bluuebunny/crossref_metadata_2025_split huggingface dataset:
Head to Head Clinical Comparison of Two Confrontation Naming Measures in Spanish Speaking People with Epilepsy
Authors: Smith J A D , Bailey K C , Chavarria V 
Published: August 2019

Abstract

Objective
The incidence of epilepsy in Hispanic, adult Spanish-speaking people with epilepsy (PWE) residing in the United States is nearly twice that of non-Hispanic US adults. Neuropsychologists are asked to discern if test findings reveal lateralization or localization regarding known epileptiform activity. Given the high stakes nature of surgical procedures (e.g., partial temporal lobectomy), it is imperative that intervention approaches are guided by valid and reliable neuropsychological measures. Identifying these measures is especially challenging in this underserved group, where test options are limited. The purpose of the present investigation was to compare the clinical utility of two confrontation naming measures, the Pontón-Satz Modified Boston Naming Test (MBNT) and the Vocabulario Sobre Dibujos subtest from the Batería III Woodcock-Muñoz.

Participants and Method
Seventy-one Hispanic, primarily immigrant, Spanish-speaking PWE underwent neuropsychological assessment which included both confrontation naming measures. Seizure lateralization was agreed upon by consensus via an interdisciplinary epilepsy conference (left hemisphere [LH] = 35, right hemisphere [RH] = 36).

Results
Analyses used education adjusted standard scores. Independent t-tests revealed that, as expected, LH Vocabulario Sobre Dibujos scores were significantly lower than RH, t(69) = 2.0, p = 0.049. Notably, LH and RH MBNT scores did not significantly differ. ROC analyses of Vocabulario Sobre Dibujos yielded adequate classification accuracy (AUC = 0.639, p &lt; .05; Sensitivity = 71%; Specificity = 89%); however, the MBNT was not significant (AUC = 0.594, p = .17).

Conclusions
Education adjusted standard scores for Vocabulario Sobre Dibujos outperformed the MBNT for detecting language impairment as well as discriminating between seizure laterality; thus, suggesting a need for further investigation and, possibly, evidence-based change in clinical neuropsychological practice with US Spanish speaking PWE.
Diagnosing Social Communication Disorder (SCD) in Multicultural Individuals: A Case Study
Authors: Jain D , Cohen M J , Fredrick-Keniston A 
Published: August 2019

Abstract

Objective
Explore the impact of culture, developmental stage, and cognitive functioning in a possible diagnosis of SCD.

Case Description
A 12-year-old South Asian, bilingual/bicultural adolescent male (X) presented with concerns regarding his executive and social functioning skills. His medical history was notable for craniosynostosis - successfully treated with craniofacial surgery at age 1 - and a diagnosis of Attention-Deficit/Hyperactivity Disorder (ADHD), combined presentation.

Diagnostic Impressions and Outcomes
X demonstrated superior intellectual performance with some inefficiencies in cognitive processing. Challenges with social interaction were not observed over the course of testing but his mother reported difficulties understanding pragmatic aspects of communication (sexual innuendos in double entendres) and recognizing when conversation had moved to a different topic. He kept a small social circle and preferred the company of older children.

Discussion
In conceptualizing X’s difficulties with social pragmatics, we must keep in mind the socio-cultural context in which he is growing up. He is the son of immigrant parents with South Asian roots. He is at an adolescent developmental stage where he is beginning to explore his individual identity while navigating the differing mores between his South Asian home culture and his American host culture. Therefore, responding to sexual innuendos may be a decision that is fraught with cultural angst over what is appropriate in one context but not the other. His gifted abilities and ADHD may make it difficult for him to remain engaged in the classroom or with similar-aged peers who don’t challenge his intellectual proclivities. His ADHD may also explain his difficulty in recognizing when the topic of conversation has changed. In deciding whether to assign a diagnosis of SCD, it is important to remember these cultural and developmental factors which could explain his difficulties in a normalizing way. These factors should also inform potential therapeutic recommendations.
A Systematic Approach to Spanish Neuropsychological Evaluation: Case Report with a Mexican Woman in an Outpatient Setting
Authors: Rivera P , Savage K , Ball A 
Published: August 2019

Abstract

Objective
The following case will demonstrate a systematic approach to neuropsychological evaluation with Spanish-speaking individuals, which includes creating a suitable test battery, interpreting results with appropriate normative samples, and incorporating personal history.

Case Description
61-year-old, right-handed, Mexican female with 2 years of formal education, and with a recent history of subarachnoid hemorrhage with hydrocephalus. She was referred by her social worker and primary care provider to discern whether the reported cognitive complaints were due to a neurocognitive condition or depression.

