bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinician knowledge, attitudes, and barriers to management of vulvovaginal atrophy: variations in primary care and gynecology
Authors: Vesco Kimberly K. , Beadle Kate , Stoneburner Ashley , Bulkley Joanna , Leo Michael C. , Clark Amanda L. 
Published: August 2018

Abstract

Objective:
Vulvovaginal atrophy is a common, but under-recognized condition affecting postmenopausal women. To guide development of an intervention to boost its detection and treatment, we surveyed primary care and gynecology clinicians practicing in an integrated healthcare system.

Methods:
We constructed a three-part survey that contained (1) eight multiple-choice knowledge questions; (2) three Likert-scale questions regarding clinicians’ likelihood of assessing for vulvovaginal atrophy symptoms at a routine (well) visit, confidence in advising patients about symptoms and counseling about therapy; and (3) a 12-item check list of potential barriers to diagnosis and treatment. Analyses were performed using multiple regression.

Results:
Of the 360 clinicians who were sent an e-mail request, 119 (90 primary care, 29 gynecology) completed the survey (33%). Responders and nonresponders did not differ by age, specialty, or clinician type. The proportion with correct responses to knowledge questions differed between primary care (63%) and gynecology (77%) (adjusted mean difference [AMD] =16, 95% CI [10-22]). Primary care clinicians were less likely than gynecology clinicians to assess for symptoms (AMD = 1.04, 95% CI [0.55-1.52]), and were less confident about their ability to advise on symptoms (AMD = 0.66, 95% CI [0.33-0.99]) and to counsel patients about treatment (AMD = 0.76, 95% CI [0.42-1.10]). Lack of time (71%) and educational materials (44%) were the most common barriers to diagnosis and treatment.

Conclusions:
Primary care and gynecology clinicians differ in their knowledge and confidence in managing vulvovaginal atrophy but report similar practice barriers. Addressing identified knowledge deficits and practice barriers may lead to improved management of vulvovaginal atrophy.
Amenorrhea after lung cancer treatment
Authors: Cathcart-Rake Elizabeth J. , Ruddy Kathryn J. , Gupta Ruchi , Kremers Walter , Gast Kelly , Su H. Irene , Partridge Ann H. , Stewart Elizabeth A. , Liu Han , He Yanqi , Yang Ping 
Published: August 2018

Abstract

Objective:
More than 5,000 premenopausal women are diagnosed with lung cancer annually in the United States. Limited data exist regarding the risk of treatment-related amenorrhea, a surrogate for infertility and early menopause, after systemic therapies for lung cancer.

Methods:
Premenopausal women diagnosed with lung cancer under age 50 were surveyed at diagnosis and annually thereafter about their menstrual status as a part of the Mayo Clinic Epidemiology and Genetics of Lung Cancer Research Program. Types of lung cancer-directed treatments were recorded, and frequencies of self-reported menopause at each survey were calculated.

Results:
A cohort of 182 premenopausal women were included in this study, with average age at lung cancer diagnosis 43 years (SD 6). Among the 85 patients who received chemotherapy, 64% self-reported that they had become menopausal within a year of diagnosis. Platinum salts were universally included in these chemotherapy regimens, and the majority of these women also received taxanes within 1 year of diagnosis. Only 15% of the 94 patients who did not receive systemic therapy within 1 year of diagnosis experienced self-reported menopause. Three patients received targeted therapy alone, two of whom remained premenopausal at the final qualifying survey, completed a median of 3 years after diagnosis.

Conclusions:
Chemotherapy for lung cancer patients appears to increase risk of early loss of menses in survivors.
Improving Outcomes in Oncological Colorectal Surgery by Prehabilitation
Authors: Bruns Emma R.J. , van Rooijen Stefanus J. , Argillander Tanja E. , van der Zaag Edwin S. , van Grevenstein Wilhelmina M.U. , van Duijvendijk Peter , Buskens Christianne J. , Bemelman Willem A. , van Munster Barbara C. , Slooter Gerrit D. , van den Heuvel Baukje 
Published: August 2018

Introduction
The cornerstone in the treatment of colorectal cancer is surgery. A surgical event poses a significant risk of decreased functional decline and impaired health-related quality of life. Prehabilitation is defined as the multimodal preoperative enhancement of a patient's condition. It may serve as a strategy to improve postoperative outcomes. Prehabilitation requires a multidisciplinary effort of medical health care professionals and a behavioral change of the patient.

