bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Three Point-of-Care Tests for Detection of Toxoplasma Immunoglobulin IgG and IgM in the United States: Proof of Concept and Challenges
Authors: Gomez Carlos A , Budvytyte Laura N , Press Cindy , Zhou Lily , McLeod Rima , Maldonado Yvonne , Montoya Jose G , Contopoulos-Ioannidis Despina G 
Published: December 2018

Abstract

Background
The cost of conventional serological testing for toxoplasmosis discourages universal adoption of prenatal monthly screening programs to prevent congenital toxoplasmosis. Point-of-care (POC) technology may constitute a cost-effective approach.

Methods
We evaluated the diagnostic accuracy of 3 Toxoplasma POC tests against gold-standard testing performed at Palo Alto Medical Foundation Toxoplasma Serology Laboratory (PAMF-TSL). The POC tests included the following: Toxo IgG/IgM Rapid Test (Biopanda) and the OnSite Toxo IgG/IgM Combo-Rapid-test that detect IgG and IgM separately, and the Toxoplasma ICT-IgG-IgM-bk (LDBIO) that detects either or both immunoglobulin IgG/IgM in combination. Samples were selected from PAMF-TSL biobank (n = 210) and Centers for Disease Control and Prevention Toxoplasma 1998 Human Serum Panel (n = 100). Based on PAMF-TSL testing, Toxoplasma-infection status was classified in 4 categories: acute infections (n = 85), chronic infections (n = 85), false-positive Toxoplasma IgM (n = 60), and seronegative (n = 80). The POC testing was performed in duplicate following manufacturer’s instructions by investigators blinded to PAMF-TSL results. Sensitivity and specificity were calculated.

Results
A total of 1860 POC tests were performed. For detection of Toxoplasma IgG, sensitivity was 100% (170 of 170; 95% confidence interval [CI], 97.8%–100%) for all 3 POC kits; specificity was also comparable at 96.3% (77 of 80; 95% CI, 89.5%–98.9%), 97.5% (78 of 80; 95% CI, 91.3%–99.6%), and 98.8% (79 of 80; 95% CI, 93.2%–99.9%). However, sensitivity for detection of Toxoplasma IgM varied significantly across POC tests: Biopanda, 62.2% (51 of 82; 95% CI, 51.4%–71.9%); OnSite, 28% (23 of 82; 95% CI, 19.5%–38.6%); and LDBIO combined IgG/IgM, 100% (82 of 82; 95% CI, 95.5%–100%). Diagnostic accuracy was significantly higher for the LDBIO POC kit. The POC kits did not exhibit cross-reactivity for false-positive Toxoplasma-IgM sera.

Conclusions
The 3 evaluated POC kits revealed optimal sensitivity for Toxoplasma-IgG antibodies. The LDBIO-POC test exhibited 100% sensitivity for the combined detection of IgG/IgM in acute and chronic Toxoplasma infection. Biopanda and Onsite POC tests exhibited poor sensitivity for Toxoplasma-IgM detection.
Burden and Characteristics of the Comorbidity Tuberculosis—Diabetes in Europe: TBnet Prevalence Survey and Case-Control Study
Authors: Sane Schepisi Monica , Navarra Assunta , Altet Gomez M Nieves , Dudnyk Andrii , Dyrhol-Riise Anne Margarita , Esteban Jaime , Giorgetti Pier Francesco , Gualano Gina , Guglielmetti Lorenzo , Heyckendorf Jan , Kaluzhenina Anna , Lange Berit , Lange Christoph , Manika Katerina , Miah Jalal , Nanovic Zorica , Pontali Emanuele , Prego Monica Rios , Solovic Ivan , Tiberi Simon , Palmieri Fabrizio , Girardi Enrico 
Published: December 2018

Abstract

Background
The growing burden of diabetes mellitus (DM) is posing a threat to global tuberculosis (TB) control. DM triples the risk of developing TB, modifies the presenting features of pulmonary TB, and worsens TB treatment outcomes. We aimed to analyze the prevalence of DM among TB patients and to describe the characteristics and clinical presentation of TB-DM patients in Europe.

