bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association Between Maternal Body Mass Index in Early Pregnancy and Incidence of Cerebral Palsy
Authors: Villamor Eduardo , Tedroff Kristina , Peterson Mark , Johansson Stefan , Neovius Martin , Petersson Gunnar , Cnattingius Sven 
Published: August 2017

(Abstracted from JAMA 2017;317(9):925–936)
Prevalence of cerebral palsy (CP) rose between 1998 and 2006, and few preventable risk factors are known for this most common pediatric motor disability. Maternal obesity, a risk factor for neonatal complications such as preterm delivery and asphyxia-related neonatal morbidities, has been suggested to be associated with CP.
Case of Nonspinal Osteomyelitis Due to Bartonella and Review of the Literature
Authors: Joychan Sonia , Kuchipudi Yamini , Danielsky Paul J. , Bovid Karen M. , Garg Deepak 
Published: August 2017

Abstract
Spine osteomyelitis resulting from Bartonella infection is well described in the literature; however, little is known about nonspinal manifestations of Bartonella osteomyelitis. Here, we describe a case of femur osteomyelitis in a 5-year-old child and review the literature related to nonspinal manifestations of Bartonella. In the 33 cases reviewed, infection of the pelvic girdle was most commonly observed (42%), followed by femur (21%) and humerus infections (21%). Fever was the most common symptom, and interestingly, 18% of patients did not have any history of cat exposure. Osteomyelitis was most commonly identified by magnetic resonance imaging; however, Bartonella serology and tissue polymerase chain reaction testing were also positive when used. Recovery for most patients occurred after combination antibiotic therapy and did not require surgical debridement. In our patient, full recovery was achieved through surgical debridement and stabilization of the bone, followed by antibiotics.
The Prevention of Recurrent Cholesteatoma in CWU Surgery: The Use of Titanium Sheeting
Authors: Black Bruce , Gutteridge Ian 
Published: August 2017

Objective:
Assessment of the outcomes of a technique of prevention of recurrent cholesteatoma in canal wall up (CWU) mastoidectomy, using titanium sheeting to repair the external auditory canal wall.

Patients:
Sixty four cholesteatoma cases were managed during a period from 2007 to 2015. The cases were unselected; the surgery was performed by the senior author. Cholesteatoma Patterns Were: Forty two attic, nine pars tensa, seven combined attic-pars tensa, three congenital, and three other. Primary surgery was undertaken in 33 cases.

Interventions:
All cases underwent CWU surgery that employed canal wall repair using fine titanium sheeting combined with overlying organic material to repair canal wall defects. Drum repairs employed cymba conchae cartilage-perichondrium composite grafts. Chain reconstruction used Spanner struts or Grace Alto PORPs or TORPS.

Results:
Two cases suffered mesotympanic residual disease, and three, mesotympanic recurrence one of which extended into the attic. Two other cases incurred atticomastoid residues. Transient myringitis occurred in three cases.

Conclusion:
The surgery was judged on its ability to avoid atticomastoid recurrence, and was regarded as highly successful. The titanium sheeting offers a relatively simple but effective technique. The mesotympanic complications are those also commonly found in both CWD and other CWU methods. As in other CWU procedures, the problems of the open cavity were avoided.
Long-acting Reversible Contraception Among Homeless Women Veterans With Chronic Health Conditions
Authors: Gawron Lori M. , Redd Andrew , Suo Ying , Pettey Warren , Turok David K. , Gundlapalli Adi V. 
Published: August 2017

Background:
US women Veterans are at increased risk of homelessness and chronic health conditions associated with unintended pregnancy. Veterans Health Administration (VHA) provision of long-acting reversible contraception (LARC) can assist in healthy pregnancy planning.

Objectives:
To evaluate perinatal risk factors and LARC exposure in ever-homeless women Veterans.

Research Design:
A retrospective cohort study of women Veterans using VHA administrative data from fiscal years 2002–2015.

Subjects:
We included 41,747 ever-homeless women Veterans age 18–44 years and 46,391 housed women Veterans matched by military service period. A subgroup of 7773 ever-homeless and 8674 matched housed women Veterans deployed in Iraq and Afghanistan [Operations Enduring Freedom/Iraqi Freedom/New Dawn (OEF/OIF/OND)] conflicts comprised a second analytic cohort.

