bluuebunny/crossref_metadata_2025_split huggingface dataset:
VISUALIZATION OF CHOROIDAL NEOVASCULARIZATION USING TWO COMMERCIALLY AVAILABLE SPECTRAL DOMAIN OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY DEVICES
Authors: Arya Malvika , Rebhun Carl B. , Cole Emily D. , Sabrosa Almyr S. , Arcos-Villegas Gabriel , Louzada Ricardo N. , Novais Eduardo A. , Lane Mark , Dang Sabin , Ávila Marcos , Witkin André J. , Baumal Caroline R. , Duker Jay S. , Waheed Nadia K. 
Published: August 2018

Purpose:
To compare the sensitivity of detection and the measured size of choroidal neovascularization (CNV) on two commercially available spectral domain optical coherence tomography angiography (OCTA) devices, the Optovue RTVue XR Avanti with AngioVue and the Zeiss Cirrus HD-OCT with AngioPlex.

Methods:
Patients with CNV lesions were imaged consecutively on both OCTA devices on the same day of their visit. 3 × 3 mm and 6 × 6 mm scans centered at the fovea were obtained. Two independent masked readers evaluated the OCTA images for CNV identification and its area measurements.

Results:
No significant differences were observed between the 2 OCTA devices in CNV area measurements on their 3 × 3 mm and 6 × 6 mm scans. However, there was suboptimal performance of their automated segmentation algorithms as compared to manually adjusted segmentation for visualizing CNV lesions.

Conclusion:
There was no significant difference in the size of the CNV lesion as measured on either commercially available spectral domain OCTA device. Both devices were comparable in their detection of CNV lesions on manual adjustment of segmentation lines. However, their automated segmentation algorithms need improvement to allow for accurate measurement of CNV lesions for routine clinical application.
Moment-to-moment changes in perceived social support and pain for men living with HIV: an experience sampling study
Authors: Crockett Kaylee B. , Turan Bulent 
Published: August 2018

Abstract
Research suggests that people living with HIV experience levels of pain disproportionate to the general population. Pain is a stressor that can negatively impact health-related quality of life. As the number of people aging with HIV increases, we must understand the dynamics of pain experiences among people living with HIV and how to effectively harness evidence-based treatments and supportive resources to enhance adaptive coping. We used an experience sampling method (also called Ecological Momentary Assessment) to assess moment-to-moment experiences of pain and social support 3 times a day for 7 days in a sample of 109 men living with HIV. Participants also responded to questionnaires assessing attachment-related insecurity and social support. In hierarchical linear modeling analyses controlling for age, race, sexual orientation, and socioeconomic status, we found that experiences of social support were associated with lower subsequent pain within-persons. On the other hand, experiences of pain were not associated with later experiences of social support. Men with higher levels of attachment-related avoidance reported more pain on average. Attachment-related avoidance also moderated the association between moment-to-moment experiences of felt social support on pain. Results suggest that within-persons, experiences of daily social support reduce experiences of pain. Between-persons, attachment style may influence how individuals make use of social support in coping with experiences of pain. These findings imply a need to assess social well-being at the clinic level and also support tailored biopsychosocial approaches to pain management in HIV care settings.
Young females with long-standing patellofemoral pain display impaired conditioned pain modulation, increased temporal summation of pain, and widespread hyperalgesia
Authors: Holden Sinéad , Straszek Christian Lund , Rathleff Michael Skovdal , Petersen Kristian Kjær , Roos Ewa M. , Graven-Nielsen Thomas 
Published: August 2018

Abstract
Patellofemoral pain (PFP) is a common and recurrent knee condition in young females, characterized by pressure hyperalgesia and reduced pain inhibitory control. This study investigated antinociceptive and pronociceptive profiles in young females with long-standing (>5 years) PFP (current-PFP), those who recovered from adolescent PFP (recovered-PFP), and pain-free controls. This preregistered, assessor-blinded, cross-sectional study included 87 females younger than 25 years: 36 current-PFP, 22 recovered-PFP, and 29 pain-free controls. The primary outcome was conditioned pain modulation (CPM) assessed by increase of cuff pain thresholds during painful cuff conditioning on the contralateral leg. Secondary outcomes included pressure pain thresholds at the knee, shin, and forearm, and temporal summation of pain, assessed by pain intensity recordings on a visual analogue scale during repeated cuff pressure pain stimulations on the leg. Compared with the recovered-PFP, the current-PFP had impaired CPM (mean difference: 11.6%; P = 0.004) and reduced pressure pain thresholds at the knee, shin, and forearm which were also reduced compared to current-PFP (mean difference: 85-225 kPa; P < 0.05). There were no differences between current-PFP and controls in CPM. Current-PFP and recovered-PFP demonstrated facilitated temporal summation of pain, compared to controls (mean difference: 0.7-0.8 visual analogue scale change; P < 0.05). Compared with controls, the recovered-PFP also had reduced pressure pain thresholds at the knee, which were higher than the current-PFP (mean difference: 110-225 kPa; P < 0.05). In conclusion, both current-PFP and recovered-PFP displayed altered pain mechanisms compared to controls with no history of knee pain, despite resolution of symptoms in the recovered-PFP group. The implications of these findings in the recurrent nature of PFP requires further studies.
The Variable Characteristics of Human Papillomavirus in Squamous Cell Carcinoma and Adenocarcinoma of Cervix in China
Authors: Chen Wen , Sun Haikui , Molijn Anco , Zeng Liang , Kang Leni , Jenkins David , Zhang Shaokai , Cui Jianfeng , Wu Zeni , Pirog Edyta , Shen Guihua , Zhang Xun , Qiao Youlin 
Published: August 2018

