bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anticipating the Impact of Human Papillomavirus Vaccination on US Cervical Cancer Prevention Strategies
Authors: Massad L. Stewart 
Published: February 2018

Abstract
Cervical cancer prevention guidelines are benchmarked to risk of cervical precancer. In younger age cohorts, vaccination against high-risk types of human papillomavirus (HPV) has reduced HPV 16/18 prevalence and cervical intraepithelial neoplasia. Lower prevalence of precancer will impair the sensitivity of cytology and colposcopy, but negative predictive value will rise. Training and skills maintenance will become more difficult as abnormalities become less common. Primary screening with HPV assays will become more attractive but will require HPV genotyping as most positive HPV tests will reflect non-16/18 infections with lower oncogenicity. Screening will begin later and will occur at longer intervals. Colposcopy and treatment thresholds will become more stringent. Historical data sets will become inappropriate for guidelines development. As women immunized using nonavalent vaccine reach screening age, these trends will become still more pronounced.
Pylera and sequential therapy for first-line Helicobacter pylori eradication: a culture-based study in real clinical practice
Authors: Fiorini Giulia , Zullo Angelo , Saracino Ilaria M. , Gatta Luigi , Pavoni Matteo , Vaira Dino 
Published: February 2018

Background and aims
Italian guideline suggests 10-day sequential or bismuth-based quadruple therapies for first-line Helicobacter pylori treatment. Comparison between these regimens is lacking. We assessed the efficacy of these therapies in clinical practice and evaluated the role of primary bacterial resistance toward clarithromycin and metronidazole.

Patients and methods
Consecutive patients with H. pylori infection were enrolled. Bacterial culture with antibiotics susceptibility testing was attempted in all cases. Patients received either a sequential therapy with esomeprazole 40 mg for 10 days plus amoxicillin 1000 mg for the first 5 days followed by clarithromycin 500 mg and tinidazole 500 mg (all twice daily) for the remaining 5 days, or bismuth-based therapy with esomeprazole 20 mg twice daily and Pylera 3 tablets four times daily for 10 days. H. pylori eradication was assessed by using 13C-urea breath test.

Results
A total of 495 patients were enrolled. Following sequential (250 patients) and quadruple (245 patients) therapies, the eradication rate were 92 and 91%, respectively, at intention-to-treat analysis and 96 and 97%, respectively, at per protocol analysis. Overall, the pattern of bacterial resistance did not significantly affect the cure rate, but the presence of clarithromycin and metronidazole dual resistance tended to reduce the success rate of both sequential (84.8 vs. 90.1%; P=0.4) and quadruple (85 vs. 94.1%; P=0.06) therapies. Adverse events occurred more frequently with the quadruple than with sequential therapy (56.9 vs. 25.8%; P<0.001).

Conclusion
In our country, sequential and bismuth-based quadruple therapy achieved similarly high eradication rates as first-line treatments for H. pylori infection in clinical practice.
Three-Year Changes in Physical Activity and Subsequent Loss of Ability to Walk 400 m in Older Adults
Authors: Martinez-Gomez David , Bandinelli Stefania , Del-Panta Vieri , Talluri Eleonora , Guralnik Jack M. , Ferrucci Luigi 
Published: February 2018

