bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multidisciplinary Discharge Timeout Checklist Improves Patient Education and Captures Discharge Process Errors
Authors: Gao Michael C. , Martin Paul B. , Motal Julius , Gingras Laura F. , Chai Christina , Maikoff Megan E. , Sarkisian Alex M. , Rosenthal Nadine , Eiss Brian M. 
Published: March 2018

Objective:
To design and implement a discharge timeout checklist, and to assess its effects on patients' understanding as well as the potential impact on preventable medical errors surrounding hospital discharges to home.

Methods:
Based on the structure successfully used for surgical procedures and using the Model for Improvement framework, we designed a discharge checklist to review and assess patients' understanding of discharge medications, catheters, home care plans, follow-up, symptoms, and who to call with problems after discharge. In parallel, we developed a process of integrating the checklist into the discharge process after routine discharge procedures were completed. We used the checklists to assess patients' level of understanding and need for additional education as well as changes in discharge documentation; we also noted whether good catches of significant errors in the discharge process occurred.

Results:
Over 6 months of study, 190 discharge timeouts out of 429 eligible discharges were completed. Additional education was provided in 53 of 190 discharge timeouts (27.8%), with 62% of this education being related to medications. Twenty-one (11.1%) discharge timeouts resulted in at least one change to the discharge documentation or a good catch.

Conclusions:
A multidisciplinary discharge timeout directly involving the patient can be effective in targeting additional areas for patient education and in potentially reducing preventable adverse events.
Sacroiliitis in Children With Familial Mediterranean Fever
Authors: Aydin Fatma , Özçakar Z. Birsin , Çakar Nilgün , Çelikel Elif , Uncu Nermin , Çelikel Acar Banu , Yalçinkaya Fatoş 
Published: March 2018

Background/Objective
Familial Mediterranean fever (FMF) is an autosomal recessive disease, characterized by recurrent, self-limited attacks of fever with serositis. Various diseases were reported to be associated with FMF. The aim of this study was to investigate the frequency and characteristics of sacroiliitis in children with FMF.

Methods
Files of FMF patients who had been seen in 2 reference hospitals in Ankara were retrospectively evaluated. Patients with FMF and concomitant sacroiliitis were included to the study. All patients had magnetic resonance imaging evidence of sacroiliitis.

Results
Among 650 FMF patients, 17 (11 females, 6 males; mean age, 13.32 ± 4.24 years) (2.6%) of them were found to have sacroiliitis. Familial Mediterranean fever diagnosis was done prior to sacroiliitis diagnosis in 11 patients (65%) and concurrently or afterward in 6 patients (35%). Ten patients had isolated sacroiliitis, and 7 had associated diseases (5 enthesitis-related arthritis, 1 psoriatic arthritis, and 1 ulcerative colitis). Arthritis (59%), arthralgia (77%), leg pain (71%), heel pain (41%), and enthesitis (29%) were common complaints. Sacroiliac tenderness was detected in 77%, and M694V mutation in almost 90% of the patients. All patients received colchicine therapy. Additionally, 14 of them were treated with nonsteroidal anti-inflammatory drugs, 10 were on sulfasalazine treatment, and 7 of them were on biological agents.

Conclusions
Sacroiliitis can be seen in patients with FMF during childhood, and M694V mutation seems to be a susceptibility factor for its development. Inflammatory low-back pain and leg and heel pain could suggest sacroiliitis.
Quantitative Assessment of Thyroid, Submandibular, and Parotid Glands Elasticity With Shear-Wave Elastography in Children
Authors: Arioz Habibi Hatice , Memis Durmaz Emine Sebnem , Qarayeva Vusale , Kandemirli Sedat Giray , Kalyoncu Ucar Ayse , Aslan Mine , Apaydin Gozde , Kurugoglu Sebuh , Adaletli Ibrahim 
Published: March 2018

Abstract
Tissue elasticity is becoming a more commonly used parameter in evaluation of parenchyma in inflammatory diseases. Considering the changes in the thyroid and salivary glands with adolescence, determination of mean elasticity ranges with a function of age is necessary to apply ultrasound elastography more widely in the pediatric population.
The thyroid, submandibular, and parotid glands of 127 healthy volunteers (66 males, 61 females; mean age = 10.3 ± 3.9 years; range = 3–17 years) were evaluated with shear-wave elastography.
The mean elasticity values for the thyroid, submandibular, and parotid glands were 14.6 ± 3.3, 11.8 ± 2.2, and 11.8 ± 2.6 kPa, respectively. There was a significant positive correlation between age and elasticity of the thyroid, submandibular, and parotid glands. There was a significant correlation between age and elasticity value of the thyroid gland adjusted for weight and height.
This study provided the baseline quantitative elasticity measures of thyroid, submandibular, and parotid glands, which would be a reference for upcoming studies. In addition, an increase in elasticity value in thyroid gland as a function of age independent of change in weight and height was demonstrated.
Systematic analysis of mouse genome reveals distinct evolutionary and functional properties among circadian and ultradian genes
Authors: Castellana Stefano , Mazza Tommaso , Kappler Martin , Capocefalo Daniele , Genov Nikolai , Biagini Tommaso , Fusilli Caterina , Scholkmann Felix , Relógio Angela , Hogenesch John B. , Mazzoccoli Gianluigi 
Published: March 2018

