bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defect in Brnym1, a magnesium-dechelatase protein, causes a stay-green phenotype in an EMS-mutagenized Chinese cabbage (Brassica campestris L. ssp. pekinensis) line
Authors: Wang Nan , Zhang Yun , Huang Shengnan , Liu Zhiyong , Li Chengyu , Feng Hui 
Published: January 2020

AbstractLeaf color is an important target trait in Chinese cabbage breeding programs. Leaf yellowing may reduce crop commercial and nutritional values. Some plants with the “stay-green” trait maintain leaf greenness during senescence and even after death. Stay-green Chinese cabbage may be a focal point of future breeding projects because it could improve crop quality and yield and prolong shelf life. A new stay-green mutant,non-yellowing mutant 1(nym1), was identified in Chinese cabbage derived from an ethyl methane sulfonate (EMS)-mutagenized population. The mutant had stay-green characteristics and a higher chlorophyll content than the wild-type during leaf senescence. The stay-green trait in the mutant Chinese cabbage was controlled by the recessive geneBrnym1. MutMap and KASP analyses showed thatBrnym1(BraA03g050600.3C) encodes an mg-dechelatase (SGR protein), which might be the causal gene of the mutation in Chinese cabbage. A nonsynonymous single nucleotide base substitution (G to A) in the third exon ofBrnym1caused an amino acid substitution from L to F in the highly conserved domain of the magnesium-dechelatase. Ectopic overexpression showed that theBrNYM1gene of wild-type Chinese cabbage complemented the SGR-defective stay-green mutantnye1-1ofArabidopsis. The magnesium-dechelatase activity in thenym1mutant was significantly downregulated compared to that in the wild type.Brnym1was relatively upregulated in the mutant during late senescence, and BrNYM1 was localized to the chloroplasts. These results indicate thatBrnym1(BraA03g050600.3C) is the causal gene of the stay-green mutation and could be of particular significance in the genetic improvement of Chinese cabbage.
LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer
Authors: Giro-Perafita A. , Luo L. , Khodadadi-Jamayran A. , Thompson M. , Akgol Oksuz B. , Tsirigos A. , Dynlacht B. D. , Sánchez I. , Esteva F. J. 
Published: January 2020

AbstractLong non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and progression. LncRNAs are differentially expressed in breast cancer subtypes. Basal-like breast cancers are generally poorly differentiated tumors, are enriched in embryonic stem cell signatures, lack expression of estrogen receptor, progesterone receptor, and HER2 (triple-negative breast cancer), and show activation of proliferation-associated factors. We hypothesized that lncRNAs are key regulators of basal breast cancers. Using The Cancer Genome Atlas, we identified lncRNAs that are overexpressed in basal tumors compared to other breast cancer subtypes and expressed in at least 10% of patients. Remarkably, we identified lncRNAs whose expression correlated with patient prognosis. We then evaluated the function of a subset of lncRNA candidates in the oncogenic process in vitro. Here, we report the identification and characterization of the chromatin-associated lncRNA, RP11-19E11.1, which is upregulated in 40% of basal primary breast cancers. Gene set enrichment analysis in primary tumors and in cell lines uncovered a correlation between RP11-19E11.1 expression level and the E2F oncogenic pathway. We show that this lncRNA is chromatin-associated and an E2F1 target, and its expression is necessary for cancer cell proliferation and survival. Finally, we used lncRNA expression levels as a tool for drug discovery in vitro, identifying protein kinase C (PKC) as a potential therapeutic target for a subset of basal-like breast cancers. Our findings suggest that lncRNA overexpression is clinically relevant. Understanding deregulated lncRNA expression in basal-like breast cancer may lead to potential prognostic and therapeutic applications.
Potential of animal models for advancing the understanding and treatment of pain in Parkinson’s disease
Authors: Buhidma Yazead , Rukavina Katarina , Chaudhuri Kallol Ray , Duty Susan 
Published: January 2020