Methods
The goal of prehabilitation is threefold: (1) to reduce postoperative complications, (2) to enhance and accelerate the recovery of the patient, and (3) to improve overall quality of life. In this article, we introduce the FIT model illustrating a possible framework toward the implementation of both evidence-based and tailor-made prehabilitation for patients undergoing surgery for colorectal cancer.

Results
The model is composed of three pillars: “facts” (how to screen patients and evidence on what content to prescribe), “integration” (data of own questionnaires assessing motivation of patients and specialists), and finally “tools” (which outcome measurements to use).

Discussion
Developing implementable methods and defining standardized outcome instruments will help establish a solid base for patient-centered prehabilitation programs. Any party introducing prehabilitation requiring multidisciplinary teamwork and behavioral change can potentially use this framework.
Patient Self-Reported Adherence to Ritonavir-Boosted Darunavir Combined With Either Raltegravir or Tenofovir Disoproxil Fumarate/Emtricitabine in the NEAT001/ANRS143 Trial
Authors: Ammassari Adriana , Stöhr Wolfgang , Antinori Andrea , Molina Jean-Michel , Schwimmer Christine , Domingo Pere , Thalme Anders , Di Pietro Massimo , Wallet Cedrick , Pozniak Anton , Richert Laura , Raffi François ,   the NEAT001/ANRS143 Trial Study Group
Published: August 2018

Background:
The NEAT001/ANRS143 trial demonstrated noninferiority of ritonavir-boosted darunavir combined with either raltegravir (RAL + DRV/r) or tenofovir disoproxil fumarate/emtricitabine (TDF/FTC + DRV/r) in HIV-positive, antiretroviral-naive adults. In post hoc analyses, however, RAL + DRV/r showed inferiority in patients with baseline CD4+ <200/mm3 and HIV-1 RNA ≥100,000 copies per milliliter. This preplanned ancillary study was conducted to assess whether differences in adherence might explain efficacy results.

Setting:
Phase III, open-label, randomized, multicenter study in 15 European countries (ClinicalTrials.gov, NCT01066962).

Methods:
Seven hundred seventy-four participants self-reported adherence (modified AIDS Clinical Trials Group questionnaire) over 96 weeks [383 RAL + DRV/r (twice daily; 5 pills/day), 391 TDF/FTC + DRV/r (once daily; 4 pills/day)]. Primary endpoint was ≥95% versus <95% adherence to prescribed doses recorded (1) over the last 4 days or (2) on the visual analogue scale over the last 30 days.

Results:
Characteristics, except age, were similar between arms; 9% had CD4+ <200 cells/mm3 and HIV-1 RNA ≥100,000 copies per milliliter. Adherence ≥95% in the last 4 days (P = 0.029) or at the visual analogue scale (P = 0.0072) was higher with TDF/FTC + DRV/r than with RAL + DRV/r. Adherence ≥95% over the last 4 days was associated with lower probability of virological failure (P = 0.015). Adherence in patients with baseline CD4+ <200 cells/mm3 and HIV-1 RNA ≥100,000 copies per milliliter was similar to the rest of the population, and not significantly associated with efficacy measures, with no significant differences between arms.

Conclusion:
Adherence was high and slightly better in the TDF/FTC + DRV/r than in the RAL + DRV/r arm. No convincing evidence was found that higher failure rate in the RAL + DRV/r arm in the subgroup with worse baseline viroimmunological status is caused by adherence differences.
Isolated Fourth Nerve Palsy in Nontraumatic Tentorial Hemorrhage
Authors: Walter Eyal , Trobe Jonathan D. 
Published: August 2018

Abstract:
A 46-year-old woman being treated with warfarin for antiphospholipid antibody syndrome experienced a rise in international normalized ratio (INR) to 5.4 and developed sudden headache and diplopia. Neuro-ophthalmologic examination disclosed a right fourth nerve palsy. Noncontrast computed tomography revealed a subdural hematoma layered along the right tentorium cerebelli, directly in the path of the nerve. With normalization of the INR, the palsy markedly improved over subsequent weeks. This is a unique case of a nontraumatic subdural hematoma causing a fourth nerve palsy.
Visual Field Mean Deviation at Diagnosis of Idiopathic Intracranial Hypertension Predicts Visual Outcome
Authors: Mikkilineni Shravani , Trobe Jonathan D. , Cornblath Wayne T. , De Lott Lindsey 
Published: August 2018

Background:
A robust predictor of visual outcome in idiopathic intracranial hypertension (IIH) would be useful in management, but there is limited information on this point. The purpose of this study was to ascertain whether visual field mean deviation on standard static perimetry performed at diagnosis in a large patient cohort is a reliable predictor of visual outcome.