ABSTRACTIn living organisms, biological clocks regulate 24 h (circadian) molecular, physiological, and behavioral rhythms to maintain homeostasis and synchrony with predictable environmental changes. Harmonics of these circadian rhythms having periods of 8 hours and 12 hours (ultradian) have been documented in several species. In mouse liver, harmonics of the 24-hour period of gene transcription hallmarked genes oscillating with a frequency two or three times faster than the circadian circuitry. Many of these harmonic transcripts enriched pathways regulating responses to environmental stress and coinciding preferentially with subjective dawn and dusk. We hypothesized that these stress anticipatory genes would be more evolutionarily conserved than background circadian and non-circadian genes. To investigate this issue, we performed broad computational analyses of genes/proteins oscillating at different frequency ranges across several species and showed that ultradian genes/proteins, especially those oscillating with a 12-hour periodicity, are more likely to be of ancient origin and essential in mice. In summary, our results show that genes with ultradian transcriptional patterns are more likely to be phylogenetically conserved and associated with the primeval and inevitable dawn/dusk transitions.
Oscillatory dynamics of perceptual to conceptual transformations in the ventral visual pathway
Authors: Clarke Alex , Devereux Barry J. , Tyler Lorraine K. 
Published: March 2018

AbstractObject recognition requires dynamic transformations of low-level visual inputs to complex semantic representations. While this process depends on the ventral visual pathway (VVP), we lack an incremental account from low-level inputs to semantic representations, and the mechanistic details of these dynamics. Here we combine computational models of vision with semantics, and test the output of the incremental model against patterns of neural oscillations recorded with MEG in humans. Representational Similarity Analysis showed visual information was represented in alpha activity throughout the VVP, and semantic information was represented in theta activity. Furthermore, informational connectivity showed visual information travels through feedforward connections, while visual information is transformed into semantic representations through feedforward and feedback activity, centered on the anterior temporal lobe. Our research highlights that the complex transformations between visual and semantic information is driven by feedforward and recurrent dynamics resulting in object-specific semantics.
Simulations and Electrostatic Analysis Suggest an Active Role for DNA Conformational Changes During Genome Packaging by Bacteriophages
Authors: Sharp Kim A. , Lu Xiang-Jun , Cingolani Gino , Harvey Stephen C. 
Published: March 2018

AbstractMotors that move DNA, or that move along DNA, play essential roles in DNA replication, transcription, recombination, and chromosome segregation. The mechanisms by which these DNA translocases operate remain largely unknown. Some double-stranded DNA (dsDNA) viruses use an ATP-dependent motor to drive DNA into preformed capsids. These include several human pathogens, as well as dsDNA bacteriophages – viruses that infect bacteria. We previously proposed that DNA is not a passive substrate of bacteriophage packaging motors but is, instead, an active component of the machinery. Computational studies on dsDNA in the channel of viral portal proteins reported here reveal DNA conformational changes consistent with that hypothesis. dsDNA becomes longer (“stretched”) in regions of high negative electrostatic potential, and shorter (“scrunched”) in regions of high positive potential. These results suggest a mechanism that couples the energy released by ATP hydrolysis to DNA translocation: The chemical cycle of ATP binding, hydrolysis and product release drives a cycle of protein conformational changes. This produces changes in the electrostatic potential in the channel through the portal, and these drive cyclic changes in the length of dsDNA. The DNA motions are captured by a coordinated protein-DNA grip-and-release cycle to produce DNA translocation. In short, the ATPase, portal and dsDNA work synergistically to promote genome packaging.
The Healthy Pregnancy Research Program: Transforming Pregnancy Research Through a ResearchKit App
Authors: Radin Jennifer M. , Steinhubl Steven R. , Su Andrew I. , Bhargava Hansa , Greenberg Benjamin , Bot Brian M. , Doerr Megan , Topol Eric J. 
Published: March 2018

