bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards self-learning based hypotheses generation in biomedical text domain
Authors: Gopalakrishnan Vishrawas , Jha Kishlay , Xun Guangxu , Ngo Hung Q , Zhang Aidong 
Published: December 2017

AbstractMotivationThe overwhelming amount of research articles in the domain of bio-medicine might cause important connections to remain unnoticed. Literature Based Discovery is a sub-field within biomedical text mining that peruses these articles to formulate high confident hypotheses on possible connections between medical concepts. Although many alternate methodologies have been proposed over the last decade, they still suffer from scalability issues. The primary reason, apart from the dense inter-connections between biological concepts, is the absence of information on the factors that lead to the edge-formation. In this work, we formulate this problem as a collaborative filtering task and leverage a relatively new concept of word-vectors to learn and mimic the implicit edge-formation process. Along with single-class classifier, we prune the search-space of redundant and irrelevant hypotheses to increase the efficiency of the system and at the same time maintaining and in some cases even boosting the overall accuracy.ResultsWe show that our proposed framework is able to prune up to 90% of the hypotheses while still retaining high recall in top-K results. This level of efficiency enables the discovery algorithm to look for higher-order hypotheses, something that was infeasible until now. Furthermore, the generic formulation allows our approach to be agile to perform both open and closed discovery. We also experimentally validate that the core data-structures upon which the system bases its decision has a high concordance with the opinion of the experts.This coupled with the ability to understand the edge formation process provides us with interpretable results without any manual intervention.Availability and implementationThe relevant JAVA codes are available at: https://github.com/vishrawas/Medline–Code_v2.Supplementary informationSupplementary data are available at Bioinformatics online.
Predictors of Secondary Role Strains Among Spousal Caregivers of Older Adults With Functional Disability
Authors: Polenick Courtney A , DePasquale Nicole 
Published: December 2017

Abstract

Background and Objectives
Aging spouses commonly care for a partner with functional disability, but little is known about how spousal caregiving may impact different life domains. This study evaluated how caregiving characteristics are associated with secondary role strains among spousal caregivers.

Research Design and Methods
This cross-sectional study examined 367 spousal caregivers and their partners from the 2011 National Health and Aging Trends Study and National Study of Caregiving. Hierarchical regressions were estimated to determine how caregiver background factors (sociodemographics, health conditions) along with primary objective (care activities, care recipient health conditions, and dementia status) and subjective (emotional caregiving difficulties, role overload) stressors are linked to care-related valued activity restriction, negative caregiving relationship quality, and care-related family disagreements. Gender differences were considered.

Results
After accounting for all predictors, older caregivers and caregivers providing more help with activities of daily living and health system interactions (e.g., scheduling appointments) were more likely to report activity restriction, whereas caregivers with more emotional difficulties reported higher negative caregiving relationship quality. Role overload was positively associated with all three secondary strains. For husbands only, caring for a partner with more chronic conditions was linked to higher negative caregiving relationship quality and caring for a partner with dementia was associated with a greater likelihood of family disagreements.

Discussion and Implications
Secondary role strains may develop through similar and unique pathways for caregiving wives and husbands. Further research is needed to identify those who could benefit from support in managing their care responsibilities alongside other life areas.
Clinical Updates in Women’s Health Care Summary: Common Dermatologic Conditions
Authors: Khorsand Kate O. , Iyer Jayasri G. , Abson Kim Gittere 
Published: December 2017

Abstract:
The skin is the largest organ in the human body, and as such, cutaneous problems constitute a common component of visits to medical professionals. The skin functions as a physiologic barrier and a major organ of homeostasis. The practicing obstetrician–gynecologist can play an important role in identifying skin diseases and initiating management. Additionally, the skin often reflects internal disease states. An astute health care provider can identify systemic conditions early, with the goal of improving management. This monograph reviews common cutaneous conditions, both benign and malignant, hair and nail disorders, and skin conditions unique to the adult woman.
Isolated Traumatic Subarachnoid Hemorrhage: An Evaluation of Critical Care Unit Admission Practices and Outcomes From a North American Perspective
Authors: Witiw Christopher D. , Byrne James P. , Nassiri Farshad , Badhiwala Jetan H. , Nathens Avery B. , da Costa Leodante B. 
Published: December 2017

Objectives:
Traumatic subarachnoid hemorrhage is a common radiographic finding associated with traumatic brain injury. The objective of this investigation is to evaluate the association between hospital-level ICU admission practices and clinically important outcomes for patients with isolated traumatic subarachnoid hemorrhage and mild clinical traumatic brain injury.

Design:
Multicenter observational cohort.

Setting:
Trauma centers participating in the American College of Surgeons Trauma Quality Improvement Program spanning January 2012 to March 2014.

