bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lack of evidence of mastitis as a causal factor for postpartum dysgalactia syndrome in sows123
Authors: Kaiser Marianne , Jacobson Magdalena , Bækbo Poul , Dahl Jan , Jacobsen Stine , Guo Yong Z , Larsen Torben , Andersen Pia H 
Published: October 2019

AbstractTo investigate the prevalence of mastitis in sows suffering from postpartum dysgalactia syndrome (PDS), we examined milk constituents and concentrations of lipopolysaccharides (LPS) obtained from the udder vein (v. epigastrica). As part of a case–cohort study, 109 sows were monitored daily from 60 h antepartum (a.p.) to 36 h postpartum (p.p.). Over time, 38 sows were diagnosed with PDS (PDS+) and were retrospectively matched with 38 healthy sows (PDS−). The study period was divided into 7 smaller time periods (A, B, C, D, E, F, G, H, and E), allowing the studied values, in period B to G, to be compared with period A that served as a baseline, and PDS+ and PDS− sows were compared within the time periods. All sows were subjected to a thorough daily clinical examination and blood was sampled from v. epigastrica for LPS detection. Milk samples were obtained for bacteriological evaluation and detection of N-acetyl-beta-d-glucosaminidase (NAGase), lactate dehydrogenase (LDH), β-glucuronidase (β-glu; for evaluation of mastitis), isocitrate (isoC), free glucose, uric acid (UA; for evaluation of the mammary energy status), β-hydroxybutyrate acid (BHBA; for evaluation of ketosis), and milk urea (for evaluation of the protein status). The results revealed that PDS+ sows had decreased concentrations of UA in milk (P &lt; 0.0001), increased heart rates (P &lt; 0.01), increased mammary edema (P &lt; 0.05), and prolonged capillary refill time in the vulvar mucosa (P &lt; 0.01) compared with PDS− sows. Compared with baseline, feces became more solid 0 to 36 h p.p. (P &lt; 0.0001) and the respiration rate decreased 12 to 24 h p.p. (P &lt; 0.0001) for both PDS+ and PDS− sows. No differences were found between PDS+ and PDS− sows for severe bacterial infections, concentrations of LPS in blood or LDH, NAGase, BHBA, free glucose, isoC, or urea in milk. Concentrations of LPS in blood were not associated with signs of mastitis or edema in the mammary glands. However, a difference over time was seen for redness (P &lt; 0.0001), warmth (P &lt; 0.0001), and hardness (P &lt; 0.05) of the 6 most anterior glands in both PDS+ and PDS− sows from 60 h a.p to 36 h p.p. The PDS− sows had greater concentrations of β-glu than the PDS+ sows, but no change over time was demonstrated for this marker. In conclusion, signs of mastitis were not consistently linked to PDS in sows. However, the cardiovascular system seemed to be compromised in PDS+ sows and the cause should be investigated to elucidate the pathogenesis of PDS.
The Use of Test-negative Controls to Monitor Vaccine Effectiveness
Authors: Chua Huiying , Feng Shuo , Lewnard Joseph A. , Sullivan Sheena G. , Blyth Christopher C. , Lipsitch Marc , Cowling Benjamin J. 
Published: October 2019

Background:The test-negative design is an increasingly popular approach for estimating vaccine effectiveness (VE) due to its efficiency. This review aims to examine published test-negative design studies of VE and to explore similarities and differences in methodological choices for different diseases and vaccines.Methods:We conducted a systematic search on PubMed, Web of Science, and Medline, for studies reporting the effectiveness of any vaccines using a test-negative design. We screened titles and abstracts and reviewed full texts to identify relevant articles. We created a standardized form for each included article to extract information on the pathogen of interest, vaccine(s) being evaluated, study setting, clinical case definition, choices of cases and controls, and statistical approaches used to estimate VE.Results:We identified a total of 348 articles, including studies on VE against influenza virus (n = 253), rotavirus (n = 48), pneumococcus (n = 24), and nine other pathogens. Clinical case definitions used to enroll patients were similar by pathogens of interest but the sets of symptoms that defined them varied substantially. Controls could be those testing negative for the pathogen of interest, those testing positive for nonvaccine type of the pathogen of interest, or a subset of those testing positive for alternative pathogens. Most studies controlled for age, calendar time, and comorbidities.Conclusions:Our review highlights similarities and differences in the application of the test-negative design that deserve further examination. If vaccination reduces disease severity in breakthrough infections, particular care must be taken in interpreting vaccine effectiveness estimates from test-negative design studies.
Nursing Students' Perceptions of Just Culture in Nursing Programs
Authors: Walker Danielle , Altmiller Gerry , Hromadik Lora , Barkell Nina , Barker Nancy , Boyd Teri , Compton Michelle , Cook Pamela , Curia Marianne , Hays Deana , Flexner Randi , Jordan Janet , Jowell Vicki , Kaulback Michelle , Magpantay-Monroe Edna , Rudolph Bethany , Toothaker Rebecca , Vottero Beth , Wallace Sharon 
Published: October 2019