Abstract
We examined the associations of maintaining or increasing physical activity (PA) for a 3-yr follow-up with subsequent incident inability to complete the 400-m walk test (i.e., mobility disability) for 6 yrs of follow-up in older adults. This study included 421 participants 65 yrs and older. The 400-m walk test was assessed at baseline and at 3-, 6-, and 9-yr follow-up. Physical activity was self-reported through a 6-point rating scale at baseline and 3-yr follow-up. Three-year cumulative PA (i.e., average at baseline and at 3-yr follow-up) and its changes (i.e., from baseline to 3-yr follow-up) were linked to subsequent incidence of mobility disability for 6 yrs of follow-up (i.e., from 3- to 9-yr follow-up), after adjustment for potential covariates. After the 3-yr period, incidence of mobility disability for the subsequent 6 yrs of follow-up occurred in 129 participants. The odds ratio (95% confidence interval) of incident mobility disability associated with 1-category increase in cumulative PA was 0.63 (0.41–0.97, P = 0.036). The odds ratio (95% confidence interval) of incident mobility disability associated with 1-category increase in changes in PA was 0.56 (0.38–0.84, P = 0.005). Hence, maintaining or increasing PA levels is associated with a reduced risk of mobility disability among older adults.
Incidence of Obstetric Anal Sphincter Injuries After Training to Protect the Perineum
Authors: Yeung Jennifer , Stecher Anna , Crisp Catrina C. , Mazloomdoost Donna , Smith Benjamin , Kleeman Steven D. , Pauls Rachel N. 
Published: February 2018

Objectives
Obstetric anal sphincter injuries (OASISs) are a devastating postpartum complication; reducing rates is paramount to improving quality of care. In Norway, implementation of a perineal protection program decreased the incidence of OASIS by 48%. We sought to assess impact on OASIS rates following a similar program.

Methods
This institutional review board–approved, retrospective cohort study was performed in an academic hospital system. The periods of analysis were November 2014 through October 2015 for the preintervention arm and November 2015 through October 2016 for the postintervention arm. From November 2 to 6, 2015, 2 Norwegian experts conducted a didactic and hands-on, on-site workshop focusing on perineal protection. The experts were then present on labor and delivery wards to reinforce perineal protection in live deliveries. Teachings were emphasized at departmental meetings for the remainder of the year. Data were extracted from electronic medical records and manually audited.

Results
The rate of vaginal delivery was similar among both periods (6504 and 6650; P = 0.059). Obstetric anal sphincter injury rates decreased from 211 (3.2%) preintervention to 189 (2.8%) after the workshop. Although this represented 32 fewer injuries, it was not statistically significant (P = 0.179). Obstetric anal sphincter injuries following forceps-assisted deliveries did decline significantly from 103 (28%) to 81 (21%) (P = 0.014). In addition, incidence of fourth-degree lacerations during resident deliveries decreased significantly from 10 (0.6%) to 3 (0.2%) (P = 0.047).

Conclusions
An educational workshop focusing on perineal support was not associated with a significant reduction in overall OASIS rates. Nevertheless, decreased forceps-related OASIS and fourth-degree lacerations rates support positive influence of the intervention.
Cranberry Supplementation Does Not Reduce Urinary Tract Infections in Patients With Indwelling Catheters After Pelvic Reconstructive Surgery
Authors: Shatkin-Margolis Abigail , Warehime Jenna , Pauls Rachel N. 
Published: February 2018

Objectives
Urinary tract infections (UTIs) are common after pelvic reconstructive surgery, likely due to high rates of urinary retention. We sought to determine if prescription of cranberry capsules reduced UTIs in postoperative patients requiring catheter use.

Methods
This was an institutional review board–approved retrospective cohort study. Two 6–month periods were compared: April to September 2015, before cranberry capsules were incorporated, and April to September 2016, after cranberry capsules were implemented. Our study population included patients discharged with a catheter after pelvic reconstructive surgery. All charts were reviewed for demographics, perioperative data, and urine cultures up to 6 weeks postoperatively. A UTI was defined as treatment with antibiotics or positive cultures. Statistical analysis was performed; logistic regression evaluated for relationships between UTI and other factors. Our a priori sample size calculation determined 88 subjects per group would be necessary.

Results
Over the 2 periods, 167 patients met inclusion criteria: 71 before and 96 after cranberry implementation. The 2 cohorts were similar in all data. Regarding incidence of UTI, rates were overall high and not significantly different between groups (76% before cranberry vs 69% with cranberry; P = 0.299). The median duration of catheter use was 8 days in both cohorts. The UTI was most likely to occur in the second week after surgery. Logistic regression revealed no associations between age, surgery type, duration of catheter use, and UTI.