AbstractPain is a commonly occurring non-motor symptom of Parkinson’s disease (PD). Treatment of pain in PD remains less than optimal and a better understanding of the underlying mechanisms would facilitate discovery of improved analgesics. Animal models of PD have already proven helpful for furthering the understanding and treatment of motor symptoms of PD, but could these models offer insight into pain in PD? This review addresses the current position regarding pain in preclinical models of PD, covering the face and predictive validity of existing models and their use so far in advancing understanding of the mechanisms contributing to pain in PD. While pain itself is not usually measured in animals, nociception in the form of thermal, mechanical or chemical nociceptive thresholds offers a useful readout, given reduced nociceptive thresholds are commonly seen in PD patients. Animal models of PD including the reserpine-treated rat and neurodegenerative models such as the MPTP-treated mouse and 6-hydroxydopamine (6-OHDA)-treated rat each exhibit reduced nociceptive thresholds, supporting face validity of these models. Furthermore, some interventions known clinically to relieve pain in PD, such as dopaminergic therapies and deep brain stimulation of the subthalamic nucleus, restore nociceptive thresholds in one or more models, supporting their predictive validity. Mechanistic insight gained already includes involvement of central and spinal dopamine and opioid systems. Moving forward, these preclinical models should advance understanding of the cellular and molecular mechanisms underlying pain in PD and provide test beds for examining the efficacy of novel analgesics to better treat this debilitating non-motor symptom.
Abbott ARCHITECT Syphilis TP Chemiluminescent Immunoassay Accurately Diagnoses Past or Current Syphilis in Pregnancy
Authors: Adhikari Emily H. , Frame Ithiel J. , Hill Emilie , Fatabhoy Rizwana , Strickland Amanda L. , Cavuoti Dominick , McIntire Donald D. , Hollaway Rita M. 
Published: January 2020

Abstract
Objective We evaluate diagnostic accuracy of the ARCHITECT chemiluminescent immunoassay (CIA) screening test in pregnancy, and evaluate pregnancy outcomes among screen-positive women.
Study Design Samples from routine prenatal rapid plasma reagin (RPR) tests were collected between June 22 and August 18, 2017 and frozen. Samples were batch-tested with the Abbott ARCHITECT syphilis TP immunoassay (CIA, index test). We calculated sensitivity, specificity, predictive value, and false positivity. We compared pregnancy and neonatal outcomes among screen-positive women.
Results Of 1,602 specimens, 35 (2.2%) were RPR + ; of those, 24 (69%) were CIA +/Treponema pallidum particle agglutination assay (TPPA)+ and 11 (31%) were CIA-/TPPA-. Of 1,567 RPR- specimens, 14 (0.9%) were CIA + ; of those, 13 (93%) were TPPA + , and one (7%) had a false positive CIA test. Sensitivity of the CIA (95% CI) was 100% (90.5–100%), specificity 99.9% (99.6–100%), positive predictive value 97.4% (86.2–99.9%), and false positive rate 0.06% (0.002–0.4%) for current or past syphilis. Among 37 CIA +/TPPA+ women, seven (19%) had RPR-negative status (Group 1), 11 (30%) had previously treated syphilis (Group 2), and 19 (51%) had active infection (Group 3). One stillbirth occurred in a woman with early, active syphilis identified at delivery; no adverse perinatal outcomes occurred among women in Groups 1 or 2.
Conclusion The ARCHITECT syphilis TP immunoassay accurately diagnoses current or past syphilis in pregnancy. Clinical history and staging remain essential using a reverse algorithm.
Motion reconstruction for optical tomography of trapped objects
Authors: Elbau Peter , Ritsch-Marte Monika , Scherzer Otmar , Schmutz Denise 
Published: January 2020

Abstract
Optical and acoustical trapping has been established as a tool for holding and moving microscopic particles suspended in a liquid in a contact-free and non-invasive manner. Opposed to standard microscopic imaging, where the probe is fixated, this technique allows imaging in a more natural environment. This paper provides a method for estimating the movement of a transparent particle which is maneuvered by tweezers (assuming that the inner structure of the probe is not subject to local movements) by making use of the assumption of a smooth movement in time. The mathematical formulation of the motion estimation leads to an infinitesimal version of the common line technique used in cryogenic electron microscopy single particle imaging to estimate the orientations of the particles in the probe.
Determination of the primary energy using an ultrathin calorimeter
Authors: Dmitrieva Elena , Fedosimova Anastasiya , Lebedev Igor , Temiraliev Abzal , Abishev Medeu , Kozhamkulov Tolegen , Mayorov Andrey , Spitaleri Claudio 
Published: January 2020