Background
While just culture is embraced in the clinical setting, just culture has not been systematically incorporated into nursing education.

Purpose
The purpose of this study was to assess prelicensure nursing student perceptions of just culture in academia.

Methods
Following a quantitative, descriptive design, the Just Culture Assessment Tool for Nursing Education (JCAT-NE) was used to measure just culture across multiple (N = 15) nursing programs.

Results
The majority of JCAT-NE respondents (78%) reported their program has a safety reporting system, 15.4% had involvement in a safety-related event, and 12% submitted an error report. The JCAT-NE mean total score was 127.4 (SD, 23.6), with a statistically significant total score decline as students progressed from the beginning (133.6 [SD, 20.52]) to the middle (129.77 [SD, 23.6]) and end (122.2 [SD, 25.43]) of their programs (χ
2[2] = 25.09, P < .001).

Conclusions
The results from this study are a call to action for nursing education to emphasize the tenets of just culture, error reporting, and quality improvement.
Knowledge and Skills Acquisition by Plastic Surgery Residents through Digital Simulation Training: A Prospective, Randomized, Blinded Trial
Authors: Kantar Rami S. , Alfonso Allyson R. , Ramly Elie P. , Cohen Oriana , Rifkin William J. , Maliha Samantha G. , Diaz-Siso J. Rodrigo , Eisemann Bradley S. , Saadeh Pierre B. , Flores Roberto L. 
Published: October 2019

Background:
Simulation is a standard component of residency training in many surgical subspecialties, yet its impact on knowledge and skills acquisition in plastic surgery training remains poorly defined. The authors evaluated the potential benefits of simulation-based cleft surgery learning in plastic surgery resident education through a prospective, randomized, blinded trial.

Methods:
Thirteen plastic surgery residents were randomized to a digital simulator or textbook demonstrating unilateral cleft lip repair. The following parameters were evaluated before and after randomization: knowledge of surgical steps, procedural confidence, markings performance on a three-dimensional stone model, and surgical performance using a hands-on/high-fidelity three-dimensional haptic model. Participant satisfaction with either educational tool was also assessed. Two expert reviewers blindly graded markings and surgical performance. Intraclass correlation coefficients were calculated. Wilcoxon signed rank and Mann-Whitney U tests were used.

Results:
Interrater reliability was strong for preintervention and postintervention grading of markings [preintervention intraclass correlation coefficient, 0.97 (p < 0.001); postintervention intraclass correlation coefficient, 0.96 (p < 0.001)] and surgical [preintervention intraclass correlation coefficient, 0.83 (p = 0.002); postintervention intraclass correlation coefficient, 0.81 (p = 0.004)] performance. Postintervention surgical knowledge (40.3 ± 4.4 versus 33.5 ± 3.7; p = 0.03), procedural confidence (24.0 ± 7.0 versus 14.7 ± 2.3; p = 0.03), markings performance (8.0 ± 2.5 versus 2.9 ± 3.1; p = 0.03), and surgical performance (12.3 ± 2.5 versus 8.2 ± 2.3; p = 0.04) significantly improved in the digital simulation group compared with before intervention, but not in the textbook group. All participants were more satisfied with the digital simulator as an educational tool (27.7 ± 2.5 versus 14.4 ± 4.4; p < 0.001).