Although maternal morbidity and mortality in the U.S. is among the worst of developed countries, pregnant women have been under-represented in research studies, resulting in deficiencies in evidence-based guidance for treatment. There are over two billion smartphone users worldwide, enabling researchers to easily and cheaply conduct extremely large-scale research studies through smartphone apps, especially among pregnant women in whom app use is exceptionally high, predominantly as an information conduit. We developed the first pregnancy research app that is embedded within an existing, popular pregnancy app for self-management and education of expectant mothers. Through the large-scale and simplified collection of survey and sensor generated data via the app, we aim to improve our understanding of factors that promote a healthy pregnancy for both the mother and developing fetus. From the launch of this cohort study on March 16, 2017 through December 17, 2017, we have enrolled 2,058 pregnant women from all 50 states. Our study population is diverse geographically and demographically, and fairly representative of U.S. population averages. We have collected 14,045 individual surveys and 11,669 days of sleep, activity, blood pressure and heart rate measurements during this time. On average, women stayed engaged in the study for 59 days and 45 percent who reached their due date filled out the final outcome survey. During the first nine months, we demonstrated the potential for a smartphone-based research platform to capture an ever-expanding array of longitudinal, objective and subjective participant-generated data from a continuously growing and diverse population of pregnant women.FundingSupported in part by the National Institutes of Health (NIH)/National Center for Advancing Translational Sciences grant UL1TR001114 and a grant from the Qualcomm Foundation.
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome
Authors: Sundaramoorthy Ramasubramanian , Hughes Amanda L. , El-Mkami Hassane , Norman David , Owen-Hughes Tom 
Published: March 2018

AbstractATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here we present structures of the yeast Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.
Subnetwork-based prognostic biomarkers exhibit performance and robustness superior to gene-based biomarkers in breast cancer
Authors: Grzadkowski Michal R. , Haider Syed , Sendorek Dorota H. , Boutros Paul C. 
Published: March 2018

AbstractBackgroundEffective classification of cancer patients into groups with differential survival remains an important and unsolved challenge. Biomarkers have been developed based on mRNA abundance data, but their replicability and clinical utility is modest. Integrating functional information, such as pathway data, has been suggested to improve biomarker performance. To date, however, the advantages of subnetwork-based biomarkers have not been quantified.ResultsWe deeply sampled the population of prognostic gene-based and subnetwork-based biomarkers in a breast cancer meta-dataset of 4,960 patients. Analysing the performance and robustness of 22,000,000 gene biomarkers and 6,250,000 subnetwork biomarkers across twenty different training:testing cohort partitions of the meta-dataset revealed that subnetwork biomarkers exhibit superior overall performance and higher concordance across partitions. We find evidence of an upper bound for optimal biomarker size of ∼200 genes or ∼100 subnetworks. Additionally, with both biomarker feature types, larger biomarkers tend to show less consistency in performance across partitions, suggestive of over-fitting. Finally, an evaluation of varying training cohort sizes quantifies the effects of training cohort size.ConclusionsMany groups are developing techniques for exploiting network-based representations of biological pathways to characterize cancer and other diseases. By considering the distribution of gene- and subnetwork-based biomarkers, we show that pathway data improves performance and replicability, and that smaller biomarkers are more robust across patient cohorts. These insights may facilitate development of clinically useful biomarkers.
Probing the Acyl Carrier Protein-Enzyme Interactions within Terminal Alkyne Biosynthetic Machinery
Authors: Su Michael , Zhu Xuejun , Zhang Wenjun 
Published: March 2018

AbstractThe alkyne functionality has attracted much interest due to its diverse chemical and biological applications. We recently elucidated an acyl carrier protein (ACP)-dependent alkyne biosynthetic pathway, however, little is known about ACP interactions with the alkyne biosynthetic enzymes, an acyl-ACP ligase (JamA) and a membrane-bound bi-functional desaturase/acetylenase (JamB). Here, we showed that JamB has a more stringent interaction with ACP than JamA. In addition, site directed mutagenesis of a non-cognate ACP significantly improved its compatibility with JamB, suggesting a possible electrostatic interaction at the ACP-JamB interface. Finally, error-prone PCR and screening of a second non-cognate ACP identified hot spots on the ACP that are important for interacting with JamB and yielded mutants which were better recognized by JamB. Our data thus not only provide insights into the ACP interactions in alkyne biosynthesis, but it also potentially aids in future combinatorial biosynthesis of alkyne-tagged metabolites for chemical and biological applications.Topical HeadingBiomolecular Engineering, Bioengineering, Biochemicals, Biofuels, and Food
Optimizing bioreactor growth of the smallest eukaryote
Authors: Smallwood Chuck R. , Hill Eric A. , Chrisler William , Brookreson Jory , Evans James E. 
Published: March 2018

