bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient and Treatment Characteristics by Infecting Organism in Cerebrospinal Fluid Shunt Infection
Authors: Simon Tamara D , Kronman Matthew P , Whitlock Kathryn B , Browd Samuel R , Holubkov Richard , Kestle John R W , Kulkarni Abhaya V , Langley Marcie , Limbrick David D , Luerssen Thomas G , Oakes Jerry , Riva-Cambrin Jay , Rozzelle Curtis , Shannon Chevis N , Tamber Mandeep , Wellons III John C , Whitehead William E , Mayer-Hamblett Nicole ,   Hydrocephalus Clinical Research Network
Published: April 2018

Abstract

Background
Previous studies of cerebrospinal fluid (CSF) shunt infection treatment have been limited in size and unable to compare patient and treatment characteristics by infecting organism. Our objective was to describe variation in patient and treatment characteristics for children with first CSF shunt infection, stratified by infecting organism subgroups outlined in the 2017 Infectious Disease Society of America’s (IDSA) guidelines.

Methods
We studied a prospective cohort of children <18 years of age undergoing treatment for first CSF shunt infection at one of 7 Hydrocephalus Clinical Research Network hospitals from April 2008 to December 2012. Differences between infecting organism subgroups were described using univariate analyses and Fisher’s exact tests.

Results
There were 145 children whose infections were diagnosed by CSF culture and addressed by IDSA guidelines, including 47 with Staphylococcus aureus, 52 with coagulase-negative Staphylococcus, 37 with Gram-negative bacilli, and 9 with Propionibacterium acnes. No differences in many patient and treatment characteristics were seen between infecting organism subgroups, including age at initial shunt, gender, race, insurance, indication for shunt, gastrostomy, tracheostomy, ultrasound, and/or endoscope use at all surgeries before infection, or numbers of revisions before infection. A larger proportion of infections were caused by Gram-negative bacilli when antibiotic-impregnated catheters were used at initial shunt placement (12 of 23, 52%) and/or subsequent revisions (11 of 23, 48%) compared with all other infections (9 of 68 [13%] and 13 of 68 [19%], respectively). No differences in reinfection were observed between infecting organism subgroups.

Conclusions
The organism profile encountered at infection differs when antibiotic-impregnated catheters are used, with a higher proportion of Gram-negative bacilli. This warrants further investigation given increasing adoption of antibiotic-impregnated catheters.
Persistent Metabolic Disturbance in the Perihemorrhagic Zone Despite a Normalized Cerebral Blood Flow Following Surgery for Intracerebral Hemorrhage
Authors: Tobieson Lovisa , Rossitti Sandro , Zsigmond Peter , Hillman Jan , Marklund Niklas 
Published: April 2018

Abstract

BACKGROUND
We hypothesized that reduced cerebral blood flow (CBF) and/or energy metabolic disturbances exist in the tissue surrounding a surgically evacuated intracerebral hemorrhage (ICH). If present, such CBF and/or metabolic impairments may contribute to ongoing tissue injury and the modest clinical efficacy of ICH surgery.

OBJECTIVE
To conduct an observational study of CBF and the energy metabolic state in the perihemorrhagic zone (PHZ) tissue and in seemingly normal cortex (SNX) by microdialysis (MD) following surgical ICH evacuation.

METHODS
We evaluated 12 patients (median age 64; range 26-71 yr) for changes in CBF and energy metabolism following surgical ICH evacuation using Xenon-enhanced computed tomography (n = 10) or computed tomography perfusion (n = 2) for CBF and dual MD catheters, placed in the PHZ and the SNX at ICH surgery.

RESULTS
CBF was evaluated at a mean of 21 and 58 h postsurgery. In the hemisphere ipsilateral to the ICH, CBF improved between the investigations (36.6 ± 20 vs 40.6 ± 20 mL/100 g/min; P < .05). In total, 1026 MD samples were analyzed for energy metabolic alterations including glucose and the lactate/pyruvate ratio (LPR). The LPR was persistently elevated in the PHZ compared to the SNX region (P < .05). LPR elevations in the PHZ were predominately type II (pyruvate normal-high; indicating mitochondrial dysfunction) as opposed to type I (pyruvate low; indicating ischemia) at 4 to 48 h (70% vs 30%) and at 49 to 84 h (79% vs 21%; P < .05) postsurgery.