Methods
We performed a cross-sectional survey on the prevalence of DM among consecutively diagnosed adult TB patients in 11 European TB referral centers located in France, Germany, Greece, Italy, Russia, Slovakia, Spain, and the United Kingdom over the period 2007–2015. We also selected DM-TB cases and TB only controls with a 1:3 ratio to perform a case-control analysis, including patients selected from the countries mentioned above plus Norway and Ukraine.

Results
Among 3143 TB enrolled patients, DM prevalence overall was 10.7% and ranged from 4.4% in Greece to 28.5% in the United Kingdom. Patients’ median ages ranged from 36 to 49 years, and all centers had &gt;60% males; the proportion of foreign-born patients varied widely across sites. In the case-control study, DM was independently associated with older age and, among older patients, with being foreign-born. Among patients with pulmonary involvement, cavities on chest imaging were more frequently observed among those with DM.

Conclusions
Diabetes mellitus represents a challenge for TB control in Europe, especially in foreign-born and in elderly patients. Specific screening strategies should be evaluated.
Microsurgical Resection of Low-Grade Spinal Cord Astrocytoma: 2-Dimensional Operative Video
Authors: Pojskić Mirza , Arnautović Kenan I 
Published: December 2018

Abstract
This video demonstrates microsurgical resection of low-grade (Grade I) thoracic spinal cord astrocytoma. Astrocytomas are the most common pediatric intramedullary tumors and occur secondary to ependymomas in adults.
1,2
The treatment goal should be radical gross total resection while preserving neurological function with intraoperative neuromonitoring.
2-4
To our knowledge, this is the first video report on microsurgical resection of low-grade spinal cord astrocytoma.
A 58-yr-old female presented with gait disturbances has been featured in this video. A spinal MRI revealed T1/T2 hyperintense intramedullary tumor at T4, suggesting spinal cord astrocytoma versus ependymoma. Dura was opened in the midline and tacked to the surrounding muscle tissue with tacking sutures. The arachnoid was opened separately with microscissors, keeping it intact for closure at the end of surgery. Liga clips were applied to hold the arachnoid to the dura. Myelotomy was done in the midline,
5
opening the posterior median sulcus over the length of the tumor and extending proximally and distally a few millimeters beyond the tumor.
3,5
The tumor reduction was achieved by coagulation or debulking. Once sufficient debulking was achieved, dissection of the tumor margins toward surrounding cord was performed. Preoperative recording of motor-evoked potentials (MEPs) compared with continuous intraoperative MEPs were essential for preserving the neurological function and quality of life. The intraoperative finding of a clear tumor plane of resection carries positive prognostic significance and reduces the risk of complications.
2,3,6

A pathohistological diagnosis showed a low-grade (Grade I) spinal cord astrocytoma (pilocytic). Follow-up MRI showed no sign of tumor or recurrence. The patient recovered fully and was neurologically intact.
Written consent was obtained directly from the patient.
Segregation and the Cost of Money: Race, Poverty, and the Prevalence of Alternative Financial Institutions
Authors: Faber Jacob William 
Published: December 2018

Abstract
Payday lenders, check cashers, and other “alternative” financial services (AFS) have garnered attention from policymakers and advocates for the poor because they are more expensive than traditional banking—constituting what some call a “Ghetto Tax.” This is the first study to explore neighborhood-level AFS geography on the national scale. Leveraging a dataset comprising the universe of AFS in 2015, I show that not only are there substantial differences in AFS presence between white and non-white neighborhoods, but that these disparities are largest in the most segregated metropolitan areas. This finding supports theories that racial segregation creates easily identifiable markets for institutions to avoid, target, and exploit. I further show that while AFS presence declines with neighborhood income, the gap between black and white neighborhoods is widest among high-income neighborhoods, reflecting the unique vulnerability of even affluent blacks to institutional marginalization. This work documents how the overlapping geographies of racial isolation and AFS prevalence shape the very cost of money for different racial groups, illustrating the importance of institutions transmitting the effects of racial isolation.
Effects of Syngenta Enogen Feed Corn containing an α-amylase trait on finishing cattle performance and carcass characteristics1
Authors: Jolly-Breithaupt M L , Harris M E , Nuttelman B L , Burken D B , MacDonald J C , Luebbe M K , Iragavarapu T K , Erickson G E 
Published: December 2018