Measures:
Descriptive statistics compared demographic, military, health conditions, and LARC exposure in ever-homeless versus housed women Veterans. Multivariable logistic regression explored factors associated with LARC exposure in the OEF/OIF/OND subgroup.

Results:
All health conditions were significantly higher in ever-homeless versus housed Veterans: mental health disorder in 84.5% versus 48.7% (P<0.001), substance abuse in 35.8% versus 8.6% (P<0.001), and medical conditions in 74.7% versus 55.6% (P<0.001). LARC exposure among all VHA users was 9.3% in ever-homeless Veterans versus 5.4% in housed Veterans (P<0.001). LARC exposure in the OEF/OIF/OND cohort was 14.1% in ever-homeless Veterans versus 8.2% in housed Veterans (P<0.001). In the OEF/OIF/OND cohort, homelessness along Veterans with medical and mental health indicators were leading LARC exposure predictors.

Conclusions:
The VHA is successfully engaging homeless women Veterans and providing LARC access. The prevalence of perinatal risk factors in ever-homeless women Veterans highlights a need for further programmatic enhancements to improve reproductive planning.
Outcomes of Robotic Sacrocolpopexy Using Only Absorbable Suture for Mesh Fixation
Authors: Linder Brian J. , Anand Mallika , Klingele Christopher J. , Trabuco Emanuel C. , Gebhart John B. , Occhino John A. 
Published: August 2017

(Abstracted from Female Pelvic Med Reconstr Surg 2017;23:13–16)
Following the introduction of abdominal sacrocolpopexy over 50 years ago, the procedure achieved excellent long-term anatomic success rates for the treating apical pelvic organ prolapse. However, the procedure is associated with significant morbidity.
Anesthesia and Developing Brains—Implications of the FDA Warning
Authors: Andropoulos Dean B. , Greene Michael F. 
Published: August 2017

(Abstracted from N Engl J Med 2017;376(10):905–907)
A recent US Food and Drug Administration (FDA) drug safety communication on the use of general anesthesia and sedation drugs in pregnant women and children younger than 3 years warned that use of anesthesia for more than 3 hours or repeated anesthesia exposure “may affect the development of children’s brains.” This warning will likely be added to the labels of many common general anesthetics and sedatives and will lead to some changes in practice.
The Tissue-Engineered Tendon-Bone Interface: In Vitro and In Vivo Synergistic Effects of Adipose-Derived Stem Cells, Platelet-Rich Plasma, and Extracellular Matrix Hydrogel
Authors: McGoldrick Rory , Chattopadhyay Arhana , Crowe Christopher , Chiou Grace , Hui Kenneth , Farnebo Simon , Davis Christopher , Le Grand Anais , Jacobs Molly , Pham Hung , Chang James 
Published: August 2017

Background:
Suboptimal healing of the tendon-bone interface remains an unsolved problem. The authors hypothesized that (1) platelet-rich plasma and prolonged in vitro incubation will produce interface scaffolds with greater reseeding of viable adipose-derived stem cells; and (2) when implanted with extracellular matrix hydrogel, constructs will display superior in vivo strength repair and biocompatibility.

Methods:
Achilles-calcaneal composite tendon-bone interface scaffold grafts were harvested from 30 Wistar rats. After physicochemical decellularization and lyophilization, scaffolds were revitalized in rat plasma or 100% activated rat platelet-rich plasma and reseeded with viable adipose-derived stem cells. For part 2 of the study, 90 Sprague-Dawley rats underwent reconstruction with one of five decellularized, lyophilized scaffold revitalization/reseeding conditions: (1) phosphate-buffered saline; (2) lyophilized, 100% activated platelet-rich plasma; (3) platelet-rich plasma and extracellular matrix hydrogel; (4) platelet-rich plasma and 14-day reseeding with ASC-luc2-eGFP cells; and (5) plasma, reseeding, and hydrogel.

Results:
In part 1, platelet-rich plasma–revitalized grafts demonstrated greater live viable adipose-derived stem cell loads at 3, 7, and 14 days and total adipose-derived stem cell loads at 7 and 14 days with visibly greater live surface cellularity, layering, migration, and penetration. In part 2, bioluminescence imaging confirmed cell viability to day 22 after implantation. Biomechanical strength testing demonstrated a significant increase in ultimate failure load for reseeded groups compared with all other groups at week 2, whereas only reseeded grafts with hydrogel remained significantly stronger at weeks 4 and 8. Histologic examination demonstrated most increased tendinous cellular invasion and fibrocartilage repopulation at 8 weeks in the reseeded group with hydrogel. Masson trichrome staining demonstrated persistence of the scaffold structure at week 8 and blinded ImageJ analysis demonstrated significantly more type III collagen in the reseeded/hydrogel group at 2, 4, and 8 weeks.

