bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reading Specialists Use Verbal Protocols as a Formative Assessment Tool
Authors: Bergeson Kristi Tamte 
Published: April 2019

AbstractPractitioners face many challenges when working with students who are experiencing difficulty with comprehension. The act of creating meaning with texts is complex, and comprehension is often measured in schools as a product of reading. Product assessments, such as answering questions or retelling a text, take place after reading, which makes it difficult to understand why and when a student may be experiencing difficulties. Using design‐based research, the author examined the implementation of verbal protocols in classrooms as a formative assessment tool for comprehension. During this two‐month study, three reading specialists drew on the landscape model of reading as a theoretical framework to better understand their students’ think‐aloud statements. Findings indicated that reading specialists implemented verbal protocols as a formative assessment tool with diagnostic interpretation about their students’ reading difficulties and were able to use this information to effectively coach students on their reading processes.
Donkey and smuggler optimization algorithm: A collaborative working approach to path finding
Authors: Shamsaldin Ahmed S. , Rashid Tarik A. , Al-Rashid Agha Rawan A. , Al-Salihi Nawzad K. , Mohammadi Mokhtar 
Published: April 2019

AbstractSwarm Intelligence is a metaheuristic optimization approach that has become very predominant over the last few decades. These algorithms are inspired by animals' physical behaviors and their evolutionary perceptions. The simplicity of these algorithms allows researchers to simulate different natural phenomena to solve various real-world problems. This paper suggests a novel algorithm called Donkey and Smuggler Optimization Algorithm (DSO). The DSO is inspired by the searching behavior of donkeys. The algorithm imitates transportation behavior such as searching and selecting routes for movement by donkeys in the actual world. Two modes are established for implementing the search behavior and route-selection in this algorithm. These are the Smuggler and Donkeys. In the Smuggler mode, all the possible paths are discovered and the shortest path is then found. In the Donkeys mode, several donkey behaviors are utilized such as Run, Face & Suicide, and Face & Support. Real world data and applications are used to test the algorithm. The experimental results consisted of two parts, firstly, we used the standard benchmark test functions to evaluate the performance of the algorithm in respect to the most popular and the state of the art algorithms. Secondly, the DSO is adapted and implemented on three real-world applications namely; traveling salesman problem, packet routing, and ambulance routing. The experimental results of DSO on these real-world problems are very promising. The results exhibit that the suggested DSO is appropriate to tackle other unfamiliar search spaces and complex problems.Highlights Donkey and Smuggler Optimization Algorithm (DSO) is a novel optimization algorithm. The DSO is inspired by Donkeys' behaviors. It has been evaluated against other algorithms. DSO solves different problems such as TSP, packet routing, and ambulance routing. The outcomes on the tests exhibit a greater manipulation of DSO. The outcomes prove that DSO has a greater searching ability.
Prevalence and Psychopathological Determinants of Sexual Dysfunction and Related Distress in Women With and Without Multiple Sclerosis
Authors: Gava Giulia , Visconti Matteo , Salvi Fabrizio , Bartolomei Ilaria , Seracchioli Renato , Meriggiola Maria Cristina 
Published: April 2019

ABSTRACT

Introduction
Sexual dysfunction (SD) is common but still underdiagnosed in women with multiple sclerosis (MS); in fact, the lack of a consistent use of validated diagnostic tools makes the prevalence of SD and related distress difficult to define precisely.

Aim
To assess the prevalence of SD in Italian women with MS compared with age-matched healthy control subjects (HC) and the association with demographic, psychological, and MS-related characteristics.

Methods
The Female Sexual Function Index (FSFI) and the Female Sexual Distress Scale were administered to 153 women with MS and 153 HC. Demographic, gynecologic, and neurologic data were obtained. Disability was assessed using the Expanded Disability Status Scale. Psychological symptoms were evaluated in MS patients with Profile of Mood State and the Beck Depression Inventory II.

Main Outcomes Measures
Prevalence of SD and sexual distress in women with MS compared with HC.