CONCLUSION
Despite normalization of CBF following ICH evacuation, an energy metabolic disturbance suggestive of mitochondrial dysfunction persists in the perihemorrhagic zone.
C5-C6 Cervical Spinal Cord Cavernous Malformation Microsurgical Resection: 2-Dimensional Operative Video
Authors: Enriquez-Marulanda Alejandro , Alturki Abdulrahman Y , Kicielinski Kimberly , Thomas Ajith J , Ogilvy Christopher S 
Published: April 2018

Abstract
We describe the case of a previously healthy 44-yr-old female patient presenting with a sudden onset of numbness, paresthesias, and decreased sensation in her lower limbs. Physical examination revealed a decreased sensation to vibration and light touch in her lower extremities, primarily in the left limb. Impaired proprioception was also evident primarily in the left toe. Full strength with 2+ reflexes was observed in all extremities. Magnetic resonance imaging demonstrated an exophytic lesion in the posterior aspect of the cervical spinal cord at the C5-C6 level, with a hemosiderin halo, consistent with a cavernous malformation. Given the evidence of past hemorrhage and the location of the lesion, microsurgical intervention was indicated. A midline cervical C5-C6 laminectomy under neurophysiologic monitoring was performed, and complete resection of the lesion was achieved with mild improvement of the sensitive symptoms and no evidence of new motor deficits. Any microsurgical resection of a cervical spinal cord lesion can be technically difficult and adequate patient selection with evaluation of the accessibility to the lesion is key.
1
Surgical resection of cavernous malformations in selected patients eliminates the risk of future hemorrhage and may achieve satisfactory outcomes comparable to patients who undergo conservative management.
2
In the following video illustration, we narrate this operative case, and highlight the nuances of this approach. Patient consent was obtained for the submission of the video to this journal.
Microsurgical Resection of Medulla Oblongata Hemangioblastoma: 2-Dimensional Operative Video
Authors: Pojskić Mirza , Arnautović Kenan I 
Published: April 2018

Abstract
This video demonstrates the microsurgical resection of brainstem hemangioblastoma. The patient is a 32-yr-old woman with Von Hippel Lindau syndrome who presented with quadriparesis and inability to swallow. Magnetic resonance imaging (MRI) of the neuroaxis revealed a brainstem cystic lesion with contrast-enhancing tumor nodule right along the posterior aspect of the lower part of medulla oblongata. The surgery was performed in the prone position with suboccipital craniectomy and partial C1 posterior arch removal. The aim of the surgery was to remove the tumor nodule.
1-12

The tumor was separated from the right dorsal nerve roots, and then progressively dissected with coagulation of arterial feeders and draining vein and division of the pia circumferentially. Postoperative MRI revealed complete resection. The patient completely recovered from her quadriparesis and difficulty swallowing.
Justification
Authors: Lane Anthony N. S. 
Published: April 2018

Abstract
The last seventy years have seen many dialogues between Roman Catholics and Protestants (mainly, but not exclusively, Lutherans) on the doctrine of justification. This article surveys eight of these dialogues, their culmination in the 1999 Joint Declaration on the Doctrine of Justification, and the impact of this last document. Also considered are nine doctrinal issues raised by the dialogues: justification as the chief article of faith; human incapacity; the definition of justification; why we are accounted righteous; remaining sin in the Christian; faith alone; lapse and restoration; merit and reward; and assurance of salvation. The conclusion is that considerable progress has been made in clearing up misunderstandings and that the two sides have drawn together. It remains to be seen how solid and lasting is this achievement.
Method in Ecumenism
Authors: Abraham William J. 
Published: April 2018