Conclusions:
Decellularized lyophilized allogeneic tendon-bone interface scaffolds can be optimized by revitalization in platelet-rich plasma, reseeding with viable adipose-derived stem cells, and supplemented by an extracellular matrix tendon hydrogel at the time of implantation. When this is done, they display greater repair strength and biocompatibility.
Clinical and Quantitative Isokinetic Comparison of Abdominal Morbidity and Dynamics following DIEP versus Muscle-Sparing Free TRAM Flap Breast Reconstruction
Authors: Uda Hirokazu , Kamochi Hideaki , Sarukawa Syunji , Sunaga Ataru , Sugawara Yasushi , Yoshimura Kotaro 
Published: August 2017

Background:
The deep inferior epigastric perforator (DIEP) flap, which is a modification of the muscle-sparing free transverse rectus abdominis musculocutaneous (TRAM) flap, is being more frequently used in an effort to reduce postoperative abdominal morbidity. However, there is no consensus as to which of these flaps is superior. The authors aimed to compare quantitative measurements of abdominal function obtained with an isokinetic dynamometer after DIEP and muscle-sparing free TRAM flap elevation.

Methods:
Patients who underwent unilateral single-pedicled DIEP (n = 42) or muscle-sparing free TRAM flap (n = 36) breast reconstruction performed by a single surgeon were included in this study. Preoperative and postoperative trunk flexion parameters were measured prospectively using an isokinetic dynamometer in all patients. The occurrence of postoperative pain, stiffness, and bulging along with patient activity level were also investigated.

Results:
At 3 months postoperatively, abdominal functions were decreased in both groups, with a larger decline in the muscle-sparing free TRAM flap group. However, at 6 months postoperatively, abdominal muscle function recovered to preoperative levels in both groups. These findings were consistent with the absence of a statistically significant difference in patient postoperative abdominal pain and stiffness, activity level, and the incidence of bulging between the two groups at 6 months postoperatively.

Conclusion:
From these results, we propose that the surgeon can select the muscle-sparing free TRAM flap, without hesitation or concern regarding abdominal morbidity, when a thick and reliable perforator does not exist and multiple thin perforators must be incorporated.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
The Dynamics of Error Processing in the Human Brain as Reflected by High-Gamma Activity in Noninvasive and Intracranial EEG
Authors: Völker Martin , Fiederer Lukas D. J. , Berberich Sofie , Hammer Jiří , Behncke Joos , Kršek Pavel , Tomášek Martin , Marusič Petr , Reinacher Peter C. , Coenen Volker A. , Helias Moritz , Schulze-Bonhage Andreas , Burgard Wolfram , Ball Tonio 
Published: August 2017

AbstractError detection in motor behavior is a fundamental cognitive function heavily relying on cortical information processing. Neural activity in the high-gamma frequency band (HGB) closely reflects such local cortical processing, but little is known about its role in error processing, particularly in the healthy human brain. Here we characterize the error-related response of the human brain based on data obtained with noninvasive EEG optimized for HGB mapping in 31 healthy subjects (15 females, 16 males), and additional intracranial EEG data from 9 epilepsy patients (4 females, 5 males). Our findings reveal a comprehensive picture of the global and local dynamics of error-related HGB activity in the human brain. On the global level as reflected in the noninvasive EEG, the error-related response started with an early component dominated by anterior brain regions, followed by a shift to parietal regions, and a subsequent phase characterized by sustained parietal HGB activity. This phase lasted for more than 1 s after the error onset. On the local level reflected in the intracranial EEG, a cascade of both transient and sustained error-related responses involved an even more extended network, spanning beyond frontal and parietal regions to the insula and the hippocampus. HGB mapping appeared especially well suited to investigate late, sustained components of the error response, possibly linked to downstream functional stages such as error-related learning and behavioral adaptation. Our findings establish the basic spatio-temporal properties of HGB activity as a neural correlate of error processing, complementing traditional error-related potential studies.Significance StatementThere is great interest to understand how the human brain reacts to errors in goal-directed behavior. An important index of cortical and subcortical information processing is fast oscillatory brain activity, particularly in the high-gamma band (above 50 Hz). Here we show that it is possible to detect signatures of errors in event-related high-gamma responses with noninvasive techniques, characterize these responses comprehensively, and validate the EEG procedure for the detection of such signals. In addition, we demonstrate the added value of intracranial recordings pinpointing the fine-grained spatio-temporal patterns in error-related brain networks. We anticipate that the optimized noninvasive EEG techniques as described here will be helpful in many areas of cognitive neuroscience where fast oscillatory brain activity is of interest.
Permissive zones for the centromere-binding protein ParB on theCaulobacter crescentuschromosome
Authors: Tran Ngat T. , Stevenson Clare E. , Som Nicolle F. , Thanapipatsiri Anyarat , Jalal Adam S. B. , Le Tung B. K. 
Published: August 2017