Results
Among women sexually active in the last month, we found an increased prevalence of SD in MS patients compared with HC subjects (42.0% vs 16.0%, P = .0001). The prevalence of dysfunctional FSFI global scores (&lt;26.55) was higher in women with MS compared with HC (49.6% vs 33.6%, P = .014). In the MS group, the prevalence of SD was similar between pre- and post-menopausal women. Both premenopausal and postmenopausal MS women presented a greater prevalence of SD if compared with the premenopausal and postmenopausal HC groups (30/79 [37.9%] vs. 5/74 [6.8%], P = .0001 and 20/40 [50.0%] vs 16/57 [28.1%], P = .03, respectively). A negative correlation was observed between the FSFI global score and age and Expanded Disability Status Scale. Depressive symptoms were more common in women with MS and SD than in those without.

Clinical Implications
This study suggests that sexual function investigation should always be a standard part of the consultation with healthcare professionals for MS.

Strength & Limitations
The strength of this study was the comparison with an age-matched healthy control group and the use of validated questionnaires to assess both sexual function and sexual distress. Larger and multicenter studies may further support our findings.

Conclusion
In our cohort, the prevalence of SD and sexual distress was higher in women with MS compared to the HC group. Age, disability, and depressive symptoms were associated with increased SD.
A glimpse into the psychological status of E.N.T inpatients in China: A cross‐sectional survey of three hospitals in different regions
Authors: Tian Jun , Li Li , Tao Chun‐Lei , Hao Rong‐Ying , Huang Fu‐Hui , Ge Xiao‐Hui , Zhang San‐Mei 
Published: April 2019

ObjectiveTo determine whether E.N.T inpatients have a higher prevalence of mental illness than the general population and whether certain diseases are more likely to be associated with mental illness than other diseases.MethodsThis cross‐sectional survey was conducted in the E.N.T departments of three hospitals in different cities in China. The psychological status of all consecutive adult inpatients was assessed within 1–2 days following hospital admission using the Symptom Checklist‐90 (SCL‐90), Zung Self‐Rating Depression Scale (SDS) and Zung Self‐Rating Anxiety Scale (SAS). Inpatients from the general surgery and pneumology departments at the same hospital were enrolled and surveyed as control groups.ResultsThe 439 patients enrolled in the final analysis accounted for 88.0% of all E.N.T inpatients during the study period. Of these patients, 16.4% were in an anxious state and 79.5% were in a depressive state. The overall anxiety (41.7 ± 9.7) and depression (55.9 ± 29.2) scores were much higher than Chinese norm (29.8 ± 10.0 and 33.5 ± 8.6, respectively), and significant differences were observed (t = 20.89, P < 0.01 and t = 13.12, P < 0.01, respectively). Although 18.7% of the E.N.T patients were psychiatric distress, these patients scored lower on the SCL‐90 than the Chinese norm. Furthermore, the patients in the E.N.T department had a higher prevalence of anxiety and depression than those in the general surgery department but a similar prevalence to those in the respiratory department.ConclusionPsychological distress, particularly anxiety and depression, are widespread in patients with otolaryngological diseases. Therefore, the identification and treatment of co‐occurring psychiatric disorders in this high risk and clinically challenging group of patients are urgent in China.
Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
Authors: Rees David J. , Hanifi Arash , Obille Angelico , Alexander Robert , Sone Eli D. 
Published: April 2019

AbstractThe European freshwater mollusk Dreissena bugensis (quagga mussel), an invasive species to North America, adheres to surfaces underwater via the byssus: a non-living protein ‘anchor’. In spite of its importance as a biofouling species, the sequence of the majority of byssal proteins responsible for adhesion are not known, and little genomic data is available. To determine protein sequence information, we utilized next-generation RNA sequencing and de novo assembly to construct a cDNA library of the quagga mussel foot transcriptome, which contains over 200,000 transcripts. Quagga mussel byssal proteins were extracted from freshly induced secretions and analyzed using LC-MS/MS; peptide spectra were matched to the transcriptome to fingerprint the entire protein primary sequences. We present the full sequences of fourteen novel quagga mussel byssal proteins, named Dreissena bugensis foot proteins 4 to 17 (Dbfp4–Dbfp17), and new sequence data for two previously observed byssal proteins Dbfp1 and Dbfp2. Theoretical masses of the newly discovered proteins range from 4.3 kDa to 21.6 kDa. These protein sequences are unique but contain features similar to glue proteins from other species, including a high degree of polymorphism, proteins with repeated peptide motifs, disordered protein structure, and block structures.
Less fit Lamium amplexicaule plants produce more dispersible seeds
Authors: Zinger Eyal , Gueijman Ariel , Obolski Uri , Ram Yoav , Ruby Eliya , Binder Mor , Yechieli Nivi , Ohad Nir , Hadany Lilach 
Published: April 2019