Conclusions
In this retrospective study, prescription of cranberry capsules did not significantly reduce UTI rates among patients with urinary catheters after pelvic reconstructive surgery.
Changes in the Vaginal Microenvironment as Related to Frequency of Pessary Removal
Authors: Fregosi Nicole J. , Hobson Deslyn T.G. , Kinman Casey L. , Gaskins Jeremy T. , Stewart J. Ryan , Meriwether Kate V. 
Published: February 2018

Objective
The aim of the study was to describe the effect of frequency of pessary removal on the vaginal microenvironment.

Methods
We performed a secondary analysis of a multicenter randomized trial of hydroxyquinoline gel in women presenting for pessary fitting. Patients had vaginal secretions analyzed at baseline, 2 weeks, and 3 months. Patients were stratified by frequency of pessary removal at least once daily, at least once weekly, and less often than once weekly. These groups were compared for prevalence of Lactobacillus predominance (primary outcome), anaerobic predominance, Mobiluncus prominence, vaginal symptoms, and bacterial vaginosis by Nugent criteria, and correction for confounding variables was performed.

Results
One hundred thirty-seven women were included in this analysis: 34 (25%) removed the pessary daily, 54 (39%) at least weekly, and 49 (36%) less often than once weekly. Women who removed the pessary less often than weekly were older (P < 0.01), using more hormone therapy (P = 0.03), and more likely to have bacterial vaginosis at baseline (P < 0.01). At 2 weeks, the predominance of Lactobacillus in the group removing pessary daily was higher (41% daily vs 24% weekly vs 9% longer, P = 0.03) and this persisted after confounder correction (P < 0.01). Women who removed their pessary less than weekly were more likely to have anaerobic predominance at 3 months (P = 0.04).

Conclusions
Women who remove their pessaries less often than once weekly have an increased prevalence of anaerobes at 3 months, but no difference in vaginal symptoms or pessary satisfaction.
J. Marion Sims and the Vesicovaginal Fistula: Historical Understanding, Medical Ethics, and Modern Political Sensibilities
Authors: Wall L. Lewis 
Published: February 2018

Objectives
To review the historical background surrounding the early work of Dr. J. Marion Sims, who developed the first consistently successful surgical technique for the repair of obstetric vesicovaginal fistulas by operating on a group of young, enslaved, African American women who had this condition between 1846 and 1849.

Methods
Review of primary source documents on Sims and his operations, early 19th century clinical literature on the treatment of vesicovaginal fistula, the introduction of ether and chloroform anesthesia into surgical practice, and the literature on the early 19th century medical ethics pertaining to surgical innovation. The goals are to understand Sims's operations within the clinical context of the 1840s and to avoid the problems of “presentism,” in which beliefs, attitudes, and practices of the 21st century are anachronistically projected backward into the early 19th century. The object is to judge Sims within the context of his time, not to hold him accountable to standards of practice which were not developed until a century after his death.

Results
A narrative of what Sims did is presented within the context of the therapeutic options available to those with fistula in the early 19th century.

Conclusions
Review of the available material demonstrates that Sims' first fistula operations were legal, that they were carried out with express therapeutic intent for the purpose of repairing these women's injuries, that they conformed to the ethical requirements of his time, and that they were performed with the patients' knowledge, cooperation, assent, and assistance.
Secretory vesicle trafficking in awake and anesthetized mice: differential speeds in axons versus synapses
Authors: Knabbe Johannes , Nassal Joris , Verhage Matthijs , Kuner Thomas 
Published: February 2018