ABSTRACTProper chromosome segregation is essential in all living organisms. InCaulobacter crescentus, the ParA-ParB-parSsystem is required for proper chromosome segregation and cell viability. The bacterial centromere-likeparSDNA locus is the first to be segregated following chromosome replication.parSis bound by ParB protein, which in turn interacts with ParA to partition the ParB-parSnucleoprotein complex to each daughter cell. Here, we investigated the genome-wide distribution of ParB on theCaulobacterchromosome using a combination ofin vivochromatin immunoprecipitation (ChIP-seq) andin vitroDNA affinity purification with deep sequencing (IDAP-seq). We confirmed two previously identifiedparSsites and discovered at least three more sites that cluster ~8 kb from the origin of replication. We showed thatCaulobacterParB nucleates atparSsites and associates non-specifically with ~10 kb flanking DNA to form a high-order nucleoprotein complex on the left chromosomal arm. Lastly, using transposon mutagenesis coupled with deep sequencing (Tn-seq), we identified a ~500 kb region surrounding the nativeparScluster that is tolerable to the insertion of a secondparScluster without severely affecting cell viability. Our results demonstrate that the genomic distribution ofparSsites is highly restricted and is crucial for chromosome segregation inCaulobacter.
Analysis of multistage in vitro fertilization data with mixed multilevel outcomes using joint modelling approaches
Authors: Wilkinson Jack , Vail Andy , Roberts Stephen A 
Published: August 2017

SummaryIn vitro fertilization comprises a sequence of interventions concerned with the creation and culture of embryos which are then transferred to the patient’s uterus. While the clinically important endpoint is birth, the responses to each stage of treatment contain additional information about the reasons for success or failure. Joint analysis of the sequential responses is complicated by mixed outcome types defined at two levels (patient and embryo). We develop three methods for multistage analysis based on joining submodels for the different responses using latent variables and entering outcome variables as covariates for downstream responses. An application to routinely collected data is presented, and the strengths and limitations of each method are discussed.
Computational pipeline for the PGV-001 neoantigen vaccine trial
Authors: Rubinsteyn Alex , Kodysh Julia , Hodes Isaac , Mondet Sebastien , Aksoy Bulent Arman , Finnigan John P , Bhardwaj Nina , Hammerbacher Jeffrey 
Published: August 2017

AbstractThis paper describes the sequencing protocol and computational pipeline for the PGV-001 personalized vaccine trial. PGV-001 is a therapeutic peptide vaccine targeting neoantigens identified from patient tumor samples. Peptides are selected by a computational pipeline which identifies mutations from tumor/normal exome sequencing and ranks mutant sequences by a combination of predicted Class I MHC affinity and abundance estimated from tumor RNA. The PGV pipeline is modular and consists of many independently usable tools and software libraries. We draw attention to three particular tools which may be useful to other groups working on neoantigen vaccination. (1) Epidisco is a workflow which orchestrates the parallel execution of the PGV pipeline, including both common steps such as alignment as well as tools which have been developed specifically for the PGV-001 trial. (2) Vaxrank uses somatic variants and tumor RNA reads to select peptides for inclusion in a patient’s vaccine. (3) Isovar is a library used by Vaxrank to determine the mutated protein sequence associated with a genomic variant from supporting tumor RNA reads. We hope that the functionality of these tools may extend beyond the specifics of the PGV-001 trial and enable other research groups in their own neoantigen investigations.
Integrative analyses of splicing in the aging brain: role in susceptibility to Alzheimer’s Disease
Authors: Raj Towfique , Li Yang I. , Wong Garrett , Ramdhani Satesh , Wang Ying-chih , Ng Bernard , Wang Minghui , Gupta Ishaan , Haroutunian Vahram , Schadt Eric E. , Zhang Bin , Young-Pearse Tracy , Mostafavi Sara , Sklar Pamela , Bennett David , De Jager Philip L. 
Published: August 2017