Abstract
An approach for measuring energy of cosmic-ray particles with energies E > 1012 eV using an ultrathin calorimeter is presented. The method is based on the analysis of the correlation dependence of the cascade size on the rate of development of the cascade process. In order to determine the primary energy, measurements are made based on the number of secondary particles in the cascade, N

e
, at two observation levels Z
1 and Z
2, separated by an absorber layer. Based on the obtained measurements, a correlation analysis of the dependence of logN

e
(Z
1) on th
e
difference d
N = logN

e
(Z
1) − logN

e
(Z
2) is carried out. The correlation curves (logN

e
from d
N) in the negative part of the dN axis are almost parallel to each other and practically do not depend on the depth of the cascade development. It makes it possible to determine the primary energy using an ultrathin calorimeter. The best option for applying the method is a calorimeter, which has a unit with a heavy target, leading to the rapid development of the cascade, and a homogeneous measuring and absorption block.
Mixed alkali effect on borosilicate glass structure with vanadyl ion as spin probe
Authors: Nagamani B , Srinivasu Ch 
Published: January 2020

Abstract
Mixed alkali borosilicate glasses doped with 2% vanadium oxide were synthesized by conventional melt-quench method. The Micro structure of the materials was analysed using XRD, SEM and EDX spectrum. Optical nature of glasses was studied by computing optical bandgaps with absorption spectral data. Covalent nature of glasses was estimated correlating optical bandgap energy with EPR spectral data. The metallization criterion of glasses was evaluated from the physical parameters. FTIR and Raman spectral techniques were used to identify the structural groups of the borates and silicates that are formed with addition of modifiers. Emission spectra were recorded at excitation wavelength of 350 nm and their thermal nature was also studied using TGA/DTA techniques.
Hermitian curvature flow on unimodular Lie groups and static invariant metrics
Authors: Lafuente Ramiro , Pujia Mattia , Vezzoni Luigi 
Published: January 2020

We investigate the Hermitian curvature flow (HCF) of leftinvariant metrics on complex unimodular Lie groups. We show that in this setting the flow is governed by the Ricci-flow type equation

∂
t

g

t

=
−

R
i
c

1
,
1

(

g
t

)

\partial _tg_{t}=-{\mathrm { Ric}}^{1,1}(g_t)

. The solution

g
t

g_t

always exists for all positive times, and

(
1
+
t

)

−
1

g
t

(1 + t)^{-1}g_t

converges as

t
→
∞

t\to \infty

in Cheeger–Gromov sense to a nonflat left-invariant soliton

(

G
¯

,

g
¯

)

(\bar G, \bar g)

. Moreover, up to homotheties on each of these groups there exists at most one left-invariant soliton solution, which is a static Hermitian metric if and only if the group is semisimple. In particular, compact quotients of complex semisimple Lie groups yield examples of compact non-Kähler manifolds with static Hermitian metrics. We also investigate the existence of static metrics on nilpotent Lie groups and we generalize a result of Enrietti, Fino, and the third author [J. Symplectic Geom. 10 (2012), no. 2, 203–223] for the pluriclosed flow. In the last part of the paper we study the HCF on Lie groups with abelian complex structures.
Implementing Low-Cost, High Accuracy DNA Barcoding From Single Molecule Sequencing to Screen Larval Tephritid Fruit Flies Intercepted at Ports of Entry
Authors: Garzón-Orduña Ivonne J , Geib Scott M , Ledezma Lisa , Bremer Forest T , Barr Norman B 
Published: January 2020

AbstractExotic fruit flies in the family Tephritidae pose a threat to U.S. agriculture and natural resources. As part of ongoing fruit fly detection and exclusion programs, invasive fruit fly adults are periodically trapped in and introduced populations are eradicated from two major fruit producing states: California and Florida. Although the pathways used by flies to enter these states are not clear, one possible introduction pathway is hand-carrying fruits and vegetables infested with eggs or larvae through ports of entry during border crossings or international air travel. These collections represent an important resource for determining what species are most commonly associated with particular ports of entry, their host plants, and source country, making the identification of the intercepted larvae fundamental. Here, we examine cytochrome c oxidase subunit I sequences obtained with Sanger DNA sequencing and Single Molecule Real-time sequencing (SMRT) technologies on a collection of hundreds of intercepted larvae and pupae that are suspected to be fruit pests found in the subfamily Dacinae, in addition to a collection of field-caught flies. Utilizing Pacific Biosciences (PacBio) Circular Consensus Sequencing, we sequenced thousands of independent amplicons in a single SMRT cell. We present our implementation of PacBio’s method by describing wet-lab procedures as well as analytical protocols to automate the process. Finally, for the intercepted material, we compared the generated SMRT data to sequences produced with Sanger and evaluate their quality as a means to identify flies. Using intercepted material, we obtained a sequencing success of over 88% with PacBio’s SMRT sequencing. As the spread of invasive insects grow, so will the size of collections of intercepted material; we found technologies such as SMRT sequencing to be excellent resources to simplify the generation of large amounts of molecular data and to reduce or eliminate all together the manipulation of the sequences.
How Good Is the Phoneme Elision Test in Assessing Reading, Spelling and Arithmetic-Related Abilities?
Authors: Barbosa-Pereira Drielle , Martins Pedro S R , Guimarães Amanda P L , Silva Emanuelle de O , Batista Luana T , Haase Vitor G , Lopes-Silva Júlia B 
Published: January 2020