Methods:
We retrospectively reviewed the automated visual field mean deviations at diagnosis and at final encounter in 79 patients with IIH examined in the neuro-ophthalmology clinics at a single academic medical center from 1999 to 2015.

Results:
Of the 79 study patients, 66 (84%) entered with visual field mean deviations of −7 dB or better. Of those 66 patients, 59 (89%) had final mean deviations of −4 dB or better and 33 (56%) had final mean deviations of −2 dB or better. The single patient who had an initial mean deviation of −7 dB or better and a poor final mean deviation (−32 dB) was nonadherent to prescribed medication. Of the 13 (21%) patients who entered with mean deviations worse than −7 dB, 11 (85%) ended up with poor visual outcomes, their final mean deviations ranging from −5 dB to −32 dB. Over half of those 13 patients had required surgery for IIH, often within 3 weeks of diagnosis, owing to severe papilledema and visual dysfunction at the time of diagnosis.

Conclusions:
Based on this retrospective study, patients with IIH who have relatively mild visual dysfunction at diagnosis are likely to have a favorable visual outcome, provided they are adherent to recommended treatment. Many of those with poor visual function at diagnosis will have unfavorable visual outcomes despite aggressive treatment.
A probable genetic origin for pit defects on the molars of Paranthropus robustus
Authors: Towle Ian , Irish Joel D. 
Published: August 2018

AbstractWe report the frequencies of linear enamel hypoplasia (LEH) and, specifically, pitting enamel hypoplasia (PEH) defects in the teeth of Paranthropus robustus, for comparison with four other South African hominin species and three extant nonhuman primate species. Unlike LEH, the lesser known PEH is characterized by multiple circular depression defects across a tooth crown and is often difficult to interpret in terms of developmental timing and etiology. Teeth in all samples were examined macroscopically with type, position and number of defects recorded. Frequencies of teeth with LEH vary among hominin species, but the differences in PEH are considerable. That is, P. robustus has much higher rates of pitting defects, with 47% of deciduous teeth and 14% of permanent teeth affected, relative to 6.7% and 4.3%, respectively, for all other hominin teeth combined; none of the extant primate samples evidence comparable rates. The defects on P. robustus molars are unlike those in other species, with entire crowns often covered in small circular depressions. The PEH is most consistent with modern human examples of amelogenesis imperfecta. Additionally, the defects are: 1) not found on anterior teeth, 2) uniform in shape and size, and 3) similar in appearance/severity on all molars. A possible reason for this form of PEH is as a side effect of selection on another phenotype that shares the same coding gene(s), i.e., a genetic origin. Recent research on the ENAM gene provides one such possibility. Paranthropus likely underwent rapid evolution in the ENAM loci, with changes in this gene contributing to larger posterior teeth and thicker enamel. This same gene is associated with amelogenesis imperfecta; therefore, pleiotropy effects, relating to high selection on this gene during Paranthropus evolution, could have yielded this unique condition.
UNCROSS2: identification of cross-talk in 16S rRNA OTU tables
Authors: Edgar Robert C. 
Published: August 2018

AbstractNext-generation amplicon sequencing is widely used for surveying biological diversity in applications such as microbial metagenomics, immune system repertoire analysis and targeted tumor sequencing of cancer-associated genes. In such studies, assignment of reads to incorrect samples (cross-talk) is a well-documented problem that is rarely considered in practice. Here, I describe UNCROSS2, an algorithm designed to detect and filter cross-talk in OTU tables generated by next-generation sequencing of the 16S ribosomal RNA gene. On eight published datasets, cross-talk rates are estimated to range from 0.4% to 1.5% mis-assigned reads. On a mock community test, UNCROSS2 identifies spurious counts due to cross-talk with sensitivity ∼80% to 90% and error rate from ∼1% to ∼20%, but it is not clear whether the accuracy of the algorithm is sufficient to decisively improve diversity rates in practice.
Real-time non-invasive intracranial state estimation using unscented Kalman filter
Authors: Park Chanki , Ryu Seungjun , Jung Bonghyun , Lee Sangpyong , Hong Changkie , Kim Yongbae , Lee Boreom 
Published: August 2018