ABSTRACTWe use deep sequencing to identify sources of variation in mRNA splicing in the dorsolateral prefrontal cortex (DLFPC) of 450 subjects from two prospective cohort studies of aging. Hundreds of aberrant pre-mRNA splicing events are reproducibly associated with Alzheimer’s Disease (AD). We also generate a catalog of splicing quantitative trait loci (sQTL) effects in the human cortex: splicing of 3,198 genes is influenced by genetic variation. sQTLs are enriched among those variants influencing DNA methylation and histone acetylation. In assessing known AD loci, we report that altered splicing is the mechanism for the effects of thePICALM, CLU,andPTK2Bsusceptibility alleles. Further, we leverage our sQTL catalog to identify genes whose aberrant splicing is associated with AD and mediated by genetics. This transcriptome-wide association study identified 21 genes with significant associations, many of which are found in AD GWAS loci, but 8 are in novel AD loci, includingFUS,which is a known amyotrophic lateral sclerosis (ALS) gene. This highlights an intriguing shared genetic architecture that is further elaborated by the convergence of old and new AD genes in autophagy-lysosomal-related pathways already implicated in AD and other neurodegenerative diseases. Overall, this study of the aging brain’s transcriptome provides evidence that dysregulation of mRNA splicing is a feature of AD and is, in some genetically-driven cases, causal.
Maternal RNA-directed DNA methylation is required for seed development inBrassica rapa
Authors: Grover Jeffrey W. , Kendall Timmy , Baten Abdul , King Graham J. , Mosher Rebecca A. 
Published: August 2017

AbstractSome organisms deploy small RNAs from accessory cells to maintain genome integrity in the zygote, a mechanism that has been proposed but not demonstrated in plants. Here we show that maternal mutations in the Pol IV-dependent small RNA pathway cause abortion of developing seeds inBrassica rapa. Surprisingly, small RNA production is required in maternal somatic tissues, but not in maternal gametes or the developing zygote. We propose that parental influence over zygotic genomes is a common strategy in eukaryotes and that outbreeding species such asB. rapaare key to understanding the role of small RNAs during reproduction.
Rare earth elements (REE) in freshwater, marine, and terrestrial ecosystems in the eastern Canadian Arctic
Authors: MacMillan Gwyneth Anne , Chételat John , Heath Joel , Mickpegak Raymond , Amyot Marc 
Published: August 2017

ABSTRACTFew ecotoxicological studies exist for rare earth elements (REEs), particularly field-based studies on their bioaccumulation and food web dynamics. REE mining has led to significant environment impacts in several countries (China, Brazil, U.S.), yet little is known about the fate and transport of these contaminants of emerging concern. To understand how REEs behave in pristine northern food webs, we measured REE concentrations and carbon and nitrogen stable isotope ratios (∂15N, ∂13C) in biota from marine, freshwater, and terrestrial ecosystems of the eastern Canadian Arctic (N=339). Northern ecosystems are potentially vulnerable to REE enrichment from prospective mining projects at high latitudes. Wildlife harvesting and tissue sampling was partly conducted by local hunters through a community-based monitoring project. Results show that REE generally follow a coherent bioaccumulation pattern for sample tissues, with some anomalies for redox-sensitive elements (Ce, Eu). Highest REE concentrations were found at low trophic levels, especially in vegetation and aquatic invertebrates. Terrestrial herbivores, ringed seal, and fish had low REE levels in muscle tissue (<0.1 nmolg-1), yet accumulation was an order of magnitude higher in all liver tissues. Age- and length-dependent REE accumulation also suggest that REE uptake is faster than elimination for some species. Overall, REE bioaccumulation patterns appear to be species- and tissue-species, with limited potential for biomagnification. This study provides novel ecotoxicological data on the behaviour of REE in ecosystems and will be useful for environmental impact assessment of REE enrichment in northern regions.