AbstractNeuronal dense core vesicles (DCVs) transport many cargo molecules like neuropeptides and neurotrophins to their release sites in dendrites or axons. The transport properties of DCVs in axons of the intact mammalian brain are unknown. We used viral expression of a DCV cargo reporter (NPY-Venus/Cherry) in the thalamus and two-photon in vivo imaging to visualize axonal DCV trafficking in thalamo-cortical projections of anesthetized and awake mice. We found an average speed of 1 μm/s, maximal speeds of up to 5 μm/s and a pausing fraction of ~11%. Directionality of transport differed between anesthetized and awake mice. In vivo microtubule +-end extension imaging using Macf18-GFP revealed microtubular growth at 0.12 μm/s and provided positive identification of antero- and retrograde axonal transport. Consistent with previous reports, anterograde transport was faster (~2.1 μm/s) than retrograde transport (~1.4 μm/s). In summary, DCVs are transported with faster maximal speeds and lower pausing fraction in vivo compared to previous results obtained in vitro. Finally, we found that DCVs slowed down upon presynaptic bouton approach. We propose that this mechanism promotes synaptic localization and cargo release.Key pointsDespite their immense physiological and pathophysiological importance, we know very little about the biology of dense core vesicle (DCV) trafficking in the intact mammalian brain.DCVs are transported at similar average speeds in the anesthetized and awake mouse brain compared to neurons in culture, yet maximal speed and pausing fraction of transport were higher.Microtubule +-end extension imaging visualized microtubular growth at 0.12 μm/s and revealed that DCVs were transported faster in the anterograde direction.DCV transport slowed down upon presynaptic bouton approach, possibly promoting synaptic localization and cargo release.Our work provides a basis to extrapolate DCV transport properties determined in cultured neurons to the intact mouse brain and reveal novel features such as slowing upon bouton approach and brain state-dependent trafficking directionality.
White matter plasticity and reading instruction: Widespread anatomical changes track the learning process
Authors: Huber Elizabeth , Donnelly Patrick M. , Rokem Ariel , Yeatman Jason D. 
Published: February 2018

AbstractWhite matter tissue properties correlate with children’s performance across domains ranging from reading, to math, to executive function. We use a longitudinal intervention design to examine experience-dependent growth in reading skills and white matter in a group of grade school aged, struggling readers. Diffusion MRI data were collected at regular intervals during an 8-week, intensive reading intervention. These measurements reveal large-scale changes throughout a collection of white matter tracts, in concert with growth in reading skill. Additionally, we identify tracts whose properties predict reading skill but remain fixed throughout the intervention, suggesting that some anatomical properties may stably predict the ease with which a child learns to read, while others dynamically reflect the effects of experience. These results underscore the importance of considering recent experience when interpreting cross-sectional anatomy-behavior correlations. Widespread changes throughout the white matter may be a hallmark of rapid plasticity associated with an intensive learning experience.
Physical exercise increases overall brain oscillatory activity but does not influence inhibitory control in young adults
Authors: Ciria Luis F. , Perakakis Pandelis , Luque-Casado Antonio , Sanabria Daniel 
Published: February 2018

AbstractExtant evidence suggests that acute exercise triggers a tonic power increase in the alpha frequency band at frontal locations, which has been linked to benefits in cognitive function. However, recent literature has questioned such a selective effect on a particular frequency band, indicating a rather overall power increase across the entire frequency spectrum. Moreover, the nature of task-evoked oscillatory brain activity associated to inhibitory control after exercising, and the duration of the exercise effect, are not yet clear. Here, we investigate for the first time steady state oscillatory brain activity during and following an acute bout of aerobic exercise at two different exercise intensities (moderate-to-high and light), by means of a data-driven cluster-based approach to describe the spatio-temporal distribution of exercise-induced effects on brain function without prior assumptions on any frequency range or site of interest. We also assess the transient oscillatory brain activity elicited by stimulus presentation, as well as behavioural performance, in two inhibitory control (flanker) tasks, one performed after a short delay following the physical exercise and another completed after a rest period of 15’ post-exercise to explore the time course of exercise-induced changes on brain function and cognitive performance. The results show that oscillatory brain activity increases during exercise compared to the resting state, and that this increase is higher during the moderate-to-high intensity exercise with respect to the light intensity exercise. In addition, our results show that the global pattern of increased oscillatory brain activity is not specific to any concrete surface localization in slow frequencies, while in faster frequencies this effect is located in parieto-occipital sites. Notably, the exercise-induced increase in oscillatory brain activity disappears immediately after the end of the exercise bout. Neither transient (event-related) oscillatory activity, nor behavioral performance during the flanker tasks following exercise showed significant between-intensity differences. The present findings help elucidate the effect of physical exercise on oscillatory brain activity and challenge previous research suggesting improved inhibitory control following moderate-to-high acute exercise.
ChIPSeqSpike: A R/Bioconductor package for ChIP-Seq data scaling according to spike-in control
Authors: Descostes Nicolas , Tsirigos Aristotelis , Reinberg Danny 
Published: February 2018