Patients:
A total of 14,146 subjects, 16 years old and older, admitted to 215 trauma centers with isolated traumatic subarachnoid hemorrhage and Glasgow Coma Scale score 13 or greater. Patients with concurrent intracranial injuries, severe injury to other body regions, or tests positive for alcohol or illicit substances were excluded.

Intervention:
ICU admission.

Measurements and Main Results:
The primary outcome was need for neurosurgical intervention, defined as insertion of an intracranial monitor/drain or craniectomy/craniotomy. Secondary outcomes describing the clinical course included hospital discharge disposition, in-hospital mortality, and length of stay. Admission to ICU was common within the cohort (44.6%), yet the need for neurosurgical intervention was rare (0.24%). Variability was high between centers and remained so after adjusting for differences in case-mix and hospital-level characteristics (median odds ratio, 4.1). No significant differences in neurosurgical interventions, mortality, or discharge disposition to home under self-care were observed between groups of the highest and lowest ICU admitting hospitals. However, those in highest admitting group “stayed” in hospital 1.13 (95% CI, 1.07–1.20; p < 0.001) times that of the lowest admitting group.

Conclusions:
Critical care admission for mild traumatic brain injury patients with isolated traumatic subarachnoid hemorrhage is frequent and highly variable despite low probability of requiring neurosurgical intervention. Reevaluation of hospital-level practices may represent an opportunity for resource optimization when managing patients with mild clinical traumatic brain injury and associated isolated traumatic subarachnoid hemorrhage.
Effect of Rehabilitation on Sleep Quality After Ablation for Atrial Fibrillation
Authors: Risom Signe Stelling , Fevejle Cromhout Pernille , Overgaard Dorthe , Hastrup Svendsen Jesper , Kikkenborg Berg Selina 
Published: December 2017

Background:
Low sleep quality is common in patients with atrial fibrillation (AF). Positive effects of cardiac rehabilitation on patients treated for AF with ablation have been found, but whether cardiac rehabilitation affects sleep quality is unknown. The objectives of this study were to investigate (1) differences in sleep quality between cardiac rehabilitation and usual care groups and (2) whether other factors could affect sleep quality.

Methods:
From the randomized CopenHeartRFA trial, 210 patients treated for AF with ablation were included. A rehabilitation program consisting of physical exercise and psychoeducational consultations was tested. Sleep quality was measured with the Pittsburg Sleep Quality Index (PSQI) questionnaire before intervention and at the end of intervention. Anxiety, depression, and European Heart Rhythm Association scores were assessed.

Results:
No difference between groups in sleep quality was found (PSQI global mean [SD] score, 6.60 [3.61] points for the cardiac rehabilitation group [n = 83] and 6.08 [3.60] points for the usual care group [n = 90]; P = .34), although improvements in sleep quality were noted in both groups. Sleep latency, duration, and efficiency were significant by type of AF at 1 month. Anxiety, depression, and higher European Heart Rhythm Association scores at 4 months were associated with a higher PSQI global mean score at the end of intervention.

Conclusion:
The rehabilitation program showed no effect on sleep quality. A large proportion of patients reported poor sleep quality, and patients reporting anxiety, depression, or AF symptoms described worse sleep quality compared with patients who did not experience anxiety, depression, or AF symptoms. More research in the field is warranted.
Open Wounds and Healed Scars
Authors: van Ee Birgit , Smits Carolien , Honkoop Aafke , Kamper Ad , Slaets Joris , Hagedoorn Mariët 
Published: December 2017

Background
Breast cancer is more prevalent among women 60 years or older than among women younger than 60 years. However, we know much more about the breast cancer experiences of younger women than of older women. Such knowledge is important, for example, to guide treatment decisions or to provide psychosocial care.

Objective
The aim of this study was to gain insight into the experiences of women with breast cancer 70 years or older.

Methods
Semistructured interviews were conducted with 21 older patients with breast cancer in the Netherlands. We used open coding and affinity diagramming to evoke the themes reflecting the experiences of these women.

Results
Four themes emerged from the data: living through and coping with breast cancer, information exchange and informed choice, support experiences, and impact on daily life. Getting breast cancer took some women by surprise. However, older women with breast cancer coped fairly well and were satisfied with the support they received, especially from oncology nurses. Disturbing treatment adverse effects and changes in appearance, comorbid diseases, lack of clear information, and/or an unsupportive environment complicated their living with breast cancer.

Conclusions
Even though many older women with breast cancer handle their disease rather well, some women do encounter difficulties. Lack of support, comorbid diseases, and treatment adverse effects warrant extra attention.