Diagnostic Impressions and Outcomes
The evaluation was administered entirely in Spanish and some exams were modified to accommodate her limited literacy skills. She exhibited deficits in executive functioning, verbal fluency, and memory. Emotional testing revealed moderate depression with anxious distress, which she attributed to significant changes in everyday life. Her family informed us that she was the “matriarch of the family” and worked as a farm field truck driver, with significant difficulties/lack of engagement in both of these roles. Therefore, diagnoses of probable major vascular neurocognitive disorder and major depressive disorder with anxious distress were assigned. With this information, her providers were able to connect the family with community resources.

Discussion
The Hispanic population continues to be the fastest growing demographic in the United States. As more clinicians will work with members of this ethnicity in outpatient settings, it is important that they incorporate culturally-relevant factors in their approach to testing and interpretation of results. Nonetheless, this case demonstrates the current challenges and limitations, including modification of exams, differences in educational system that underlie test construction, and patient’s history. Recommendations for future areas of study and practice will also be discussed.
Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?
Authors: Palacios Catalina , García-R Silvana , Parra Juan Luis , Cuervo Andrés M , Stiles F Gary , McCormack John E , Cadena Carlos Daniel 
Published: August 2019

AbstractEcological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.
Fast and accurate correction of optical mapping data via spaced seeds
Authors: Salmela Leena , Mukherjee Kingshuk , Puglisi Simon J , Muggli Martin D , Boucher Christina 
Published: August 2019

AbstractMotivationOptical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes. The challenge faced in error correction is in determining pairs of Rmaps that originate from the same region of the same genome.ResultsWe create an efficient method for determining pairs of Rmaps that contain significant overlaps between them. Our method relies on the novel and nontrivial adaption and application of spaced seeds in the context of optical mapping, which allows for spurious and deleted cut sites to be accounted for. We apply our method to detecting and correcting these errors. The resulting error correction method, referred to as Elmeri, improves upon the results of state-of-the-art correction methods but in a fraction of the time. More specifically, cOMet required 9.9 CPU days to error correct Rmap data generated from the human genome, whereas Elmeri required less than 15 CPU hours and improved the quality of the Rmaps by more than four times compared to cOMet.Availability and implementationElmeri is publicly available under GNU Affero General Public License at https://github.com/LeenaSalmela/Elmeri.Supplementary informationSupplementary data are available at Bioinformatics online.
DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases
Authors: Li Tingyang , Tripathi Ashootosh , Yu Fengan , Sherman David H , Rao Arvind 
Published: August 2019

Abstract

Summary
DDAP is a tool for predicting the biosynthetic pathways of the products of type I modular polyketide synthase (PKS) with the focus on providing a more accurate prediction of the ordering of proteins and substrates in the pathway. In this study, the module docking domain (DD) affinity prediction performance on a hold-out testing dataset reached 0.88 as measured by the area under the receiver operating characteristic (ROC) curve (AUC); the Mean Reciprocal Ranking (MRR) of pathway prediction reached 0.67. DDAP has advantages compared to previous informatics tools in several aspects: (i) it does not rely on large databases, making it a high efficiency tool, (ii) the predicted DD affinity is represented by a probability (0–1), which is more intuitive than raw scores, (iii) its performance is competitive compared to the current popular rule-based algorithm. DDAP is so far the first machine learning based algorithm for type I PKS DD affinity and pathway prediction. We also established the first database of type I modular PKSs, featuring a comprehensive annotation of available docking domains information in bacterial biosynthetic pathways.

Availability and implementation
The DDAP database is available at https://tylii.github.io/ddap. The prediction algorithm DDAP is freely available on GitHub (https://github.com/tylii/ddap) and released under the MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences
Authors: Wang Jun , Du Pu-Feng , Xue Xin-Yu , Li Guang-Ping , Zhou Yuan-Ke , Zhao Wei , Lin Hao , Chen Wei 
Published: August 2019

Abstract

Summary
Many efforts have been made in developing bioinformatics algorithms to predict functional attributes of genes and proteins from their primary sequences. One challenge in this process is to intuitively analyze and to understand the statistical features that have been selected by heuristic or iterative methods. In this paper, we developed VisFeature, which aims to be a helpful software tool that allows the users to intuitively visualize and analyze statistical features of all types of biological sequence, including DNA, RNA and proteins. VisFeature also integrates sequence data retrieval, multiple sequence alignments and statistical feature generation functions.

Availability and implementation
VisFeature is a desktop application that is implemented using JavaScript/Electron and R. The source codes of VisFeature are freely accessible from the GitHub repository (https://github.com/wangjun1996/VisFeature). The binary release, which includes an example dataset, can be freely downloaded from the same GitHub repository (https://github.com/wangjun1996/VisFeature/releases).