Abstract
Two experiments evaluated the effects of feeding a new corn hybrid, containing an α-amylase enzyme trait, Syngenta Enogen Feed Corn (SYT-EFC), on feedlot performance and carcass characteristics at two locations. Experiment 1 utilized 300 calffed steers (298.5 ± 16.3 kg of BW) at the University of Nebraska–Lincoln Eastern Nebraska Research and Extension Center Mead, NE. Treatments were designed as a 2 × 2 + 1–factorial arrangement with factors consisting of 1) corn type (SYT-EFC or conventional [CON]) and 2) byproduct type (with or without Sweet Bran [SB]), or a BLEND of STY-EFC and CON without SB. In Exp. 2, 240 crossbred, calf-fed steers (287.6 ± 15.4 kg of BW) were utilized at the University of Nebraska–Lincoln Panhandle Research and Extension Center near Scottsbluff, NE. Steers were fed SYT-EFC, CON, BLEND, or CON with a commercial α-amylase enzyme supplement (CON-E). In Exp. 1, there was an interaction for ADG (P = 0.05) and G:F (P = 0.02). Steers fed SYT-EFC with SB had greater ADG and G:F than CON; however, in diets without SB, SYT-EFC and CON were not different resulting in a 10.1% change in G:F when steers were fed SYT-EFC in SB compared with CON and only 1.6% change between SYT-EFC and CON without SB. Energy values, based on performance data, resulted in a 6.5% and 8.3% change in NEm and NEg, respectively, for steers fed SYT-EFC and CON with SB and 1.6% change for both NEm and NEg for steers fed SYT-EFC and CON without SB. For the main effect of corn trait, steers fed SYT-EFC had greater marbling scores, fat depth, and calculated yield grade compared with CON (P ≤ 0.03). In diets without SB, there was no difference between SYT-EFC, CON, or BLEND for DMI, final BW, ADG, G:F, NEm, or NEg (P ≥ 0.35). In Exp. 2, cattle fed SYT-EFC, BLEND, or CON-E had greater final BW, ADG, and G:F than cattle fed CON (P ≤ 0.03). On average, NEm and NEg were 4.9% and 7.0% greater, respectively, for steers fed amylase enzyme treatments compared with CON (P ≤ 0.01). Hot carcass weights were greater in steers fed α-amylase treatments compared with CON (P &lt; 0.01). Feeding Syngenta Enogen Feed Corn, which contains an α-amylase enzyme trait, at both locations improved feed efficiency in finishing cattle diets containing WDGS or SB.
Developmental regulators FlbE/D orchestrate the polarity site-to-nucleus dynamics of the fungal bZIP FlbB
Authors: Otamendi Ainara , Perez-de-Nanclares-Arregi Elixabet , Oiartzabal Elixabet , Cortese Marc S. , Espeso Eduardo A. , Etxebeste Oier 
Published: December 2018

AbstractPermanently polarized cells have developed transduction mechanisms linking polarity-sites with gene regulation in the nucleus. In neurons, one mechanism is based on long-distance retrograde migration of transcription factors (TFs).Aspergillus nidulansFlbB is the only known fungal TF shown to migrate retrogradely to nuclei from the polarized region of fungal cells known as hyphae. There, FlbB controls developmental transitions by triggering the production of asexual multicellular structures. FlbB dynamics in hyphae is orchestrated by regulators FlbE and FlbD. At least three FlbE domains are involved in the acropetal transport of FlbB, with a final MyoE/actin filament-dependent step from the subapex to the apex. Experiments employing a T2A viral peptide-containing chimera (FlbE::mRFP::T2A::FlbB::GFP) suggest that apical FlbB/FlbE interaction is inhibited in order to initiate a dynein-dependent FlbB transport to nuclei. FlbD controls the nuclear accumulation of FlbB through a cMyb domain and a C-terminal LxxLL motif. Overall, results elucidate a highly dynamic pattern of FlbB interactions, which enable timely developmental induction. Furthermore, this system establishes a reference for TF-based long-distance signaling in permanently polarized cells.
Acquisition of visual priors and induced hallucinations in chronic schizophrenia
Authors: Valton Vincent , Karvelis Povilas , Richards Katie L. , Seitz Aaron R. , Lawrie Stephen M. , Seriès Peggy 
Published: December 2018