AbstractPhotosynthetic organisms are adept at circumventing nutrient deprivation. Microalgae in particular present novel adaptations to nutrient and light starvation since they can scavenge external and internal nutrient pools to redistribute energy resources for survival. In this report, a turbidostatic photobioreactor was used to characterize environmental conditions and nutrient requirements for cultures of the smallest free-living eukaryote Ostreococcus tauri. Optimized growth conditions were identified that enable 4-times faster phototrophic growth-rates while increasing total biomass 10-fold. By achieving phototrophic doubling times shorter than 6 hours, these results highlight the potential of this smallest eukaryote for future industrial bioproduct applications.
Automated classification of synaptic vesicles in electron tomograms ofC. elegansusing machine learning
Authors: Kaltdorf Kristin Verena , Theiss Maria , Markert Sebastian Matthias , Zhen Mei , Dandekar Thomas , Stigloher Christian , Kollmannsberger Philip 
Published: March 2018

1.AbstractSynaptic vesicles (SVs) are a key component of neuronal signaling and fulfil different roles depending on their composition. In electron micrograms of neurites, two types of vesicles can be distinguished by morphological criteria, the classical “clear core” vesicles (CCV) and the typically larger “dense core” vesicles (DCV), with differences in electron density due to their diverse cargos. Compared to CCVs, the precise function of DCVs is less defined. DCVs are known to store neuropeptides, which function as neuronal messengers and modulators [1]. InC. elegans, they play a role in locomotion, dauer formation, egg-laying, and mechano- and chemosensation [2]. Another type of DCVs, also referred to as granulated vesicles, are known to transport Bassoon, Piccolo and further constituents of the presynaptic density in the center of the active zone (AZ), and therefore are important for synaptogenesis [3].To better understand the role of different types of SVs, we present here a new automated approach to classify vesicles. We combine machine learning with an extension of our previously developed vesicle segmentation workflow, the ImageJ macro 3D ART VeSElecT. With that we reliably distinguish CCVs and DCVs in electron tomograms ofC. elegansNMJs using image-based features. Analysis of the underlying ground truth data shows an increased fraction of DCVs as well as a higher mean distance between DCVs and AZs in dauer larvae compared to young adult hermaphrodites. Our machine learning based tools are adaptable and can be applied to study properties of different synaptic vesicle pools in electron tomograms of diverse model organisms.2.Author summaryVesicles are important components of the cell, and synaptic vesicles are central for neuronal signaling. Two types of synaptic vesicles can be distinguished by electron microscopy: the classical “clear core” vesicles (CCVs) and the typically larger “dense core” vesicles (DCVs). The distinct appearance of vesicles is caused by their different cargos. To rapidly distinguish between both vesicle types, we present here a new automated approach to classify vesicles in electron tomograms. We combine machine learning with an extension of our previously developed vesicle segmentation workflow, an ImageJ macro, to reliably distinguish CCVs and DCVs using specific image-based features. The approach was trained and validated using data-sets that were hand curated by microscopy experts. Our technique can be transferred to more extensive comparisons in both stages as well as to other neurobiology questions regarding synaptic vesicles.
Lymphocyte activation gene 3 (Lag3) expression is increased in prion infections but does not modify disease progression
Authors: Liu Yingjun , Sorce Silvia , Nuvolone Mario , Domange Julie , Aguzzi Adriano 
Published: March 2018

AbstractPrion diseases, Alzheimer’s disease and Parkinson’s disease (PD) are fatal degenerative disorders that share common neuropathological and biochemical features, including the aggregation of pathological protein conformers. Lymphocyte activation gene 3 (Lag3, also known as CD223) is a member of the immunoglobulin superfamily of receptors expressed on peripheral immune cells, microglia and neurons, which serves as a receptor for α-synuclein aggregates in PD. Here we examined the possible role of Lag3 in the pathogenesis of prion diseases. Through quantitative real-time PCR and RNA-sequencing, we found that the expression levels of Lag3 were relatively low in the adult mouse brains, yet its expression was increased after prion infection. However, we failed finding significant differences regarding the incubation time, PrPSc load, neurodegeneration, astrocyte and microglia reactions and inflammatory gene expression between the Lag3 knockout mice and wild-type littermate controls after prion infection. We conclude that loss of Lag3 has no significant influence on prion disease pathogenesis. Considering that Lag3 is an immune checkpoint receptor, our results suggest that immune checkpoint inhibition (an increasingly prevalent therapeutic modality against many types of cancer) might not exert positive or negative effects on the progression of prion diseases.