Supplementary information
Supplementary data are available at Bioinformatics online.
MKP1 phosphatase is recruited by CXCL12 in glioblastoma cells and plays a role in DNA strand breaks repair
Authors: Dedobbeleer Matthias , Willems Estelle , Lambert Jeremy , Lombard Arnaud , Digregorio Marina , Lumapat Paul Noel , Di Valentin Emmanuel , Freeman Stephen , Goffart Nicolas , Scholtes Felix , Rogister Bernard 
Published: August 2019

Abstract
Glioblastoma (GBM) is the most frequent and aggressive primary tumor in the central nervous system. Previously, the secretion of CXCL12 in the brain subventricular zones has been shown to attract GBM cells and protect against irradiation. However, the exact molecular mechanism behind this radioprotection is still unknown. Here, we demonstrate that CXCL12 modulates the phosphorylation of MAP kinases and their regulator, the nuclear MAP kinase phosphatase 1 (MKP1). We further show that MKP1 is able to decrease GBM cell death and promote DNA repair after irradiation by regulating major apoptotic players, such as Jun-N-terminal kinase, and by stabilizing the DNA repair protein RAD51. Increases in MKP1 levels caused by different corticoid treatments should be reexamined for GBM patients, particularly during their radiotherapy sessions, in order to prevent or to delay the relapses of this tumor.
Optimization of Insect Odorant Receptor Trafficking and Functional Expression Via Transient Transfection in HEK293 Cells
Authors: Miazzi Fabio , Hoyer Carolin , Sachse Silke , Knaden Markus , Wicher Dieter , Hansson Bill S , Lavista-Llanos Sofia 
Published: August 2019

Abstract
Insect odorant receptors (ORs) show a limited functional expression in various heterologous expression systems including insect and mammalian cells. This may be in part due to the absence of key components driving the release of these proteins from the endoplasmic reticulum and directing them to the plasma membrane. In order to mitigate this problem, we took advantage of small export signals within the human HCN1 and Rhodopsin that have been shown to promote protein release from the endoplasmic reticulum and the trafficking of post-Golgi vesicles, respectively. Moreover, we designed a new vector based on a bidirectional expression cassette to drive the functional expression of the insect odorant receptor coreceptor (Orco) and an odor-binding OR, simultaneously. We show that this new method can be used to reliably express insect ORs in HEK293 cells via transient transfection and that is highly suitable for downstream applications using automated and high-throughput imaging platforms.
Cytomegalovirus Viremia Associated With Increased Mortality in Cryptococcal Meningitis in Sub-Saharan Africa
Authors: Skipper Caleb , Schleiss Mark R , Bangdiwala Ananta S , Hernandez-Alvarado Nelmary , Taseera Kabanda , Nabeta Henry W , Musubire Abdu K , Lofgren Sarah M , Wiesner Darin L , Rhein Joshua , Rajasingham Radha , Schutz Charlotte , Meintjes Graeme , Muzoora Conrad , Meya David B , Boulware David R 
Published: August 2019

AbstractBackgroundCryptococcal meningitis and tuberculosis are both important causes of death in persons with advanced human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). Cytomegalovirus (CMV) viremia may be associated with increased mortality in persons living with HIV who have tuberculosis. It is unknown whether concurrent CMV viremia is associated with mortality in other AIDS-related opportunistic infections.MethodsWe prospectively enrolled Ugandans living with HIV who had cryptococcal meningitis from 2010–2012. Subsequently, we analyzed stored baseline plasma samples from 111 subjects for CMV DNA. We compared 10-week survival rates among those with and without CMV viremia.ResultsOf 111 participants, 52% (58/111) had detectable CMV DNA (median plasma viral load 498 IU/mL, interquartile range [IQR] 259–2390). All samples tested were positive on immunoglobin G serology. The median CD4+ T cell count was 19 cells/µL (IQR 9–70) and did not differ by the presence of CMV viremia (P = .47). The 10-week mortality rates were 40% (23/58) in those with CMV viremia and 21% (11/53) in those without CMV viremia (hazard ratio 2.19, 95% confidence interval [CI] 1.07–4.49; P = .03), which remained significant after a multivariate adjustment for known risk factors of mortality (adjusted hazard ratio 3.25, 95% CI 1.49–7.10; P = .003). Serum and cerebrospinal fluid cytokine levels were generally similar and cryptococcal antigen-specific immune stimulation responses did not differ between groups.ConclusionsHalf of persons with advanced AIDS and cryptococcal meningitis had detectable CMV viremia. CMV viremia was associated with an over 2-fold higher mortality rate. It remains unclear whether CMV viremia in severely immunocompromised persons with cryptococcal meningitis contributes directly to this mortality or may reflect an underlying immune dysfunction (ie, cause vs effect).Clinical Trials RegistrationNCT01075152.
Chlorhexidine Bathing to Prevent Central Line–Associated Bloodstream Infections in Hematology Units: A Prospective, Controlled Cohort Study
Authors: Tien Kuei-Lien , Sheng Wang-Huei , Shieh Shiouh-Chu , Hung Yen-Ping , Tien Hwei-Fang , Chen Yi-Hsuan , Chien Li-Jung , Wang Jann-Tay , Fang Chi-Tai , Chen Yee-Chun 
Published: August 2019

Abstract

Background
Chlorhexidine (CHG) bathing decreases the incidence of bloodstream infections in intensive care units, but its effect has been understudied in patients with hematological malignancies in noncritical care units.