AbstractProminent theories suggest that symptoms of schizophrenia stem from learning deficiencies resulting in distorted internal models of the world. To further test these theories, we here use a visual statistical learning task known to induce rapid implicit learning of the stimulus statistics (Chalk et al., 2010). In this task, participants are presented with a field of coherently moving dots and need to report the presented direction of the dots (estimation task) and whether they saw any dots or not (detection task). Two of the directions were more frequently presented than the others. In controls, the implicit acquisition of the stimuli statistics influences their perception in two ways: 1-motion directions are perceived as being more similar to the most frequently presented directions than they really are (estimation biases); 2-in the absence of stimuli, participants sometimes report perceiving the most frequently presented directions (a form of hallucinations). Such behaviour is consistent with probabilistic inference, i.e. combining learnt perceptual priors with sensory evidence. We investigated whether patients with chronic, stable, treated schizophrenia (n=20) differ from controls (n=23) in the acquisition of the perceptual priors and/or their influence on perception. We found that, although patients were slower than controls, they showed comparable acquisition of perceptual priors, correctly approximating the stimulus statistics. This suggests that patients have no statistical learning deficits in our task. This may reflect our patients relative wellbeing on antipsychotic medication. Intriguingly, however, patients made significantly fewer hallucinations of the most frequently presented directions than controls and fewer prior-based lapse estimations. This suggests that prior expectations had less influence on patients’ perception than on controls when stimuli were absent or below perceptual threshold.
Predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks
Authors: Zhang Kaiming , Pan Xiaoyong , Yang Yang , Shen Hong-Bin 
Published: December 2018

AbstractCircular RNAs (circRNAs), with their crucial roles in gene regulation and disease development, have become a rising star in the RNA world. A lot of previous wet-lab studies focused on the interaction mechanisms between circRNAs and RNA-binding proteins (RBPs), as the knowledge of circRNA-RBP association is very important for understanding functions of circRNAs. Recently, the abundant CLIP-Seq experimental data has made the large-scale identification and analysis of circRNA-RBP interactions possible, while no computational tool based on machine learning has been developed yet.We present a new deep learning-based method, CRIP (CircRNAs Interact with Proteins), for the prediction of RBP binding sites on circRNAs, using only the RNA sequences. In order to fully exploit the sequence information, we propose a stacked codon-based encoding scheme and a hybrid deep learning architecture, in which a convolutional neural network (CNN) learns high-level abstract features and a recurrent neural network (RNN) learns long dependency in the sequences. We construct 37 datasets including sequence fragments of binding sites on circRNAs, and each set corresponds to one RBP. The experimental results show that the new encoding scheme is superior to the existing feature representation methods for RNA sequences, and the hybrid network outperforms conventional classifiers by a large margin, where both the CNN and RNN components contribute to the performance improvement. To the best of our knowledge, CRIP is the first machine learning-based tool specialized in the prediction of circRNA-RBP interactions, which is expected to play an important role for large-scale function analysis of circRNAs.
Identification of QTL for leaf angle at canopy-wide levels in maize
Authors: Tang Dengguo , Chen Zhengjie , Ni Jixing , Jiang Qin , Li Peng , Wang Le , Zhou Jinhong , Li Chenyang , Liu Jian 
Published: December 2018