Abstract
Method can mean either the steps taken to achieve church unity or the principles appropriate to the study of ecumenism. Most ecumenists have sought organic unity; they have hoped that agreement on the issue of authority would further this end. This turned out to be impossible, and recently there has been a shift from epistemology to pneumatology. This shift allows for a third option beyond the claims of Catholicism and Orthodoxy, on the one hand, and Magisterial Protestantism, on the other, as regards ecclesial continuity. We can think of the creation of the church as the reinstantiation of primitive Christianity in the wake of Pentecost. Messianic Judaism provides telling warrant for pursuing this option. This shift also provides fresh hope for ecumenism by moving beyond conciliar conversations about doctrine, and calling instead for gift-sharing—that is, the realistic sharing of what we actually think are gifts for the common good.
Orthodox
Authors: Grdzelidze Tamara 
Published: April 2018

Abstract
This chapter aims to clarify the role of the Orthodox Church in the ecumenical movement. Historically present in the movement from the beginning, and theologically challenging the understanding of unity in the movement right up to the present day, the Orthodox tradition has shown ambivalence in relation to other Christians and especially with regard to their claims to ecclesiality. An ecclesiological challenge has become the most remarkable characteristic of the Orthodox in the inter-Christian context. Nevertheless, the Orthodox tradition has demonstrated the capacity to reach agreements through dialogue in spite of difficulties associated with other Christian traditions such as the relativization of the inherited tradition. Among achievements on the way to Christian unity is rapprochement between the two Orthodox families, Eastern and Oriental. Many questions remain to be answered within the Orthodox Church in order to bring new breath into inter-Christian dialogue.
Targeted Reactivation of FMR1 Transcription in Fragile X Syndrome Embryonic Stem Cells
Authors: Haenfler Jill M. , Skariah Geena , Rodriguez Caitlin M. , Rocha Andre Monteiro da , Parent Jack M. , Smith Gary D. , Todd Peter K. 
Published: April 2018

ABSTRACTFragile X Syndrome (FXS) is the most common inherited cause of intellectual disability and autism. It results from expansion of a CGG nucleotide repeat in the 5’ untranslated region of FMR1. Large expansions elicit repeat and promoter hyper-methylation, heterochromatin formation, FMR1 transcriptional silencing, and loss of the Fragile X protein, FMRP. Efforts aimed at correcting the sequelae resultant from FMRP loss have thus far proven insufficient, perhaps because of FMRP’s pleiotropic functions. As the repeats do not disrupt the FMRP coding sequence, reactivation of endogenous FMR1 gene expression could correct the proximal event in FXS pathogenesis. Here we utilize the CRISPR/dCAS9 system to selectively re-activate transcription from the silenced FMR1 locus. Fusion of the transcriptional activator VP192 to dCAS9 robustly enhances FMR1 transcription and increases FMRP levels when targeted directly to the CGG repeat in human cells. Using a previously uncharacterized FXS human embryonic stem cell (hESC) line which acquires transcriptional silencing with serial passaging, we achieved locus-specific transcriptional re-activation of FMR1 mRNA expression despite promoter and repeat methylation. These studies demonstrate that FMR1 mRNA expression can be selectively reactivated in human patient cells, creating a pathway forward for therapeutic development in Fragile X Syndrome.
A Novel Household Water Insecurity Scale: Procedures and Psychometric Analysis among Postpartum Women in Western Kenya
Authors: Boateng Godfred O. , Collins Shalean M. , Mbullo Patrick , Wekesa Pauline , Onono Maricianah , Neilands Torsten B. , Young Sera L. 
Published: April 2018

