediatric cardiothoracic services: making it happen
Authors: Wray Jo , Oldham Geralyn 
Published: January 2020

AbstractObjectivePatient experience is a core component of quality and service improvement. In the case of child health, it is parents who often report on their experiences of the child’s healthcare. However, these parent experiences are rarely used to drive change. Our aim was to develop and implement the systematic collection of parent experience data across a range of cardiothoracic services, using quality improvement methodology to implement change.DesignPlan-Do-Study-Act methodology was used to develop parent-reported experience measures. Setting: Specialist children’s hospital.ParticipantsParents of children under the care of one of a number of cardiothoracic services at the hospital.Intervention(s)Completion of questionnaires about hospital experience comprising quantitative and qualitative questions.Main Outcome Measure(s)Response rates and completion of a specific-measurable-achievable-realistic-timely (SMART) action plan by the individual clinical teams.ResultsDuring the first cycle 17 surveys were developed for different clinical services and questionnaires sent/given to 1876 parents. The overall response rate was 30% (15–100%). Clinical teams developed SMART plans following eight (47%) surveys; three teams have reviewed and reported back on their progress against their plan and started on the second cycle of questionnaires. Challenges included lack of resources (time, finances and electronic data collection tools) and problems with actioning SMART plans. However, teams engaged positively, recognizing the importance of parent experience and actively seeking solutions to problems.ConclusionsParent-reported experience measures are practical and acceptable quality improvement tools in healthcare but challenges need to be addressed, primarily related to resources, training and sustainability.
Constitutive activation of the EGFR–STAT1 axis increases proliferation of meningioma tumor cells
Authors: Ferluga Sara , Baiz Daniele , Hilton David A , Adams Claire L , Ercolano Emanuela , Dunn Jemma , Bassiri Kayleigh , Kurian Kathreena M , Hanemann Clemens O 
Published: January 2020

Abstract

Background
Meningiomas are the most frequent primary brain tumors of the central nervous system. The standard of treatment is surgery and radiotherapy, but effective pharmacological options are not available yet. The well-characterized genetic background stratifies these tumors in several subgroups, thus increasing diversification. We identified epidermal growth factor receptor–signal transducer and activator of transcription 1 (EGFR–STAT1) overexpression and activation as a common identifier of these tumors.

Methods
We analyzed STAT1 overexpression and phosphorylation in 131 meningiomas of different grades and locations by utilizing several techniques, including Western blots, qPCR, and immunocytochemistry. We also silenced and overexpressed wild-type and mutant forms of the gene to assess its biological function and its network. Results were further validated by drug testing.

Results
STAT1 was found widely overexpressed in meningioma but not in the corresponding healthy controls. The protein showed constitutive phosphorylation not dependent on the JAK–STAT pathway. STAT1 knockdown resulted in a significant reduction of cellular proliferation and deactivation of AKT and ERK1/2. STAT1 is known to be activated by EGFR, so we investigated the tyrosine kinase and found that EGFR was also constitutively phosphorylated in meningioma and was responsible for the aberrant phosphorylation of STAT1. The pharmaceutical inhibition of EGFR caused a significant reduction in cellular proliferation and of overall levels of cyclin D1, pAKT, and pERK1/2.

Conclusions
STAT1–EGFR-dependent constitutive phosphorylation is responsible for a positive feedback loop that causes its own overexpression and consequently an increased proliferation of the tumor cells. These findings provide the rationale for further studies aiming to identify effective therapeutic options in meningioma.
Clinical Features and Outcomes of Bloodstream Infections Caused by New Delhi Metallo-β-Lactamase–Producing Enterobacterales During a Regional Outbreak
Authors: Falcone Marco , Tiseo Giusy , Antonelli Alberto , Giordano Cesira , Di Pilato Vincenzo , Bertolucci Pietro , Parisio Eva Maria , Leonildi Alessandro , Aiezza Noemi , Baccani Ilaria , Tagliaferri Enrico , Righi Lorenzo , Forni Silvia , Sani Spartaco , Mechi Maria Teresa , Pieralli Filippo , Barnini Simona , Rossolini Gian Maria , Menichetti Francesco 
Published: January 2020