AbstractLeaf angle (LA) is one of the most important canopy architecture related traits of maize (Zea mays L.). Currently, there is an urgent need to elucidate the genetic mechanism of LA at canopy-wide levels for optimizing dense-planting canopy architecture. In present study, one RIL population derived from two parent lines which show distinct plant architecture was used to perform QTL mapping for LA at eight leaves below the tassel under three environments. Dozens of QTL for LA at eight leaves were identified, which were mapped on all maize chromosomes except for the tenth chromosome. Among them, there were nine common QTL as they were identified for LA more than 1 leaves or in two or three environments. And individual QTL could explain 1.29% - 20.14% of the phenotypic variation and affect LA of 1-8 leaves, including qLA5.1 affected LA of all eight leaves, qLA3.1 affected LA of the upper leaves (1stLA to 4thLA), and qLA9.1 could affect LA of the lower leaves (5thLA to 8thLA). Furthermore, the results indicated that the genetic architecture of LA at eight leaves was different. Specifically, 8thLA was mainly affected by major and minor QTL; 1stLA, 4thLA and 5thLA were affected by epistatic interactions beside major and minor QTL; while the other four LAs were simultaneously affected by major QTL, minor QTL, epistatic interactions and environments. These results provide a comprehensive understanding of genetic basis of LA at canopy-wide levels, which will be beneficial to design ideal plant architecture under dense planting in maize.Author contribution statementJ. L. and D. T. designed and supervised the study, D. T., Z.C., J.N., Q.J., P.L., L.W., J.Z., C.L. performed the phenotypic data collection. D. T. analyzed the data and drafted the manuscript, D. T. and Z.C. revised and finalized the manuscript. All the authors read and approved the manuscript.Key messageDozens of QTL for leaf angle of eight consecutive leaves were identified in the RIL population across three environments, providing the information that optimization of canopy architecture at various canopy levels.
A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing
Authors: Kingan Sarah B. , Heaton Haynes , Cudini Juliana , Lambert Christine C. , Baybayan Primo , Galvin Brendan D. , Durbin Richard , Korlach Jonas , Lawniczak Mara K. N. 
Published: December 2018

AbstractA high-quality reference genome is a fundamental resource for functional genetics, comparative genomics, and population genomics, and is increasingly important for conservation biology. PacBio Single Molecule, Real-Time (SMRT) sequencing generates long reads with uniform coverage and high consensus accuracy, making it a powerful technology for de novo genome assembly. Improvements in throughput and concomitant reductions in cost have made PacBio an attractive core technology for many large genome initiatives, however, relatively high DNA input requirements (∼5 µg for standard library protocol) have placed PacBio out of reach for many projects on small organisms that have lower DNA content, or on projects with limited input DNA for other reasons. Here we present a high-quality de novo genome assembly from a single Anopheles coluzzii mosquito. A modified SMRTbell library construction protocol without DNA shearing and size selection was used to generate a SMRTbell library from just 100 ng of starting genomic DNA. The sample was run on the Sequel System with chemistry 3.0 and software v6.0, generating, on average, 25 Gb of sequence per SMRT Cell with 20 hour movies, followed by diploid de novo genome assembly with FALCON-Unzip. The resulting curated assembly had high contiguity (contig N50 3.5 Mb) and completeness (more than 98% of conserved genes are present and full-length). In addition, this single-insect assembly now places 667 (>90%) of formerly unplaced genes into their appropriate chromosomal contexts in the AgamP4 PEST reference. We were also able to resolve maternal and paternal haplotypes for over 1/3 of the genome. By sequencing and assembling material from a single diploid individual, only two haplotypes are present, simplifying the assembly process compared to samples from multiple pooled individuals. The method presented here can be applied to samples with starting DNA amounts as low as 100 ng per 1 Gb genome size. This new low-input approach puts PacBio-based assemblies in reach for small highly heterozygous organisms that comprise much of the diversity of life.
Lipopolysaccharide (LPS) induces increased epidermal green autofluorescence of mouse
Authors: Li Yujia , Zhang Mingchao , Tao Yue , Ying Weihai 
Published: December 2018

AbstractOur recent studies have suggested that characteristic ‘Pattern of Autofluorescence (AF)’ of each disease could be a novel biomarker for non-invasive diagnosis of multiple major diseases such as acute ischemic stroke. It is necessary to determine if increased epidermal green AF may be produced by major pathological factors such as inflammation. In our current study, we used C57BL/6Slac mice exposed to LPS to test our hypothesis that inflammation may induce increased epidermal green AF: LPS rapidly induced significant increases in the epidermal green AF of the mice’s ears at 1 hr after LPS injection. LPS also dose-dependently increased the epidermal green AF. The AF intensity had a linear relationship with the LPS dosages at both 3 and 7 days after the LPS administration. The AF images exhibited the characteristic structure of the keratinocytes in Stratum Spinosum, suggesting that the origin of the increased AF was keratin 1 and/or keratin 10. Collectively, our current study has provided the first evidence indicating that inflammation can rapidly and dose-dependently induce increased epidermal green AF, suggesting that the green AF may be the first biomarker for non-invasive and rapid detection of systemic inflammation. Since inflammation is a key pathological factor of numerous diseases, our finding has highlighted the value of the epidermal AF as a novel diagnostic biomarker for numerous diseases.