AbstractTheory predicts that less fit individuals would disperse more often than fitter ones (Fitness Associated Dispersal, FAD hypothesis). To test this prediction under laboratory conditions, an entire life cycle of Lamium amplexicaule plants and the preferences of its dispersal agent, Messor ebeninus ants, were tracked. Characterization of individual L. amplexicaule plant revealed high variability in spot cover on the surface of the seeds, where less fit plants produce “unspotted seeds” (see Fig. 1 in Introduction). Unspotted L. amplexicaule seeds showed higher variation in germination time and lower germination rate. Moreover, M. ebeninus ants preferably collected these unspotted seeds. Our results show that low fitness L. amplexicaule plants produce seeds with higher potential for dispersal, supporting the FAD hypothesis in a plant-animal system.
Retinal microvasculature and cerebral small vessel disease in the Lothian Birth Cohort 1936 and Mild Stroke Study
Authors: McGrory Sarah , Ballerini Lucia , Doubal Fergus N. , Staals Julie , Allerhand Mike , Valdes-Hernandez Maria del C. , Wang Xin , MacGillivray Tom , Doney Alex S. F. , Dhillon Baljean , Starr John M. , Bastin Mark E. , Trucco Emanuele , Deary Ian J. , Wardlaw Joanna M. 
Published: April 2019

AbstractResearch has suggested that the retinal vasculature may act as a surrogate marker for diseased cerebral vessels. Retinal vascular parameters were measured using Vessel Assessment and Measurement Platform for Images of the Retina (VAMPIRE) software in two cohorts: (i) community-dwelling older subjects of the Lothian Birth Cohort 1936 (n = 603); and (ii) patients with recent minor ischaemic stroke of the Mild Stroke Study (n = 155). Imaging markers of small vessel disease (SVD) (white matter hyperintensities [WMH] on structural MRI, visual scores and volume; perivascular spaces; lacunes and microbleeds), and vascular risk measures were assessed in both cohorts. We assessed associations between retinal and brain measurements using structural equation modelling and regression analysis. In the Lothian Birth Cohort 1936 arteriolar fractal dimension accounted for 4% of the variance in WMH load. In the Mild Stroke Study lower arteriolar fractal dimension was associated with deep WMH scores (odds ratio [OR] 0.53; 95% CI, 0.32–0.87). No other retinal measure was associated with SVD. Reduced fractal dimension, a measure of vascular complexity, is related to SVD imaging features in older people. The results provide some support for the use of the retinal vasculature in the study of brain microvascular disease.
Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants
Authors: Everson Todd M. , Marsit Carmen J. , Michael O’Shea T. , Burt Amber , Hermetz Karen , Carter Brian S. , Helderman Jennifer , Hofheimer Julie A. , McGowan Elisabeth C. , Neal Charles R. , Pastyrnak Steven L. , Smith Lynne M. , Soliman Antoine , DellaGrotta Sheri A. , Dansereau Lynne M. , Padbury James F. , Lester Barry M. 
Published: April 2019

AbstractNeonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in buccal cell DNA methylation (DNAm) associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N = 536). We tested whether epigenetic age, age acceleration, or DNAm levels at individual loci differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations may be informative for infant neurobehavior.
Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Authors: Liu Yuanhang , Chanana Pritha , Davila Jaime I. , Hou Xiaonan , Zanfagnin Valentina , McGehee Cordelia D. , Goode Ellen L. , Polley Eric C. , Haluska Paul , Weroha S. John , Wang Chen 
Published: April 2019