Abstract
Limited data about New Delhi metallo-β-lactamase (NDM) bacteremia are available. Blood isolates from 40 patients with NDM bacteremia were studied for antibiotic susceptibility and whole-genomic sequencing. NDM bacteremia has high 30-day mortality. In most cases, aztreonam-avibactam is active in vitro. Ceftazidime-avibactam plus aztreonam may represent a feasible therapeutic option.
Comparative Evaluation of 3-Dimensional High Definition and 2-Dimensional 4-K Ultra-High Definition Endoscopy Systems in Endonasal Skull Base Surgery
Authors: Uozumi Yoichi , Taniguchi Masaaki , Nakai Tomoaki , Kimura Hidehito , Umehara Toru , Kohmura Eiji 
Published: January 2020

Abstract

BACKGROUND
The differences between 3-dimensional (3D) high definition (HD) and 2-dimensional (2D) 4-K ultra-HD (4K) endoscopy and their respective advantages remain unclear.

OBJECTIVE
To evaluate the utility of these endoscopy systems in endonasal skull base surgery.

METHODS
Consecutive series of endoscopic endonasal surgeries performed after introduction of 3D/HD and 2D/4K systems (July 2017) were retrospectively evaluated. Sporadic cases treated with either system, or a conventional 2D standard definition (SD) system, during the rental period from March 2016 were also included. Objective comparisons between the systems were made for newly diagnosed Knosp grade 0 to 3 pituitary adenomas. Surgical procedures were divided into nasal, sphenoidal, and intradural phases, and the surgical procedural time was compared for each phase. The time required for and accuracy of suturing the sellar floor dura was also evaluated.

RESULTS
A total of 74 cases were treated with 3D/HD and/or 2D/4K, and 12 cases with 2D/SD. 3D/HD was advantageous in the nasal phase because of its intuitive depth perception. 2D/4K was advantageous in the intradural phase because of its superior image quality. Surgical time of the nasal phase with 3D/HD, and that of the intradural phase with 2D/4K, were significantly shorter than that with 2D/SD. The time required for and accuracy of sellar floor dural suturing showed a trend toward improving in the order of 2D/SD, 2D/4K, and 3D/HD.

CONCLUSION
3D/HD and 2D/4K endoscopy systems have different advantages, which are useful in distinct surgical phases. Understanding the characteristics of endoscopy systems is important for selecting the most appropriate system for distinct surgical situations.
Pain Agreements and Time-to-Event Analysis of Substance Misuse in a Primary Care Chronic Pain Program
Authors: Ghodke Ameer , Ives Timothy J , Austin Anna E , Bennett William C , Patel Naishal Y , Eshet Sharon A , Chelminski Paul R 
Published: January 2020

Abstract

Background
Types and correlates of pain medication agreement (PMA) violations in the primary care setting have not been analyzed.

Methods
A retrospective analysis was completed to examine patient characteristics and correlates of PMA violations, a proxy for substance misuse, over a 15-year period in an outpatient General Medicine Pain Service within the Division of General Medicine and Clinical Epidemiology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill. Patients who signed the PMA were managed for chronic pain from 2002 through 2017 (N = 1,210). The incidence of PMA violations was measured over a 15-year span. Substance misuse was defined a priori in the study as urine toxicology screen positive for illicit or nonprescribed controlled substances, patient engagement in prescription alteration, doctor-shopping, or diversion.

Results
Most patients received a prescription for a controlled substance (77.4%). During enrollment, 488 (40.3%) patients had one or more violations of their PMA. One-third (33.4%) of pain service patients had a violation within 365 days of signing the agreement. Active tobacco smokers had double the incidence of agreement violation within the first 30 days of enrollment. Almost one-half (49.8%) of violations were due to inconsistent use of controlled substances. Patients with any prior DWI/DUI or drug-related offense had a significantly increased rate of substance misuse (P &lt; 0.0001).

Conclusions
PMA violations were common among a population of patients managed for chronic nonmalignant pain. Universal opioid prescribing precautions, including PMAs, require further investigation to assess their roles in mitigating the potential patient and societal harms associated with opioid prescribing.
Relationship between Stunting, Wasting, Underweight and Geophagy and Cognitive Function of Children
Authors: Mireku Michael O , Cot Michel , Massougbodji Achille , Bodeau-Livinec Florence 
Published: January 2020

Abstract

Objectives
The aim of this study was to investigate the relationship between anthropometric characteristics and both geophagy and cognitive function of children.