Objective
A hospital-based multicenter, retrospective study was conducted to compare the distribution of human papillomavirus (HPV) in squamous cell carcinoma (SCC) and cervical adenocarcinoma (CADC) in China.

Methods
Paraffin-embedded tissue blocks diagnosed as SCC and CADC across China were collected, as well as the total number of diagnosed invasive cervical cancer of the 9 selected centers. DNA enzyme immunoassay, reverse hybridization, and multiplex type-specific polymerase chain reaction were used for HPV genotyping.

Results
The ratios of CADC to SCC were increasing from 2005 to 2010, in parallel with HPV prevalence in CADC. In 630 patients with SCC (mean ± SD age, 45.40 ± 10.30) and 718 patients with CADC (mean ± SD age, 46.09 ± 10.59) recruited, HPV prevalence rates were 97.6% and 74.5%, respectively. Human papillomavirus viral load for SCC is significantly higher than that for CADC. Most common HPV types distributed in SCC and CADC were HPV-16 (78.5%, 75.1%–81.6%; 47.1%, 42.9%–51.3%), HPV-18 (8.0%, 6.1%–10.4%; 41.1%, 37.0%–45.3%), HPV-52 (2.3%, 1.4%–3.8%; 5.6%, 4.0%–7.9%), and HPV-45 (1.1%, 0.6%–2.3%; 3.9%, 2.6%–5.9%). Different diagnostic mean ± SD age for HPV-16/HPV-18 versus other high-risk HPV types were observed: SCC (44.5 ± 9.94 vs 51.0 ± 10.83, p < .05) and CADC (44.1 ± 9.44 vs 47.4 ± 10.41, p = .006). For HPV-negative cases, mean ± SD age was 46.1 ± 10.73 in SCC and 50.3 ± 11.85 in CADC, which were older than the positive (45.4 ± 10.31, 44.5 ± 9.64). HPV-16 and HPV-18 were the most frequent HPV types in both histological types, and HPV-18 was more frequent in CADC than in SCC.

Conclusions
Human papillomavirus infection was identified more often in SCC than in CADC. Women with HPV-associated cancers, especially HPV-16/HPV-18, were of a younger age at diagnosis when compared with non–HPV-associated cancers.
The role of transjugular intrahepatic portosystemic shunt in the management of portal vein thrombosis: a systematic review and meta-analysis
Authors: Valentin Nelson , Korrapati Praneet , Constantino Joseph , Young Ari , Weisberg Ilan 
Published: August 2018

Background
The role of transjugular intrahepatic portosystemic shunt (TIPS) in the management of portal vein thrombosis (PVT) remains controversial. This study aimed to conduct a systematic review and meta-analysis to evaluate the role of TIPS for the management of PVT in adult patients with liver disease.

Patients and methods
Multiple databases were searched through April 2017. Data were gathered to estimate the rates of technical success, portal vein recanalization, portal patency, hepatic encephalopathy, and mean change in portal pressure gradient in patients with PVT who underwent TIPS. Estimates were pooled across studies using the random effects model.

Results
Eighteen studies were included in the analysis. The pooled technical success rate was 86.7% [95% confidence interval (CI)=78.6–92.1%]. Rate of portal vein recanalization was 84.4% (95% CI=78.4–89.0%). The rate of complete recanalization was 73.7% (95% CI=64.3–81.3%). Portal patency was 86.9% (95% CI=79.7–91.8%). Mean change in portal pressure gradient was 14.5 mmHg (95% CI=11.3–17.7 mmHg). Hepatic encephalopathy was 25.3% (95% CI=19.2–32.6%). The number of major adverse events reported across studies was low. The majority of the analyses were not associated with substantial heterogeneity.