Conclusion:
The authors present evidence suggesting that digital cognitive simulators lead to significant improvement in surgical knowledge, procedural confidence, markings performance, and surgical performance.
Classifying post-traumatic stress disorder using the magnetoencephalographic connectome and machine learning
Authors: Zhang Jing , Richardson J. Don , Dunkley Benjamin T. 
Published: October 2019

AbstractGiven the subjective nature of conventional diagnostic methods for post-traumatic stress disorder (PTSD), an objectively measurable biomarker is highly desirable. Macroscopic neural circuits measured using magnetoencephalography (MEG) has previously been shown to be indicative of the PTSD phenotype and severity. In the present study, we employed a machine learning-based classification framework using MEG neural synchrony to distinguish combat-related PTSD from trauma-exposed controls. Support vector machine (SVM) was used as the core classification algorithm. A recursive random forest feature selection step was directly incorporated in the nested SVM cross validation process (CV-SVM-rRF-FS) for identifying the most important features for PTSD classification. For the five frequency bands tested, the nested CV-SVM-rRF-FS analysis selected the minimum numbers of edges per frequency that could serve as a PTSD signature and be used as the basis for SVM modelling. Many of the selected edges have been reported previously to be core in PTSD pathophysiology, with frequency-specific patterns also observed. Furthermore, the independent partial least squares discriminant analysis suggested low bias in the nested CV-SVM-rRF-FS process. The final SVM models built with selected features showed excellent PTSD classification performance (area-under-curve value up to 0.9). Testament to its robustness when distinguishing individuals from a heavily-traumatised control group, these developments for a classification model for PTSD also provide a comprehensive machine learning-based computational framework for classifying other mental health challenges using MEG connectome profiles.
Dynamic interactions of influenza viruses in Hong Kong during 1998-2018
Authors: Yang Wan , Lau Eric H. Y. , Cowling Benjamin J. 
Published: October 2019

AbstractInfluenza epidemics cause substantial morbidity and mortality every year worldwide. Currently, two influenza A subtypes, A(H1N1) and A(H3N2), and type B viruses co-circulate in humans and infection with one type/subtype could provide cross-protection against the others. However, it remains unclear how such ecologic competition via cross-immunity and antigenic mutations that allow immune escape impact influenza epidemic dynamics at the population level. Here we develop a comprehensive model-inference system and apply it to study the evolutionary and epidemiological dynamics of the three influenza types/subtypes in Hong Kong, a city of global public health significance for influenza epidemic and pandemic control. Utilizing long-term influenza surveillance data since 1998, we are able to estimate the strength of cross-immunity between each virus-pairs, the timing and frequency of punctuated changes in population immunity in response to antigenic mutations in influenza viruses, and key epidemiological parameters over the last 20 years including the 2009 pandemic. We find evidence of cross-immunity in all types/subtypes, with strongest cross-immunity from A(H1N1) against A(H3N2). Our results also suggest that A(H3N2) may undergo antigenic mutations in both summers and winters and thus monitoring the virus in both seasons may be important for vaccine development. Overall, our study reveals intricate epidemiological interactions and underscores the importance of simultaneous monitoring of population immunity, incidence rates, and viral genetic and antigenic changes.
Association of rs12722 COL5A1 with Pulmonary Tuberculosis infection: a preliminary case-control study in a Kazakhstani population
Authors: Zhetkenev Sanzhar , Khassan Ayauly , Khamzina Armanay , Issanov Alpamys , Crape Byron , Akilzhanova Ainur , Kozhamkulov Ulan , Yerezhepov Dauren , Chan Chee Kai 
Published: October 2019