Study design
The study prospectively followed singleton children whose mothers participated in the MiPPAD clinical trial in Allada, Benin, from birth to age 12 months. Anthropometric measurements were taken at birth and 9 and 12 months. Wasting, stunting and underweight were defined as weight-for-length, length-for-age and weight-for-age Z-scores less than −2, respectively. Cognitive and motor functions were assessed using the Mullen Scales of Early Learning. Parent-reported geophageous habits of children were collected when the children were 12 months. Multiple linear and logistic regressions were used to analyse the data.

Results
A total of 632 children (49.7% girls) were involved in the study. Stunting, wasting and underweight were observed in 14.1%, 13.6% and 17.7%, respectively, at 9 months and 17.3%, 12.7% and 17.2%, respectively, at 12 months. The prevalence of geophagy among the children was 48.2%. Impaired growth at 9 and 12 months was consistently associated with low cognitive and gross motor (GM) score. Children stunted at 9 months had lower GM scores at 12 months compared with their non-stunted peers (β = −3.48, 95% confidence interval −6.62 to −0.35).

Conclusions
Stunting, wasting and underweight are associated with cognitive and GM deficits in infants. In this setting, impaired growth was not associated with geophagy. Further research evaluating geophagy and growth prospectively and concurrently from birth to 36 months is needed.
Bayesian spatio-temporal models for mapping TB mortality risk and its relationship with social inequities in a region from Brazilian Legal Amazon
Authors: Alves Josilene D , Chiaravalloti-Neto Francisco , Arroyo Luiz H , Arcoverde Marcos A M , Santos Danielle T , Berra Thaís Z , Alves Luana S , Ramos Antônio C V , Campoy Laura T , Belchior Aylana S , Assis Ivaneliza S , Nunes Carla , Forati Regina C , Serrano-Gallardo Pilar , Arcêncio Ricardo A 
Published: January 2020

AbstractBackgroundReducing TB mortality is a great challenge in Brazil due to its territorial extension, cultural variations and economic and political crises, which impact the health system. This study aimed to estimate in space and time the risk of TB mortality and test its relationship with social inequities.MethodsThis was an ecological study that included deaths from TB between 2006 and 2016 in Cuiabá, Brazilian Legal Amazon. Bayesian models based on the integrated nested Laplace approximation approach were used to estimate spatio-temporal RRs. RRs for TB mortality were obtained according to the covariables representative of social inequities.ResultsThe risk of TB mortality was stable between 2006 and 2016 and high-risk areas were identified throughout the municipality studied. Regarding social inequities, income was an important factor associated with TB mortality risk, as an increase of 1 SD in income resulted in a 35.4% (RR 0.646; CI 95% 0.476 to 0.837) decrease in risk.ConclusionsThe results provided evidence of areas with higher TB mortality risks that have persisted over time and are related to social inequities. Advancing social policies and protections in these areas will contribute to achieving the WHO's End TB strategy.
Research presented at the 14th International Symposium on Tardigrada: progress in studies on water bears
Authors: Møbjerg Nadja , Michalczyk Łukasz , Mcinnes Sandra J , Christenhusz Maarten J M 
Published: January 2020

AbstractThe 14th International Symposium on Tardigrada took place in Copenhagen, Denmark from 30 July to 3 August 2018. Approximately 140 participants, representing 28 countries from five continents attended the meeting, and there were 58 talks and 74 posters of which 20 were selected for the Symposium Proceedings published in this special issue. The studies span phylogenomics, systematics, anatomy, morphology, reproductive biology, cryobiology, ecology, diet, microbial interactions and biogeography, taking the next step forward in broadening and deepening our understanding of tardigrade biology.
Validation of Emotional Stimuli Flashcards for Conducting ‘Response to Reward’ fMRI study among Malaysian students
Authors: Nasser Nisha Syed , Sharifat Hamed , Rashid Aida Abdul , Hamid Suzana Ab , Rahim Ezamin Abdul , Mohamad Mazlyfarina , Tyagi Rohit , Ismail Siti Irma Fadhilah , Mooi Ching Siew , Suppiah Subapriya 
Published: January 2020