Conclusion
The use of TIPS in the management of PVT is feasible and effective in achieving a significant and sustainable reduction in clot burden with a low risk of major complications. TIPS should be considered as a viable treatment option in patients with PVT. Given the limited amount of randomized comparative studies reported, additional trials are warranted to assess the safety and efficacy of TIPS as a treatment modality in PVT, in comparison to other treatment options, such as anticoagulation.
Crohn’s and Colitis Foundation of America Partners Patient-Powered Research Network
Authors: Chung Arlene E. , Vu Maihan B. , Myers Kelly , Burris Jessica , Kappelman Michael D. 
Published: August 2018

Background:
To build a Patient-Powered Research Networks (PPRN) that prioritizes the needs of its members who have inflammatory bowel diseases (IBD), we sought to better understand patients’ preferences for what are the essential features that will facilitate and sustain engagement.

Methods:
We conducted a two-phase qualitative study. Seven focus groups involving 62 participants with IBD were conducted (phase 1). Focus group results informed the phase 2 cognitive interviews, which included 13 phone interviews. Topics included experiences with IBD and research, PPRN engagement, patient-generated health data, and resources/tools to facilitate self-management. All focus groups and interviews were digitally recorded, transcribed verbatim, and analyzed in ATLAS.ti 7.5. Thematic categories were derived from the data, and codes were grouped into emergent themes and relationships.

Results:
Four major themes emerged through inductive coding: (1) the impact of knowing; (2) participation barriers and challenges; (3) engagement and collaboration; and (4) customizable patient portal features/functionalities. Participants were motivated to participate in the PPRN because the knowledge gained from research studies would benefit both society and the individual. Main concerns included credibility of online resources, pharmaceutical industry profiting from their data, data security, and participation expectations. Participants wanted a true and equal partnership in every phase of building a PPRN. Participants felt it was important to have access to personal health records and be able to track health status and symptoms.

Conclusion:
Partnering with participants throughout PPRN development was critical to understanding the needs and preferences of patients with IBDs and for shaping engagement strategies and the portal’s design.
MoodNetwork
Authors: Sylvia Louisa G. , Hearing Casey M. , Montana Rebecca E. , Gold Alexandra K. , Walsh Samantha L. , Janos Jessica A. , Tovey Roberta E. , Deckersbach Thilo , Nierenberg Andrew A. 
Published: August 2018

Introduction:
Research has often been viewed as a passive process by which participants enroll in studies developed by researchers. It is becoming clearer that to understand the nuances of mood episodes and how to prevent them, we need to conduct large clinical trials that have the power to investigate moderators and mediators, or catalysts and mechanisms of change. MoodNetwork, the first online, patient-centered research community for individuals with mood disorders, aims to change the way that traditional research has been conducted by involving patients, their caregivers, and advocates in the process of research. The aim of this report is to share lessons learned from developing MoodNetwork.

Methods:
Participants enroll by completing a demographic survey and consent form. Once enrolled, participants are encouraged to complete optional surveys about their mood disorders and areas of research priority. Stakeholder and advocacy partners developed the website, web-based surveys, and recruitment materials.

Results:
MoodNetwork has enrolled 4103 participants to date. Of this sample, 96.9% report experiencing depression and 79.7% endorse symptoms of mania or hypomania. Participants rated reducing stigma and alleviating symptoms as their 2 largest research priorities. Recruitment has been slower than expected. Recruiting a diverse sample has been challenging, and this impacts the Network’s ability to conduct comparative effectiveness research studies.

Discussion:
We discuss lessons learned from recruiting individuals with mood disorders to MoodNetwork, an innovative approach to conducting clinical trials. We identify and review 5 strategies for increasing enrollment as well as future directions.
A Novel Stakeholder Engagement Approach for Patient-centered Outcomes Research
Authors: Kim Katherine K. , Khodyakov Dmitry , Marie Kate , Taras Howard , Meeker Daniella , Campos Hugo O. , Ohno-Machado Lucila 
Published: August 2018

Introduction/Objectives:The engagement of patients and other stakeholders is a critical element in the design of patient-centered outcomes research studies. However, methodology for scalable engagement in research management particularly activities such as operationalization of principles and setting of priorities is not well-developed. The objective of this study is to describe a novel approach for scalable stakeholder engagement in research aligned with the Patient-Centered Outcomes Research Institute (PCORI) engagement principles, which was evaluated in a national clinical data research network.Materials and Methods:Patient, patient advocate, clinician, and researcher stakeholders were recruited from clinical sites, as well as social media sites related to the 3 conditions of focus, heart failure, obesity, and Kawasaki disease. The engagement strategy was designed, implemented, and mapped to the PCORI engagement principles. Evaluation included internal assessment and quantitative measures of online engagement.Results:We operationalized the PCORI principles with 12 stakeholder engagement strategies and convened stakeholder advisory boards and online research prioritization panels to determine research priorities in a rigorous, deliberative process. A total of 46 advisors (20 patients) and 339 panelists (159 patients) actively participated. There were not significant differences between patients and clinicians in level of online engagement. Nonetheless, while patients reported a slightly greater challenge with following online discussion, they overall had a more favorable opinion about use of the online format.Discussion/Conclusion:An efficient way to engage large numbers of representative stakeholders in research is a necessary first step to assure the public of trustworthy use of data networks for health research. This paper describes a comprehensive approach to engagement in patient-centered outcomes research management that informs ongoing development of rigorous methodologies in this area.
Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon
Authors: Jesús Suárez-Moo Pablo de , Vovides Andrew P. , Griffith M. Patrick , Barona-Gómez Francisco , Cibrián-Jaramillo Angélica 
Published: August 2018

AbstractCycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from sevenDioonspecies and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species ofDioonthat we evaluated, suggesting a recent divergence ofDioonpopulations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched withNostocspp andCalothrixspp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.
Brood-holding causes workers to pay attention to the queen in the carpenter ant Camponotus japonicus
Authors: Hara Kenji 
Published: August 2018

[Abstract]Brood accumulation, a fundamental behavior of offspring care in the carpenter ant Camponotus japonicus, is driven by alternation of ‘holding run’ and ‘empty-handed run’ behaviors. In the holding run, a worker holds a brood with her mandibles and carries it to the queen (holding run). After releasing it beside the queen, she hurries back to another brood (empty-handed run). To address the motivation for the brood-accumulation task, in this study, I observed these behaviors under experimental conditions. When workers performed the task in a situation that involved selection between their own and unfamiliar queens, they ran in significantly more restrictive ways during the holding run than during the empty-handed run. Hence, ‘holding’ represents a different motivational state than ‘empty-handed’. In a second experiment, the workers were suddenly presented with an unfamiliar floor during the task. Regardless of whether they were holding or empty-handed, their running traces on the familiar floor were simple, whereas on the unfamiliar floor they were more complex. These results show that holding workers would pay attention to the queen, exploiting cues on the floor to restrict their responses to the queen.
PconsC4: fast, free, easy, and accurate contact predictions
Authors: Michel Mirco , Hurtado David Menéndez , Elofsson Arne 
Published: August 2018

AbstractMotivationResidue contact prediction was revolutionized recently by the introduction of direct coupling analysis (DCA). Further improvements, in particular for small families, have been obtained by the combination of DCA and deep learning methods. However, existing deep learning contact prediction methods often rely on a number of external programs and are therefore computationally expensive.ResultsHere, we introduce a novel contact predictor, PconsC4, which performs on par with state of the art methods. PconsC4 is heavily optimized, does not use any external programs and therefore is significantly faster and easier to use than other methods.AvailabilityPconsC4 is freely available under the GPL license from https://github.com/ElofssonLab/PconsC4. Installation is easy using the pip command and works on any system with Python 3.5 or later and a modern GCC compiler.Contactarne@bioinfo.se
A galling insect activates plant reproductive programs during gall development
Authors: Schultz Jack C. , Edger Patrick P. , J.A. Body Mélanie , Appel Heidi M. 
Published: August 2018

AbstractSome insects can redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We tested this hypothesis using RNA sequencing (RNAseq) to quantify the transcriptional responses of wild grapevine (Vitis ripariaMichx.) leaves to a galling parasite, phylloxera(Daktulosphaira vitifolia(Fitch 1855)). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology (GO) categories were significantly enriched in developing galls, and that expression of many candidate genes involved in floral development were significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall appears to be phenotypically and transcriptionally similar to the carpel, due to the parasite hijacking underlying genetic machinery in the host plant.
The genome ofDrosophila innubilareveals lineage-specific patterns of selection in immune genes
Authors: Hill Tom , Koseva Boryana S. , Unckless Robert L. 
Published: August 2018

AbstractPathogenic microbes can exert extraordinary evolutionary pressure on their hosts. They can spread rapidly and sicken or even kill their host to promote their own proliferation. Because of this strong selective pressure, immune genes are some of the fastest evolving genes across metazoans, as highlighted in mammals and insects.Drosophila melanogasterserves as a powerful model for studying host/pathogen evolution. WhileDrosophila melanogasterare frequently exposed to various pathogens, little is known aboutD. melanogaster’s ecology, or if they are representative of otherDrosophilaspecies in terms of pathogen pressure. Here, we characterize the genome ofDrosophila innubila, a mushroom-feeding species highly diverged fromD. melanogasterand investigate the evolution of the immune system. We find substantial differences in the rates of evolution of immune pathways betweenD. innubilaandD. melanogaster. Contrasting what was previously found forD. melanogaster, we find little evidence of rapid evolution of the antiviral RNAi genes and high rates of evolution in the Toll pathway. This suggests that, while immune genes tend to be rapidly evolving in most species, the specific genes that are fastest evolving may depend either on the pathogens faced by the host and/or divergence in the basic architecture of the host’s immune system.