Methods
Adults with hematological malignancies hospitalized for cytotoxic chemotherapy in noncritical care units were offered daily 2% CHG bathing. We compared outcomes of patients who chose CHG bathing (CHG group) with outcomes of those who did not choose CHG bathing (usual-care group). The primary outcome was gram-positive cocci–related, skin flora–related, or central line–associated bloodstream infection. The negative control outcome was gut-origin bacteremia.

Results
The CHG group (n = 485) had a crude incidence rate of the primary outcome that was 60% lower than the rate for the usual-care group (n = 408; 3.4 vs 8.4 per 1000 patient-days, P = .02) but had a similar crude incidence rate of the negative control outcome (4.5 vs 3.2 per 1000 patient-days; P = .10). In multivariable analyses, CHG bathing was associated with a 60% decrease in the primary outcome (adjusted hazard ratio [HR], 0.4; P &lt; .001). In contrast, CHG bathing had no effect on the negative control outcome (adjusted HR, 1.1; P = .781). CHG bathing was well tolerated by participants in the CHG group.

Conclusions
CHG bathing could be a highly effective approach for preventing gram-positive cocci–related, skin flora–related, or central line–associated bacteremia in patients with hematological malignancies who are hospitalized for cytotoxic chemotherapy in noncritical care units.
The Crafts–Harley view of German industrialization: an independent estimate of the income side of net national product, 1851–1913
Authors: Pfister Ulrich 
Published: August 2019

AbstractNovel information on land rent is used to estimate the income side of German net national product (NNP) in 1851–1913 without recourse to output side aggregates. The new series shows higher values during the initial part of the period of observation, which narrows the wedge that opens up between existing estimates of NNP before the 1880s. The results support a modified Crafts–Harley view of the first phase of German industrialization: despite rapid catch-up growth of industrial leading sectors from the 1840s to the 1870s, the pace of aggregate growth accelerated only gradually. The initially small size of the modern sector and the simultaneity of the first phase of industrialization and the first wave of globalization account for this paradox. The labor share remained largely constant; the decline of the land share in NNP was compensated by a rise of the capital share.
Five-year outcomes following timely primary percutaneous intervention, late primary percutaneous intervention, or a pharmaco-invasive strategy in ST-segment elevation myocardial infarction: the FAST-MI programme
Authors: Danchin Nicolas , Popovic Batric , Puymirat Etienne , Goldstein Patrick , Belle Loïc , Cayla Guillaume , Roubille François , Lemesle Gilles , Ferrières Jean , Schiele François , Simon Tabassome ,   the FAST-MI Investigators
Published: August 2019

Abstract

Aims
ST-segment elevation myocardial infarction (STEMI) guidelines recommend primary percutaneous coronary intervention (pPCI) as the default reperfusion strategy when feasible ≤120 min of diagnostic ECG, and a pharmaco-invasive strategy otherwise. There is, however, a lack of direct evidence to support the guidelines, and in real-world situations, pPCI is often performed beyond recommended timelines. To assess 5-year outcomes according to timing of pPCI (timely vs. late) compared with a pharmaco-invasive strategy (fibrinolysis with referral to PCI centre).

Methods and results
The French registry of Acute ST-elevation and non-ST-elevation Myocardial Infarction (FAST-MI) programme consists of nationwide observational surveys consecutively recruiting patients admitted for acute myocardial infarction every 5 years. Among the 4250 STEMI patients in the 2005 and 2010 cohorts, those with reperfusion therapy and onset-to-first call time &lt;12 h (n = 2942) were included. Outcomes at 5 years were compared according to type of reperfusion strategy and timing of pPCI, using Cox multivariable analyses and propensity score matching. Among those, 1288 (54%) patients had timely pPCI (≤120 min from ECG), 830 (28%) late pPCI (&gt;120 min), and 824 (28%) intravenous fibrinolysis. Five-year survival was higher with a pharmaco-invasive strategy (89.8%) compared with late pPCI [79.5%; adjusted hazard ratio (HR) 1.51; 1.13–2.02] and similar to timely pPCI (88.2%, adjusted HR 1.02; 0.75–1.38). Concordant results were observed in propensity score-matched cohorts and for event-free survival.

Conclusion
A substantial proportion of patients have pPCI beyond recommended timelines. As foreseen by the guidelines, these patients have poorer 5-year outcomes, compared with a pharmaco-invasive strategy.