AbstractMotivationChromatin Immuno-Precipitation followed by Sequencing (ChlP-Seq) is used to determine the binding sites of any protein of interest. ChIP-Seq data suffer from being more qualitative than quantitative. The recent use of Spike-in controls along with the standard protocol tackled this problem. However, no dedicated tool is available for a robust evaluation of this new ChIP-seq approachResultsWe developed ChIPSeqSpike, an R/Bioconductor package that enables ChIP-Seq spike-in normalization, assessment and analysis. Ready to use scaled bigwig files and scaling factors values are obtained as output. ChIPSeqSpike also provides tools for ChIP-Seq spike-in assessment and analysis through a versatile collection of graphical functions.AvailabilityThe package is implemented in R (as of version 3.4) and is available from Bioconductor at the URL: https://www.bioconductor.org/packages/3.7/bioc/html/ChIPSeqSpike.html, where installation and usage instructions can be found.Contactnicolas.descostes@nyumc.org
RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding
Authors: Humble Emily , Dasmahapatra Kanchon K , Martinez-Barrio Alvaro , Gregório Inês , Forcada Jaume , Polikeit Ann-Christin , Goldsworthy Simon D , Goebel Michael E , Kalinowski Joern , Wolf Jochen , Hoffman Joseph I 
Published: February 2018

ABSTRACTRecent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level ofr2= 0.09 by around 26 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organisation.
Reaction of Hydrogen sulfide homeostasis genes under biotic and abiotic stress condition in rice – computational approach
Authors: Alagarasan Ganesh , Ramalingam Jegadeesan 
Published: February 2018

AbstractGaseous molecules are widespread signaling compounds, regulating the cell development process in all major plant parts. For many decades, hydrogen sulfide molecule is considered mainly for its deleterious effects on plant system. The increasing recent experimental evidence and phenomenal concepts on H2S molecule further advance our understanding of H2S interaction with plant tissues. In addition, the H2S messenger molecule is found to have positive effects on plant growth, in limited condition, to maintain the balanced homeostasis. To meet the increasing demand, and to sustain the crop yield, various crop improvement programs have been followed. However, there is a concern that traditional plant improvement method and increasing climate change has a negative impact on crop production. A major approach to combating plant stress is to evaluate and explore the alternate source mechanism(s). Towards this aim, it will be valuable to characterize the genes involved in H2S homeostasis in the staple food crop rice pan-genome. In this research, we identified 15 H2S homeostasis genes in rice and used it for the ~3k rice pan-genome analysis to find out the genetic relatedness based on single nucleotide polymorphism data. Multidimensional scale plot of 15 H2S homeostasis genes among the rice cultivars, and RNA-seq experimental data analysis under various biotic and abiotic stress shows the functional genes involved in biotic and abiotic stress. This study provides new insights into plant stress management in crop breeding and suggests how H2S gene(s) can be utilized to improve the agronomic traits in rice and other food crops.