AbstractObjectiveThe aim of this study was to investigate the psychometric properties and diagnostic accuracy of phoneme elision task (PET).MethodWe assessed cross-sectionally 470 Brazilian children (54.3% girls) aged between 7 and 11 years (mean age = 8.83, sd = 0.85), from the 2nd to 4th grades. Children were assessed in their phonemic awareness ability, as well as intelligence, general school achievement, both verbal and visuospatial working memory, single-word reading, and nonsymbolic magnitude comparison. Beyond the psychometric properties and diagnostic accuracy of PET, we also provided reference values.ResultsOur data suggest that PET is composed mainly of one single construct, with high item reliability and precision (KR-20 above 0.90). In general, items have acceptable discriminability, considering item-total correlations. Overall PET is generally a good screening tool for reading and spelling difficulties (SD), as well as to identify children with learning difficulties in the early grades. However, it is not a reliable measure for screening math learning difficulties. Finally, PET shows good convergent and divergent validity.ConclusionsWe provide evidence about the psychometric properties and diagnostic accuracy of a PET. Results contribute to the assessment of phonemic awareness in Brazilian children, in both clinical and research contexts. The PET can be used as a screening tool for reading and SD, which could lead to early interventions.
Estimating disease onset from change points of markers measured with error
Authors: Lee Unkyung , Carroll Raymond J , Marder Karen , Wang Yuanjia , Garcia Tanya P 
Published: January 2020

Summary
Huntington disease is an autosomal dominant, neurodegenerative disease without clearly identified biomarkers for when motor-onset occurs. Current standards to determine motor-onset rely on a clinician’s subjective judgment that a patient’s extrapyramidal signs are unequivocally associated with Huntington disease. This subjectivity can lead to error which could be overcome using an objective, data-driven metric that determines motor-onset. Recent studies of motor-sign decline—the longitudinal degeneration of motor-ability in patients—have revealed that motor-onset is closely related to an inflection point in its longitudinal trajectory. We propose a nonlinear location-shift marker model that captures this motor-sign decline and assesses how its inflection point is linked to other markers of Huntington disease progression. We propose two estimating procedures to estimate this model and its inflection point: one is a parametric method using nonlinear mixed effects model and the other one is a multi-stage nonparametric approach, which we developed. In an empirical study, the parametric approach was sensitive to correct specification of the mean structure of the longitudinal data. In contrast, our multi-stage nonparametric procedure consistently produced unbiased estimates regardless of the true mean structure. Applying our multi-stage nonparametric estimator to Neurobiological Predictors of Huntington Disease, a large observational study of Huntington disease, leads to earlier prediction of motor-onset compared to the clinician’s subjective judgment.
Thalamic-Medial Temporal Lobe Connectivity Underpins Familiarity Memory
Authors: Kafkas Alex , Mayes Andrew R , Montaldi Daniela 
Published: January 2020