AbstractIntracranial pressure (ICP) monitoring is desirable as a first-line measure to assist decision-making in cases of increased ICP. Clinically, non-invasive ICP monitoring is also required to avoid infection and hemorrhage in patients. The relationships among the arterial blood pressure (Pa), ICP, cerebral blood flow, and its velocity (QCBFv) measured by transcranial Doppler ultrasound measurement have been reported. However, real-time non-invasive ICP estimation using these modalities is less well documented. Here, we present a novel algorithm for real-time and non-invasive ICP monitoring with QCBFv and Pa, called direct-current (DC)-ICP. This technique is compared with invasive ICP for 11 traumatic-brain-injury patients admitted to Cheju Halla Hospital and Gangnam Severance Hospital from July 2017 to June 2018. The inter-subject correlation coefficient between true and estimate was 0.70. The AUCs of the ROCs for prediction of increased ICP for the DC-ICP methods are 0.816. Thus, QCBFv monitoring can facilitate reliable real-time ICP tracking with our novel DC-ICP algorithm, which can provide valuable information under clinical conditions.
e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines
Authors: Rojas-Macias Miguel A. , Mariethoz Julien , Andersson Peter , Jin Chunsheng , Venkatakrishnan Vignesh , Aoki Nobuyuki P. , Shinmachi Daisuke , Ashwood Christopher , Madunic Katarina , Zhang Tao , Miller Rebecca L. , Horlacher Oliver , Struwe Weston B. , Levander Fredrik , Kolarich Daniel , Rudd Pauline M. , Wuhrer Manfred , Kettner Carsten , Packer Nicolle H. , Aoki-Kinoshita Kiyoko F. , Lisacek Frédérique , Karlsson Niclas G. 
Published: August 2018

ABSTRACTGlycomics targets released glycans from proteins, lipids and proteoglycans. High throughput glycomics is based on mass spectrometry (MS) that increasingly depends on exchange of data with databases and the use of software. This requires an agreed format for accurately recording of experiments, developing consistent storage modules and granting public access to glycomic MS data. The introduction of the MIRAGE (Mimimum Requirement for A Glycomics Experiment) reporting standards for glycomics was the first step towards automating glycomic data recording. This report describes a glycomic e-infrastructure utilizing a well established glycomics recording format (GlycoWorkbench), and a dedicated web tool for submitting MIRAGE-compatible MS information into a public experimental repository, UniCarb-DR. The submission of data to UniCarb-DR should be a part of the submission process for publications with glycomics MSn that conform to the MIRAGE guidelines. The structure of this pipeline allows submission of most MS workflows used in glycomics.
Where did you come from, where did you go: Refining Metagenomic Analysis Tools for HGT characterisation
Authors: Seiler Enrico , Trappe Kathrin , Renard Bernhard Y. 
Published: August 2018

AbstractHorizontal gene transfer (HGT) has changed the way we regard evolution. Instead of waiting for the next generation to establish new traits, especially bacteria are able to take a shortcut via HGT that enables them to pass on genes from one individual to another, even across species boundaries. Existing HGT detection approaches usually first identify genes of foreign nature, e.g., using composition-based methods, and then exploit phylogenetic discrepancies of the corresponding gene tree compared to a species tree. These approaches depend on fully sequenced HGT organisms and computable phylogenetic species trees. The tool Daisy offers a different approach based on read mapping that provides complementary evidence compared to existing methods at the cost of relying on the acceptor and donor references of the HGT organism being known. Acceptor and donor identification is akin to species identification in metagenomic samples based on sequencing reads, a problem addressed by metagenomic profiling tools. However, acceptor and donor references have certain properties such that these methods can not be directly applied. We propose DaisyGPS, a mapping-based pipeline that is able to identify acceptor and donor candidates of an HGT organism based on sequencing reads. To do that, DaisyGPS leverages metagenomic profiling strategies and refines them for HGT candidate identification. These candidates can then be further evaluated by tools like Daisy to establish HGT regions. We successfully validated our approach on both simulated and real data, and show its benefits in an investigation of MRSA outbreak data. DaisyGPS is freely available from https://gitlab.com/rki_bioinformatics/.
Reconstructing meaning from bits of information
Authors: Kivisaari Sasa L. , Vliet Marijn van , Hultén Annika , Lindh-Knuutila Tiina , Faisal Ali , Salmelin Riitta 
Published: August 2018