ABSTRACTBackgroundLung cavitation is the classic hallmark of TB, which facilitates the disease development and transmission. It involves the degradation of lung parenchyma which is mainly made up of collagen fibers by metalloproteinases (MMPs) produced by activated monocyte-derived cells, neutrophils and stromal cells.ObjectiveThe following population-based preliminary case-control study of adults with TB and controls without TB will check the possible association between rs1800012 in COL1A1, rs1272222 in COL5A1 genes to human TB susceptibility in Kazakhstan.MethodsIn this case-control study including 165 samples we examined the associations between TB disease status and demographic variables along with single nucleotide polymorphisms related to COLA1 and COL5A1. The unadjusted χ2 and adjusted logistic regression was performed to find out relationships between SNPS and other predictors.ResultsPreliminary findings suggest that there is a statistically significant association of age (OR=0.44, 95% CI:0.21-0.92, p-value=0.03), social status (OR=0.42, 95% CI:0.201 −0.87, p-value=0.020), HIV status(OR=6.9, 95% CI:1.86 - 25.6, p-value=0.004) and heterozygous rs12722 SNP (OR=2.45, 95% CI:1.16 −5.16 p-value=0.019) polymorphism of COL5A1 gene with TB susceptibility.ConclusionThe association of collagen genes with TB pathogenesis indicates that anti TB programs should develop new drug regimens that include MMP inhibitors. Therapeutic targeting of MMPs will prevent extracellular matrix degradation and granuloma maturation.
Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer
Authors: Xia Li C , Van Hummelen Paul , Kubit Matthew , Lee Hojoon , Bell John M , Grimes Susan M. , Wood-Bouwens Christina , Greer Stephanie U. , Barker Tyler , Haslem Derrick S , Ford James , Fulde Gail , Ji Hanlee P , Nadauld Lincoln D 
Published: October 2019

ABSTRACTDNA copy number aberrations (CNA) were frequently observed in colorectal cancers (CRC). There is an urgent call for CNA-based biomarkers in clinics, in particular for Stage III CRC, if combined with imaging or pathologic evidence, promise more precise care at the timing. We conducted this Stage III specific biomarker discovery with a cohort of 134 CRCs, and with a newly developed high-efficiency CNA profiling protocol. Specifically, we developed the profiling protocol for tumor-normal matched tissue samples based on low-coverage clinical whole-genome sequencing (WGS). We demonstrated the protocol’s accuracy and robustness by a systematic benchmark with microarray, high-coverage whole-exome and -genome approaches, where the low-coverage WGS-derived CNA segments were highly accordant (PCC>0.95) with those derived from microarray, and they were substantially less variable if compared to exome-derived segments. A lasso-based model and multivariate cox regression analysis identified a chromosome 17p loss, containing the TP53 tumor suppressor gene, that was significantly associated with reduced survival (P=0.0139, HR=1.688, 95% CI = [1.112-2.562]), which was validated by an independent cohort of 187 Stage III CRCs. In summary, the new low-coverage WGS protocol has high sensitivity, high resolution and low cost and the identified 17p-loss is an effective poor prognosis marker for Stage III patients.
Out of the abyss: Genome and metagenome mining reveals unexpected environmental distribution of abyssomicins
Authors: Iglesias Alba , Latorre-Pérez Adriel , Stach James E. M. , Porcar Manuel , Pascual Javier 
Published: October 2019

AbstractNatural products have traditionally been discovered through the screening of culturable microbial isolates from all sort of environments. The sequencing revolution allowed the identification of dozens of biosynthetic gene clusters (BGCs) within single bacterial genomes, either from cultured or uncultured strains. However, we are still far from fully exploiting the microbial reservoir, as most of the species are non-model organisms with complex regulatory systems and yet recalcitrant to be engineered. Today, genomic and metagenomic data produced by laboratories worldwide covering the most different natural and artificial environments on Earth, are an invaluable source of raw information from which natural product biosynthesis can be accessed. In the present work, we describe the environmental distribution and evolution of the abyssomicin BGC through the analysis of publicly available genomic and metagenomic data. Our results demonstrate that the selection of a pathway-specific enzyme to direct the genome mining is an excellent strategy that led to the identification of 74 new Diels-Alderase homologs and unveiled a surprising prevalence of the abyssomicin BGC within terrestrial habitats, mainly soil and plant-associated, where we have identified five complete and 12 partial new abyssomicin BGCs and 23 new potential abyssomicin BGCs. Our results strongly support the potential of genome and metagenome mining as a key preliminary tool to inform bioprospecting strategies aiming at the identification of new bioactive compounds such as -but not restricted to-abyssomicins.
Identification and Utilization of Copy Number Information for Correcting Hi-C Contact Map of Cancer Cell Line
Authors: Khalil Ahmed Ibrahim Samir , Muzaki Siti Rawaidah Mohammad , Chattopadhyay Anupam , Sanyal Amartya 
Published: October 2019