AbstractAs patient derived xenograft (PDX) models are increasingly used for preclinical drug development, strategies to account for the nonhuman component of PDX RNA expression data are critical to its interpretation. A bioinformatics pipeline to separate donor tumor and mouse stroma transcriptome profiles was devised and tested. To examine the molecular fidelity of PDX versus donor tumors, we compared mRNA differences between paired PDX-donor tumors from nine ovarian cancer patients. 1,935 differentially expressed genes were identified between PDX and donor tumors. Over 90% (n = 1767) of these genes were down-regulated in PDX models and enriched in stroma-specific functions. Several protein kinases were also differentially expressed in PDX tumors, e.g. PDGFRA, PDGFRB and CSF1R. Upon in silico removal of these PDX-donor tumor differentially expressed genes, a stronger transcriptional resemblance between PDX-donor tumor pairs was seen (average correlation coefficient increases from 0.91 to 0.95). We devised and validated an effective bioinformatics strategy to separate mouse stroma expression from human tumor expression for PDX RNAseq. In addition, we showed most of the PDX-donor differentially expressed genes were implicated in stromal components. The molecular similarities and differences between PDX and donor tumors have implications in future therapeutic trial designs and treatment response evaluations using PDX models.
c-Myb regulates tumorigenic potential of embryonal rhabdomyosarcoma cells
Authors: Kaspar Petr , Prochazka Jan , Efenberkova Michaela , Juhasz Attila , Novosadova Vendula , Sedlacek Radislav 
Published: April 2019

AbstractRhabdomyosarcomas (RMS) are a heterogeneous group of mesodermal tumors, the most common sub-types are embryonal (eRMS) and alveolar (aRMS) rhabdomyosarcoma. Immunohistochemical analysis revealed c-Myb expression in both eRMS and aRMS. c-Myb has been reported to be often associated with malignant human cancers. We therefore investigated the c-Myb role in RMS using cellular models of RMS. Specific suppression of c-Myb by a lentiviral vector expressing doxycycline (Dox)-inducible c-Myb shRNA inhibited proliferation, colony formation, and migration of the eRMS cell line (RD), but not of the aRMS cell line (RH30). Upon c-Myb knockdown in eRMS cells, cells accumulated in G0/G1 phase, the invasive behaviour of cells was repressed, and elevated levels of myosin heavy chain, marker of muscle differentiation, was detected. Next, we used an RD-based xenograft model to investigate the role of c-Myb in eRMS tumorigenesis in vivo. We found that Dox administration did not result in efficient suppression of c-Myb in growing tumors. However, when c-Myb-deficient RD cells were implanted into SCID mice, we observed inefficient tumor grafting and attenuation of tumor growth during the initial stages of tumor expansion. The presented study suggests that c-Myb could be a therapeutic target in embryonal rhabdomyosarcoma assuming that its expression is ablated.
Increased nurse workload is associated with bloodstream infections in very low birth weight infants
Authors: Küng Erik , Waldhör Thomas , Rittenschober-Böhm Judith , Berger Angelika , Wisgrill Lukas 
Published: April 2019

AbstractNeonatal sepsis is a major cause of morbidity and mortality in very low birth weight infants (VLBWI). Nurse workload considerably affects infection rates in intensive care units. However, data concerning the impact of staff workload on bloodstream infections (BSI) in VLBWI are scarce. The aim of the study was to examine the association between nurse workload and BSI in VLBWI. VLBWI admitted to our neonatal intensive care unit during 2016–2017 were retrospectively analysed. Association between nurse workload, determined by a standardized nursing score, and the BSI occurrence was investigated. A higher nurse workload was significantly associated with higher occurrence of BSI (p = 0.0139) in VLBWI. An assumed workload of 120% or higher, representing the need for additional nurses in our NICU setting, is associated with an elevated risk for BSI in this vulnerable population OR 2.32 (95% CI: 1.42–3.8, p = 0.0005). In conclusion, nurse understaffing is associated with a higher risk for BSI in VLBWI.
Pulsed Near Infrared Transcranial and Intranasal Photobiomodulation Significantly Modulates Neural Oscillations: a pilot exploratory study
Authors: Zomorrodi Reza , Loheswaran Genane , Pushparaj Abhiram , Lim Lew 
Published: April 2019