Implications for Practice
Nurses’ close attention to women at risk and early intervention could help relieve individual suffering, while taking these womens’ strengths into account can enhance self-management.
Screening for distress in survivorship
Authors: Girgis Afaf , Smith Allan B. , Durcinoska Ivana 
Published: December 2017

Purpose of review
The current review provides an overview of recent research and other initiatives aimed at increasing and/or systematizing screening for distress in cancer survivors. It is timely given an increasing drive internationally to implement distress screening as part of routine cancer care.

Recent findings
Screening using brief validated tools is recommended and the single-item distress thermometer continues to be the international screening tool of choice. Although debate continues regarding the most appropriate cut-off distress thermometer score to identify clinically distressed patients, review of checked items from the accompanying problem list can pinpoint sources of distress, to inform targeted intervention. An integrated approach should include screening, and if required, assessment/referral and intervention. However, whilst distress screening is associated with some impact on referral, especially its timeliness, delivery of evidence-based treatments to address identified distress may be limited by patients declining help and a lack of support services.

Summary
Although screening for distress in routine care holds promise for reducing costs and enhancing health system efficiency, its implementation across cancer services is variable. Further research is required to evaluate screening implementation and sustainability in routine care, as well as the feasibility of distress screening in long-term cancer survivors who are no longer in regular contact with cancer centres.
Intelligent use of antiepileptic drugs is beneficial to patients
Authors: Cheng Jocelyn Y. , French Jacqueline A. 
Published: December 2017

Purpose of review
To describe the most important issues a clinician must consider whenever selecting and administering antiepileptic drugs (AEDs). There is no available algorithm that identifies how to individualize selection of AEDs. Proper selection and administration can make an enormous difference in both effectiveness and tolerability.

Recent findings
Many principles of AED selection remain unchanged. Selection of AEDs must be based on understanding of epilepsy syndrome and seizure type, comorbidities, risk of adverse events, as well as on patient characteristics such as age and sex. Recently personalized medicine through genetics has become a reality for a subset of patients, to select optimal drugs, and avoid side effects. Selection of AEDs for women can be performed to avoid teratogenic agents, as safer AEDs have been identified. There is evidence supporting use of controlled release AED formulations, whenever available. Whenever selecting an optimal dose, physicians should attend to the principle of ‘start low, go slow.’ ‘Intelligent use’ includes not only appropriate drug selection, but also optimal and individualized dose adjustment. Drug optimization involves appropriate titration, dose schedule, individualization of therapeutic range and rescue planning

Summary
Intelligent drug use, individualized to patient characteristics, can guide management for optimal seizure control.
Correcting values of DNA sequence similarity for errors in sequencing
Authors: Hackmann Timothy J. 
Published: December 2017

AbstractThe similarity between two DNA sequences is one of the most important measures in bioinformatics, but errors introduced during sequencing make values of similarity lower than they should be. Here we develop a method to correct raw sequence similarity for sequencing errors and estimate the original sequence similarity. Our method is simple and consists of a single equation with terms for 1) raw sequence similarity and 2) error rates (e.g., from Phred quality scores). We show the importance of this correction for 16S ribosomal DNA sequences from bacterial communities, where 97% similarity is a frequent threshold for clustering sequences for analysis. At that threshold and typical error rate of 0.2%, correcting for error increases similarity by 0.36 percentage points. This result shows that, if uncorrected, sequencing error would increase similarity thresholds and generate false clusters for analysis. Our method could be used to adjust thresholds for cluster-based analyses. Alternatively, because it requires no clustering to correct sequence similarity, it could usher in a new age of analyzing ribosomal DNA sequences without clustering.
Impaired expected value computations coupled with overreliance on prediction error learning in schizophrenia
Authors: Hernaus D , Gold JM , Waltz JA , Frank MJ 
Published: December 2017

AbstractBackgroundWhile many have emphasized impaired reward prediction error (RPE) signaling in schizophrenia, multiple studies suggest that some decision-making deficits may arise from overreliance on RPE systems together with a compromised ability to represent expected value. Guided by computational frameworks, we formulated and tested two scenarios in which maladaptive representation of expected value should be most evident, thereby delineating conditions that may evoke decision-making impairments in schizophrenia.MethodsIn a modified reinforcement learning paradigm, 42 medicated people with schizophrenia (PSZ) and 36 healthy volunteers learned to select the most frequently rewarded option in a 75-25 pair: once when presented with more deterministic (90–10) and once when presented with more probabilistic (60–40) pairs. Novel and old combinations of choice options were presented in a subsequent transfer phase. Computational modeling was employed to elucidate contributions from RPE systems (“actor-critic”) and expected value (“Q-leaming”).ResultsPSZ showed robust performance impairments with increasing value difference between two competing options, which strongly correlated with decreased contributions from expected value-based (“Q-leaming”) learning. Moreover, a subtle yet consistent contextual choice bias for the “probabilistic” 75 option was present in PSZ, which could be accounted for by a context-dependent RPE in the “actor-critic”.ConclusionsWe provide evidence that decision-making impairments in schizophrenia increase monotonically with demands placed on expected value computations. A contextual choice bias is consistent with overreliance on RPE-based learning, which may signify a deficit secondary to the maladaptive representation of expected value. These results shed new light on conditions under which decisionmaking impairments may arise.
A jump distance based parameter inference scheme for particulate trajectories in biological settings
Authors: Menssen Rebecca , Mani Madhav 
Published: December 2017