AbstractMotivationHi-C and its variant techniques have been developed to capture the spatial organization of chromatin. Normalization of Hi-C contact maps is essential for accurate modeling and interpretation of genome-wide chromatin conformation. Most Hi-C correction methods are originally developed for normal cell lines and mainly target systematic biases. In contrast, cancer genomes carry multi-level copy number variations (CNVs). Copy number influences interaction frequency between genomic loci. Therefore, CNV-driven bias needs to be corrected for generating euploid-equivalent chromatin contact maps.ResultsWe developed HiCNAtra framework that extracts read depth (RD) signal from Hi-C or 3C-seq reads to generate the high-resolution CNV profile and use this information to correct the contact map. We proposed the “entire restriction fragment” counting for better estimation of the RD signal and generation of CNV profiles. HiCNAtra integrates CNV information along with other systematic biases for explicitly correcting the interaction matrix using Poisson regression model. We demonstrated that RD estimation of HiCNAtra recapitulates the whole-genome sequencing (WGS)-derived coverage signal of the same cell line. Benchmarking against OneD method (only explicit method to target CNV bias) showed that HiCNAtra fared better in eliminating the impact of CNV on the contact maps.Availability and implementationHiCNAtra is an open source software implemented in MATLAB and is available athttps://github.com/AISKhalil/HiCNAtra.
Occasion setters determine responses of putative dopamine neurons to discriminative stimuli
Authors: Aquili Luca , Bowman Eric M. , Schmidt Robert 
Published: October 2019

AbstractMidbrain dopamine (DA) neurons are involved in the processing of rewards and reward-predicting stimuli, possibly analogous to reinforcement learning reward prediction errors. Here we studied the activity of putative DA neurons (n=41) recorded in the ventral tegmental area of rats (n=6) performing a behavioural task involving occasion setting. In this task an occasion setter (OS) indicated that the relationship between a discriminative stimulus (DS) and reinforcement is in effect, so that reinforcement of bar pressing occurred only after the OS (tone or houselight) was followed by the DS (houselight or tone). We found that responses of putative DA cells to the DS were enhanced when preceded by the OS, as were behavioural responses to obtain rewards. Surprisingly though, we did not find a population response of putative DA neurons to the OS, contrary to predictions of standard temporal-difference models of DA neurons. However, despite the absence of a population response, putative DA neurons exhibited a heterogeneous response on a single unit level, so that some units increased and others decreased their activity as a response to the OS. Similarly, putative non-DA cells did not respond to the DS on a population level, but with heterogeneous responses on a single unit level. The heterogeneity in the responses of putative DA cells may reflect how DA neurons encode context and point to local differences in DA signalling.
Differences in directed functional brain connectivity related to age, sex and mental health
Authors: Lund Martina J. , Alnæs Dag , Schwab Simon , van der Meer Dennis , Andreassen Ole A. , Westlye Lars T. , Kaufmann Tobias 
Published: October 2019

AbstractObjectiveFunctional interconnections between brain regions define the ‘connectome’ which is of central interest for understanding human brain function. Resting-state functional magnetic resonance (rsfMRI) work has revealed changes in static connectivity related to age, sex, cognitive abilities and psychiatric symptoms, yet little is known how these factors may alter the information flow. The commonly used approach infers functional brain connectivity using stationary coefficients yielding static estimates of the undirected connection strength between brain regions. Dynamic graphical models (DGMs) are a multivariate model with dynamic coefficients reflecting directed temporal associations between nodes, and can yield novel insight into directed functional connectivity. Here, we leveraged this approach to test for associations between edge-wise estimates of direction flow across the brain connectome and age, sex, intellectual abilities and mental health.MethodsWe applied DGM to investigate patterns of information flow in data from 984 individuals from the Human Connectome Project (HCP) and 10,249 individuals from the UK Biobank.ResultsOur analysis yielded patterns of directed connectivity in independent HCP and UK Biobank data similar to those previously reported, including that the cerebellum consistently receives information from other networks. We show robust associations between information flow and age and sex for several connections, with strongest effects of age observed in the sensorimotor network. Visual, auditory and sensorimotor nodes were also linked to mental health.DiscussionOur findings support the use of DGM as a measure of directed connectivity in rsfMRI data and provide new insight into the shaping of the connectome during aging.