AbstractTranscranial photobiomodulation (tPBM) is the application of low levels of red or near-infrared (NIR) light to stimulate neural tissues. Here, we administer tPBM in the form of NIR light (810 nm wavelength) pulsed at 40 Hz to the default mode network (DMN), and examine its effects on human neural oscillations, in a randomized, sham-controlled, double-blinded trial. Using electroencephalography (EEG), we found that a single session of tPBM significantly increases the power of the higher oscillatory frequencies of alpha, beta and gamma and reduces the power of the slower frequencies of delta and theta in subjects in resting state. Furthermore, the analysis of network properties using inter-regional synchrony via weighted phase lag index (wPLI) and graph theory measures, indicate the effect of tPBM on the integration and segregation of brain networks. These changes were significantly different when compared to sham stimulation. Our preliminary findings demonstrate for the first time that tPBM can be used to non-invasively modulate neural oscillations, and encourage further confirmatory clinical investigations.
The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility
Authors: Calandra Ivan , Schunk Lisa , Bob Konstantin , Gneisinger Walter , Pedergnana Antonella , Paixao Eduardo , Hildebrandt Andreas , Marreiros Joao 
Published: April 2019

AbstractMany archeologists are skeptical about the capabilities of use-wear analysis to infer on the function of archeological tools, mainly because the method is seen as subjective, not standardized and not reproducible. Quantitative methods in particular have been developed and applied to address these issues. However, the importance of equipment, acquisition and analysis settings remains underestimated. One of those settings, the numerical aperture of the objective, has the potential to be one of the major factors leading to reproducibility issues. Here, experimental flint and quartzite tools were imaged using laser-scanning confocal microscopy with two objectives having the same magnification but different numerical apertures. The results demonstrate that 3D surface texture ISO 25178 parameters differ significantly when the same surface is measured with objectives having different numerical apertures. It is, however, unknown whether this property would blur or mask information related to use of the tools. Other acquisition and analyses settings are also discussed. We argue that to move use-wear analysis toward standardization, repeatability and reproducibility, the first step is to report all acquisition and analysis settings. This will allow the reproduction of use-wear studies, as well as tracing the differences between studies to given settings.
Isotopic evidence for temperate oceans during the Cambrian Explosion
Authors: Wotte Thomas , Skovsted Christian B. , Whitehouse Martin J. , Kouchinsky Artem 
Published: April 2019

AbstractThe Cambrian Explosion was a key event in the evolution of life on Earth. This event took place at a time when sea surface temperatures have been proposed to reach about 60 °C. Such high temperatures are clearly above the upper thermal limit of 38 °C for modern marine invertebrates and preclude a major biological revolution. To address this dichotomy, we performed in situ δ18O analyses of Cambrian phosphatic brachiopods via secondary ion mass spectrometry (SIMS). The δ18Ophosphate data, which are considered to represent the most primary δ18Oseawater signature, were identified by evaluating the diagenetic alteration of the analyzed shells. Assuming ice-free conditions for the Cambrian ocean and no change in δ18Oseawater (-1.4‰ to -1‰; V-SMOW) through time, our temperatures vary between 35 °C ± 12 °C and 41 °C ± 12 °C. They are thus clearly above (1) recent subequatorial sea surface temperatures of 27 °C–35 °C and (2) the upper lethal limit of 38 °C of marine organisms. Our new data can therefore be used to infer a minimal depletion in early Cambrian δ18Oseawater relative to today of about -3‰. With this presumption, our most pristine δ18Ophosphate values translate into sea surface temperatures of about 30 °C indicating habitable temperatures for subequatorial oceans during the Cambrian Explosion.
Studying the rigidity of red blood cells induced by Plasmodium falciparum infection
Authors: Paul Apurba , Ramdani Ghania , Tatu Utpal , Langsley Gordon , Natarajan Vasant 
Published: April 2019

AbstractWe study the effect of different chemical moieties on the rigidity of red blood cells (RBCs) induced by Plasmodium falciparum infection, and the bystander effect previously found. The infected cells are obtained from a culture of parasite-infected RBCs grown in the laboratory. The rigidity of RBCs is measured by looking at the Brownian fluctuations of individual cells in an optical-tweezers trap. The results point towards increased intracellular cyclic adenosine monophosphate (cAMP) levels as being responsible for the increase in rigidity.