ABSTRACTOne type of biological data that needs more quantitative analytical tools is particulate trajectories. This type of data appears in many different contexts and across scales in biology: from the trajectory of bacteria performing chemotaxis to the mobility of ms2 spots within nuclei. Presently, most analyses performed on data of this nature has been limited to mean square displacement (MSD) analyses. While simple, MSD analysis has several pitfalls, including difficulty in selecting between competing models, handling systems with multiple distinct sub-populations, and parameter extraction from limited time-series data. Here, we provide an alternative to MSD analysis using the jump distance distribution (JDD). The JDD resolves several issues: one can select between competing models of motion, have composite models that allow for multiple populations, and have improved error bounds on parameter estimates when data is limited. A major consequence is that you can perform analyses using a fraction of the data required to get similar results using MSD analyses, thereby giving access to a larger range of temporal dynamics when the underlying stochastic process is not stationary. In this paper, we construct and validate a derivation of the JDD for different transport models, explore the dependence on dimensionality of the process, and implement a parameter estimation and model selection scheme. We demonstrate the power of this scheme through an analysis of bacterial chemotaxis data, highlighting the interpretation of results and improvements upon MSD analysis. We expect that our proposed scheme provides quantitative insights into a broad spectrum of biological phenomena requiring analysis of particulate trajectories.
Rap2 and TNIK control Plexin-dependent synaptic tiling in C. elegans
Authors: Chen Xi , Shibata Akihiro C.E. , Hendi Ardalan , Kurashina Mizuki , Fortes Ethan , Weilinger Nicholas L , MacVicar Brian , Murakoshi Hideji , Mizumoto Kota 
Published: December 2017

AbstractDuring development, neurons form synapses with their fate-determined targets. While we begin to elucidate the mechanisms by which extracellular ligand-receptor interactions enhance synapse specificity by inhibiting synaptogenesis, our knowledge about their intracellular mechanisms remains limited. Here we show that Rap2 GTPase (rap-2) and its effector, TNIK (mig-15), act downstream of Plexin (plx-1) to restrict presynaptic assembly and to form tiled synaptic innervation in C. elegans. Both constitutively GTP- and GDP-forms of rap-2 mutants exhibit synaptic tiling defects as plx-1 mutants, suggesting that cycling of the RAP-2 nucleotide state is critical for synapse inhibition. Consistently, RAP-2 activity is locally suppressed by PLX-1. Excessive ectopic synapse formation in mig-15 mutants causes a severe synaptic tiling defect. Conversely, overexpression of mig-15 strongly inhibited synapse formation, suggesting that mig-15 is a negative regulator of synapse formation. These results reveal that subcellular regulation of small GTPase activity by Plexin shapes proper synapse patterning in vivo.
The genomic false shuffle: epigenetic maintenance of topological domains in the rearranged gibbon genome
Authors: Lazar Nathan H. , Nevonen Kimberly A. , O’Connell Brendan , Green Richard E. , Meyer Thomas J. , Okhovat Mariam , Carbone Lucia 
Published: December 2017

AbstractThe relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons. We find that gibbon rearrangements occur at TAD boundaries, independent of the parameters used to identify TADs. This overlap is supported by a remarkable genetic and epigenetic similarity between BOS and TAD boundaries, namely presence of CpG islands and SINE elements, and enrichment in CTCF and H3K4me3 binding. Cross-species comparisons reveal that regions orthologous to BOS also correspond with boundaries of large (400-600kb) TADs in human and other mammalian species. The co-localization of rearrangement breakpoints and TAD boundaries may be due to higher chromatin fragility at these locations and/or increased selective pressure against rearrangements that disrupt TAD integrity. We also examine the small portion of BOS that did not overlap with TAD boundaries and gave rise to novel TADs in the gibbon genome. We postulate that these new TADs generally lack deleterious consequences. Lastly, we show that limited epigenetic homogenization occurs across breakpoints, irrespective of their time of occurrence in the gibbon lineage. Overall, our findings demonstrate remarkable conservation of chromatin interactions and epigenetic landscape in gibbons, in spite of extensive genomic shuffling.