AbstractOur ability to measure household-level food insecurity has revealed its critical role in a range of physical, psychosocial, and health outcomes. Currently, there is no analogous, standardized instrument for quantifying household-level water insecurity, which prevents us from understanding both its prevalence and consequences. Therefore, our objectives were to develop and validate a household water insecurity scale appropriate for use in our cohort in western Kenya. We used a range of qualitative techniques to develop a preliminary set of 29 household water insecurity questions, and administered those questions at 15 and 18 months postpartum, concurrent with a suite of other survey modules. These data were complemented by data on quantity of water used and stored, and microbiological quality. Inter-item and item-total correlations were performed to reduce scale items to 20. Exploratory factor and parallel analyses were used to determine the latent factor structure; a unidimensional scale was hypothesized and tested using confirmatory factor and bifactor analyses, along with multiple statistical fit indices. Reliability was assessed using Cronbach’s alpha and the coefficient of stability, which produced a coefficient alpha of 0.97 at 15 and 18 months postpartum and a coefficient of stability of 0.62. Predictive, convergent and discriminant validity of the final household water insecurity scale were supported, based on relationships with food insecurity, perceived stress, per capita household water use, and time and money spent acquiring water. The resultant scale is a valid and reliable instrument. It can be used in this setting to test a range of hypotheses about the role of household water insecurity in numerous physical and psychosocial health outcomes, to identify the households most vulnerable to water insecurity, and to evaluate the effects of water-related interventions. To extend its applicability, we encourage efforts to develop a cross-culturally valid scale using robust qualitative and quantitative techniques.
A multiplexed homology-directed DNA repair assay reveals the impact of ~1,700 BRCA1 variants on protein function
Authors: Starita Lea M. , Islam Muhtadi M. , Banerjee Tapahsama , Adamovich Aleksandra I. , Gullingsrud Justin , Fields Stanley , Shendure Jay , Parvin Jeffrey D. 
Published: April 2018

AbstractLoss-of-function mutations in BRCA1 confer a predisposition to breast and ovarian cancer. Genetic testing for mutations in the BRCA1 gene frequently reveals a missense variant for which the impact on the molecular function of the BRCA1 protein is unknown. Functional BRCA1 is required for homology directed repair (HDR) of double-strand DNA breaks, a key activity for maintaining genome integrity and tumor suppression. Here we describe a multiplex HDR reporter assay to simultaneously measure the effect of hundreds of variants of BRCA1 on its role in DNA repair. Using this assay, we measured the effects of ~1,700 amino acid substitutions in the first 302 residues of BRCA1. Benchmarking these results against variants with known effects, we demonstrate accurate discrimination of loss-of-function versus benign variants. We anticipate that this assay can be used to functionally characterize BRCA1 missense variants at scale, even before the variants are observed in results from genetic testing.
Robustness of bristle number to temperature and genetic background varies with bristle type and is regulated by miR-9a
Authors: Matamoro-Vidal A. , Tully T. , Courtier-Orgogozo V. 
Published: April 2018

AbstractRobustness is the invariance of a given phenotype when faced with a given incoming genetic or environmental variation. Such essential property is being studied in a wide diversity of traits in many organisms but it is difficult to compare the results obtained on the robustness of different traits with each other given the differences that exist between traits in the way they are measured, in their genetic architecture and development. In this study, we assessed robustness of bristle number to incoming genetic and environmental variation for eight bristle types in the fruit fly Drosophila melanogaster, allowing for a straightforward comparison of the robustness observed between bristle types. We measured the response of bristle number mean and variance to changes in temperature and in the number of copies of two genes (scute and miR-9a) known to be involved in bristle development. Many combinations between the three factors were tested, thus allowing to test for the effect of each factor in different contexts for the two other factors – to which we refer herein as different backgrounds. We have found different responses between bristle types, suggesting that they present different levels of robustness to the factors tested. In addition, we have found that temperature and miR-9a affect more generally the variance of the traits rather than their means, thus fulfilling a criteria usually admitted to identify robustness factors.
The Fair Proportion is a Shapley Value on phylogenetic networks too
Authors: Coronado Tomás M. , Riera Gabriel , Rosselló Francesc 
Published: April 2018

AbstractThe Fair Proportion of a species in a phylogenetic tree is a very simple measure that has been used to assess its value relative to the overall phylogenetic diversity represented by the tree. It has recently been proved by Fuchs and Jin to be equal to the Shapley Value of the coallitional game that sends each subset of species to its rooted Phylogenetic Diversity in the tree. We prove in this paper that this result extends to the natural translations of the Fair Proportion and the rooted Phylogenetic Diversity to rooted phylogenetic networks. We also generalize to rooted phylogenetic networks the expression for the Shapley Value of the unrooted Phylogenetic Diversity game on a phylogenetic tree established by Haake, Kashiwada and Su.
Loss of YAP/TAZ impaired the proliferation and differentiation ability of neural progenitor cells
Authors: Kong Shanshan 
Published: April 2018

AbstractYAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif) are downstream effectors of the Hippo pathway, they activate the expression of transcriptional targets that promote cell growth, cell proliferation, and prevent apoptosis. Here I examined the function of YAP/TAZ in mouse neocortex development through conditional deletion of Yap and Taz by Emx1-Cre. Loss of YAP/TAZ cause the hydrocephalus after birth, leads to aberrant development and dilated ventricle in adult stage, this phenotype can be detected as early as P0. YAP/TAZ are expressed in Sox2+ neural progenitor cells, when YAP/TAZ are deleted, the neuroepithelial cell junctions are disrupted; the numbers of Sox2+ cell and Tbr2+ cell are reduced and the ratio of tbr2/Sox2 is also reduced at E15.5. Results of cell cycle analyzing experiments display YAP/TAZ deletion increased the cell cycle exit. The improperly increased expression of Tuj1+ in progenitor cells in the YAP/TAZ deleted cortex indicates the premature of Sox2+ progenitor cells. Together, our results reveal that YAP/TAZ deletion changed the polarity of neuroepithelial cells, and increased the cell cycle exit, reduced the differentiation of Sox2+ cells into Tbr2+ cells through promoting the premature of Tuj1+ cells. These results define the functions of YAP/TAZ in keeping the cell polarity neural progenitors and ensuring their proliferation and differentiation, and also reveal the roles of YAP/TAZ in developing cortex.
Network-based assessment of the vulnerability of Italian regions to bovine brucellosis
Authors: Darbon Alexandre , Valdano Eugenio , Poletto Chiara , Giovannini Armando , Savini Lara , Candeloro Luca , Colizza Vittoria 
Published: April 2018

AbstractThe endemic circulation of bovine brucellosis in cattle herds has a markedly negative impact on economy, due to decreased fertility, increased abortion rates, reduced milk and meat production. It also poses a direct threat to human health. In Italy, despite the long lasting efforts and the considerable economic investment, complete eradication of this disease still eludes the southern regions, as opposed to the northern regions that are disease-free. Here we introduced a novel quantitative network-based approach able to fully exploit the highly resolved databases of cattle trade movements and outbreak reports to yield estimates of the vulnerability of a cattle market to brucellosis. Tested on the affected regions, the introduced vulnerability indicator was shown to be accurate in predicting the number of bovine brucellosis outbreaks, thus confirming the suitability of our tool for epidemic risk assessment. We evaluated the dependence of regional vulnerability to brucellosis on a set of factors including premises spatial distribution, trading patterns, farming practices, herd market value, compliance to outbreak regulations, and exploring different epidemiological conditions. Animal trade movements were identified as a major route for brucellosis spread between farms, with an additional potential risk attributed to the use of shared pastures. By comparing the vulnerability of disease-free regions in the north to affected regions in the south, we found that more intense trade and higher market value of the cattle sector in the north, likely inducing more efficient biosafety measures, together with poor compliance to trade restrictions following outbreaks in the south were key factors explaining the diverse success in eradicating brucellosis. Our modeling scheme is both synthetic and effective in gauging regional vulnerability to brucellosis persistence. Its general formulation makes it adaptable to other diseases and host species, providing a useful tool for veterinary epidemiology and policy assessment.
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs
Authors: Shi Junchao , Ko Eun-A , Sanders Kenton M. , Chen Qi , Zhou Tong 
Published: April 2018

AbstractHigh-throughput RNA-seq has revolutionized the process of small RNA (sRNA) discovery, leading to a rapid expansion of sRNA categories. In addition to the previously well-characterized sRNAs such as microRNAs (miRNAs), Piwi-interacting RNA (piRNAs), and small nucleolar RNA (snoRNAs), recent emerging studies have spotlighted on tRNA-derived sRNAs (tsRNAs) and rRNA-derived sRNAs (rsRNAs) as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline optimized for rRNA- and tRNA- derived sRNAs (SPORTS1.0). SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users’ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate which is consistent with their highly modified nature. SPORTS1.0 is an open-source software and can be publically accessed at https://github.com/junchaoshi/sports1.0.