AbstractProblematic Instagram Use (PIGU) is a specific-Internet-addiction disorder observed among the youth of today. fMRI, is able to objectively assess regional brain activation in response to addiction-specific rewards, e.g. viewing picture flashcards. Pictures uploaded onto Instagram by PIGUs have often been associated with risky behaviours in their efforts to gain more ‘Likes’, thus it is hypothesized that PIGUs are more drawn to ‘Negative-Emotional’ cues. To date, there is no local database with addiction-specific cues.ObjectiveTo conduct an out-of-scanner validation study to create a database of pictures using ‘Negative-Emotional’ cues that evoke responses of arousal among PIGUs.MethodForty-four Malaysian undergraduate students (20 PIGUs, 24 controls) were randomly recruited based on the evaluation using the Smartphone-Addiction-Scale-Malay version (SAS-M) and modified Instagram Addiction Test (IGAT); and fulfilled Lin et al. (2016) definition of addiction. They were administered 200 content-specific pictures that were multidimensional i.e. arousal (excitation/relaxation effects), approach-avoidance (motivational direction) and emotional valence (positive/negative feelings) to describe the PIGUs perception of the psychological properties of the pictures using a 9-point Likert scale.ResultsPIGUs viewing ‘Negative-Emotional’ cues demonstrated significant positive correlations between arousal & valence (z = 4.834, p < .001, effect size = 0.69) and arousal & avoidance-approach (z = 4.625, p < .001, effect size= 0.66) as compared to controls and were more frequently aroused by ‘Negative-Emotional’ type of stimuli.ConclusionA database of validated, addiction-specific pictures can be developed to potentiate any future cue-induced response to reward fMRI studies to assess PIGU.
Venous Thromboembolism and Intracranial Hemorrhage in Patients with High-grade Glioma
Authors: Borges Clara , Lemos Carlota , Soares Pedro , Silva Roberto , Fernandes Catarina , Costa Andreia , Caeiro Cláudia , Sarmento Cristina 
Published: January 2020

AbstractBackgroundPatients with high-grade glioma (HGG) are at increased risk of venous thromboembolism (VTE), throughout the course of disease. Prophylactic anticoagulation is not established among patients with HGG, outside of perioperative context, due to potential for intracranial hemorrhage (ICH) and the limited data available for predictive VTE scores in primary brain tumors. The aim of this study was to characterize VTE prevalence in adult patients with HGG and assess ICH risk during therapeutic anticoagulation.MethodsRetrospective analysis of patients diagnosed with HGG at our institution, between 2009 and 2018. All adult patients proposed to systemic treatment were included into this study. Exclusion criteria was anticoagulation previous to diagnosis. VTE was defined as any radiographic-confirmed thrombus in the venous system. Risk factors of interest for VTE and bleeding risk scores were analyzed by chi-squared test and multivariate logistic regression. Survival analysis was performed using Kaplan-Meier method.ResultsA total of 410 patients were included of whom 31 (7,8%) developed a VTE, including 22 deep vein, 6 pulmonary and 3 central venous thrombosis. Twenty-nine patients with VTE had a WHO grade 4 glioma and 2 patients had grade 3 (anaplastic astrocytoma and oligodendroglioma).In 22 cases, the VTE occurred during systemic treatment, more frequently during Temozolomide (n=15), followed by Irinotecan+Bevacizumab (n=6), Lomustine+Bevacizumab (n=1) and PCV (n=1). The median time between diagnosis and VTE was 10,11 months (95CI 6,46-14,79). Khorana score, age, ECOG performance status, smoking and obesity did not significantly differ in the VTE population. All VTE were initially treated with low molecular weight heparin (LMWH), of which 64.5% maintained LMWH, and the remainder switched to warfarin (19.4%) or to direct oral anticoagulant (16.1%). Six patients (19,4%) had spontaneous ICH under anticoagulation. Patients with grade 3 glioma (p=0,032) had significantly higher rates of ICH than grade 4. Patients with higher ECOG had significantly higher risk of ICH (OR 3,23 (95CI 1,18-8,81), p=0,022). HAS-BLED and ACCP bleeding scores were not associated with ICH. There was no significant difference in overall survival for TVE or ICH.ConclusionAccording to our data, ICH occurred in nearly 20% anticoagulated patients with HGG, as described in literature, and did not correlate with poorer prognosis. High ECOG performance status was an independent risk factor for ICH. Further effort towards better prediction models for VTE and ICH in HGG is warranted.