AbstractWe can easily identify a dog merely by the sound of barking or an orange by its citrus scent. In this work, we study the neural underpinnings of how the brain combines bits of information into meaningful object representations. Modern theories of semantics posit that the meaning of words can be decomposed into a unique combination of individual semantic features (e.g., “barks”, “has citrus scent”). Here, participants received clues of individual objects in form of three isolated semantic features, given as verbal descriptions. We used machine-learning-based neural decoding to learn a mapping between individual semantic features and BOLD activation patterns. We discovered that the recorded brain patterns were best decoded using a combination of not only the three semantic features that were presented as clues, but a far richer set of semantic features typically linked to the target object. We conclude that our experimental protocol allowed us to observe how fragmented information is combined into a complete semantic representation of an object and suggest neuroanatomical underpinnings for this process.
Enemy release mitigates inbreeding depression in native and invasive Silene latifolia populations: experimental insight into the role of inbreeding × environment interactions in invasion success
Authors: Schrieber Karin , Wolf Sabrina , Wypior Catherina , Höhlig Diana , Keller Stephen R. , Hensen Isabell , Lachmuth Susanne 
Published: August 2018

AbstractInbreeding and enemy infestation are common in plants and can synergistically reduce their performance. This inbreeding × environment (I×E) interaction may be of particular importance for the success of plant invasions if introduced populations experience a release from attack by natural enemies relative to their native conspecifics. Using native and invasive plant populations, we investigate whether inbreeding affects infestation damage, whether inbreeding depression in performance is mitigated by enemy release and whether genetic differentiation among native and invasive plants modifies these I×E interactions. We used the plant invader Silene latifolia and its natural enemies as a study system. We performed two generations of experimental out- and inbreeding within eight native (European) and eight invasive (North American) S. latifolia populations under controlled conditions using field-collected seeds. Subsequently, we exposed the offspring to an enemy exclusion and inclusion treatment in a common garden in the species’ native range to assess the interactive effects of population origin (range), breeding treatment and enemy treatment on infestation damage as well as plant performance. Inbreeding increased flower and leaf infestation damage in plants from both ranges, but had opposing effects on fruit damage in native versus invasive plants. Both inbreeding and enemy infestation had negative effects on plant performance, whereby inbreeding depression in fruit number was higher in enemy inclusions than exclusions in plants from both ranges. Moreover, the magnitude of inbreeding depression in fruit number was lower in invasive than native populations. Our results support that inbreeding increases enemy susceptibility of S. latifolia, which magnifies inbreeding depression in the presence of enemies. Enemy release in the invaded habitat may thus increase the persistence of inbred founder populations and thereby contribute to successful invasion. Moreover, our findings emphasize that genetic differentiation among native and invasive plants can shape the magnitude and even the direction of inbreeding effects.
The Desmosome is a Mesoscale Lipid Raft-Like Membrane Domain
Authors: Lewis Joshua D , Caldara Amber L , Zimmer Stephanie E , Seybold Anna , Strong Nicole L , Stahley Sara N , Frangakis Achilleas S , Levental Ilya , Wahl James K , Mattheyses Alexa L , Sasaki Takashi , Nakabayashi Kazuhiko , Hata Kenichiro , Matsubara Yoichi , Ishida-Yamamoto Akemi , Amagai Masayuki , Kubo Akiharu , Kowalczyk Andrew P 
Published: August 2018

SummaryDesmogleins are cadherin family adhesion molecules essential for epidermal integrity. Previous studies have shown that desmogleins associate with lipid rafts, but the significance of this association was not clear. Here, we report that the desmoglein transmembrane domain (TMD) is the primary determinant of raft association. Further, we identify a novel mutation in the DSG1 TMD (G562R) that causes severe dermatitis, multiple allergies, and metabolic wasting (SAM) syndrome. Molecular modeling predicts that this G to R mutation shortens the DSG1 TMD, and experiments directly demonstrate that this mutation compromises both lipid raft association and desmosome incorporation. Finally, cryo-electron tomography (cryo-ET) indicates that the lipid bilayer within the desmosome is ~10% thicker than adjacent regions of the plasma membrane. These findings suggest that differences in bilayer thickness influence the organization of adhesion molecules within the epithelial plasma membrane, with cadherin TMDs recruited to the desmosome via establishment of a specialized mesoscale lipid raft-like membrane domain.