Abstract
The neural basis of memory is highly distributed, but the thalamus is known to play a particularly critical role. However, exactly how the different thalamic nuclei contribute to different kinds of memory is unclear. Moreover, whether thalamic connectivity with the medial temporal lobe (MTL), arguably the most fundamental memory structure, is critical for memory remains unknown. We explore these questions using an fMRI recognition memory paradigm that taps familiarity and recollection (i.e., the two types of memory that support recognition) for objects, faces, and scenes. We show that the mediodorsal thalamus (MDt) plays a material-general role in familiarity, while the anterior thalamus plays a material-general role in recollection. Material-specific regions were found for scene familiarity (ventral posteromedial and pulvinar thalamic nuclei) and face familiarity (left ventrolateral thalamus). Critically, increased functional connectivity between the MDt and the parahippocampal (PHC) and perirhinal cortices (PRC) of the MTL underpinned increases in reported familiarity confidence. These findings suggest that familiarity signals are generated through the dynamic interaction of functionally connected MTL-thalamic structures.
Bacterial Infections Associated With Substance Use Disorders, Large Cohort of United States Hospitals, 2012–2017
Authors: McCarthy Natalie L , Baggs James , See Isaac , Reddy Sujan C , Jernigan John A , Gokhale Runa H , Fiore Anthony E 
Published: January 2020

Abstract

Background
Rises in the incidence of bacterial infections, such as infective endocarditis (IE), have been reported in conjunction with the opioid crisis. However, recent trends for IE and other serious infections among persons with substance use disorders (SUDs) are unknown.

Methods
Using the Premier Healthcare Database, we identified hospitalizations from 2012 through 2017 among adults with primary discharge diagnoses of bacterial infections and secondary SUD diagnoses, using International Classification of Diseases, Clinical Modification Ninth and Tenth Revision codes. We calculated annual rates of infections with SUD diagnoses and evaluated temporal trends. Blood and cardiac tissue specimens were identified from IE hospitalizations to describe the microbiology distribution and temporal trends among hospitalizations with and without SUDs.

Results
Among 72 481 weighted IE admissions recorded, SUD diagnoses increased from 19.9% in 2012 to 39.4% in 2017 (P &lt; .0001). Hospitalizations with SUDs increased from 1.1 to 2.1 per 100 000 persons for IE, 1.4 to 2.4 per 100 000 persons for osteomyelitis, 0.5 to 0.9 per 100 000 persons for central nervous system abscesses, and 24.4 to 32.9 per 100 000 persons for skin and soft tissue infections. For adults aged 18–44 years, IE-SUD hospitalizations more than doubled, from 1.6 in 2012 to 3.6 in 2017 per 100 000 persons. Among all IE-SUD hospitalizations, 50.3% had a Staphylococcus aureus infection, compared with 19.4% of IE hospitalizations without SUDs.

Conclusions
Rates of hospitalization for serious infections among persons with SUDs are increasing, driven primarily by younger age groups. The differences in the microbiology of IE hospitalizations suggest that SUDs are changing the epidemiology of these infections.
Clinical Exome Studies Have Inconsistent Coverage
Authors: Gotway Garrett , Crossley Eric , Kozlitina Julia , Xing Chao , Fan Judy , Hornbuckle Callie , Thies Jenny , Michel Donnice , Quinn Christine , Scheuerle Angela E , Umana Luis A , Uhles Crescenda L , Park Jason Y 
Published: January 2020

Abstract

BACKGROUND
Exome sequencing has become a commonly used clinical diagnostic test. Multiple studies have examined the diagnostic utility and individual laboratory performance of exome testing; however, no previous study has surveyed and compared the data quality from multiple clinical laboratories.

METHODS
We examined sequencing data from 36 clinical exome tests from 3 clinical laboratories. Exome data were compared in terms of overall characteristics and coverage of specific genes and nucleotide positions. The sets of genes examined included genes in Consensus Coding Sequence (CCDS) (n = 17723), a subset of genes clinically relevant to epilepsy (n = 108), and genes that are recommended for reporting of secondary findings (n = 57; excludes X-linked genes).

RESULTS
The average exome nucleotide coverage (≥20×) of each laboratory varied at 96.49% (CV = 3%), 96.54% (CV = 1%), and 91.68% (CV = 4%), for laboratories A, B, and C, respectively. For CCDS genes, the average number of completely covered genes varied at 12184 (CV = 29%), 11687 (CV = 13%), and 5989 (CV = 37%), for laboratories A, B, and C, respectively. With smaller subsets of genes related to epilepsy and secondary findings, the CV revealed low consistency, with a maximum CV seen in laboratory C for both epilepsy genes (CV = 60%) and secondary findings genes (CV = 71%).

CONCLUSIONS
Poor consistency in complete gene coverage was seen in the clinical exome laboratories surveyed. The degree of consistency varied widely between the laboratories.