bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Droplet Digital PCR Human mtDNA Assay for Global Fecal Source Tracking
Authors: Zhu Kevin , Suttner Brittany , Konstantinidis Konstantinos T. , Brown Joe 
Published: October 2019

AbstractHuman mitochondrial DNA (mtDNA) provides a promising target for microbial source tracking because it is unique to humans and universal across human individuals. We developed a droplet digital PCR (ddPCR) assay, hCYTB484, targeting the cytochrome b gene of the human mtDNA and compared the performance of the hCYTB484 assay with a widely used assay targeting human-associated Bacteroides, the HF183/BacR287 assay. We also defined and validated the analytical limit of detection and analytical lower limit of quantification; these analytical limits determine the concentration levels above which samples are declared to be positive and quantifiable for the target, respectively. We found both assays to be highly specific (95%) against cow and pig feces; however, the hCYTB484 was more sensitive when tested against individual human feces from US, Bangladesh, and Mozambique (100% versus a mean of 51% across the 3 countries). To further compare the performance of the two assays, we utilized a receiver operating characteristic curve, showing that the hCYTB484 marker was widely distributed across human feces from the 3 different geographical regions tested and in higher quantities than the HF183/BacR287 marker. The higher performance of the hCYTB484 marker in individual feces is a desirable characteristic in the detection of fecal pollution from sources to which fewer individuals contribute, such as non-sewered types of sanitation that serve most of Earth’s population and carry the highest risk of exposure to fecal-oral pathogens.ImportanceThe usefulness of an ideal human-specific, culture- and library-independent marker to the microbial source tracking field is reflected by the numerous efforts to develop such markers; however, thus far, microbial-based markers of this type have exhibited variable source-specificity across geographies and variable sensitivity across scales of fecal waste. Most of the world’s population is served by non-sewered forms of sanitation that also carry the highest risk of exposure to fecal-oral pathogens. This reality underscores the need for markers of human fecal contamination that have high sensitivity in fecal pollution sources to which fewer individuals contribute to, such as fecal sludges found in pit latrines. We show that human mtDNA-based methods can be highly source-specific and highly sensitive in smaller scales of fecal pollution, providing a useful addition to the microbial source tracking toolbox by complementing the variable performance of microbial-based markers.
Real‐world experiences of apremilast in clinics for Japanese patients with psoriasis
Authors: Saruwatari Hiroshi 
Published: October 2019

AbstractPsoriasis, though not an immediately life‐threatening disorder, still lowers quality of life and disrupts daily functions. While many treatments for psoriasis exist, few are convenient and safe long term; even if sufficiently effective, treatments themselves often decrease quality of life and make long‐term treatment adherence difficult. Approved in Japan in December 2016, apremilast was expected to function as a simple, long‐term, systemic therapeutic agent for psoriasis. We report on the clinical outcomes of administrating apremilast for 2 years as observed in 46 psoriatic patients at the Saruwatari Dermatology Clinic between March 2017 and February 2019. We believe the ease of clinic consultation (as compared with large general hospital consultation) draws patients who are busy or have mild symptoms, and consequently poor adherence to regular visits and treatment, reflecting realistic conditions. Major adverse events with apremilast treatment were diarrhea (37.0%) and nausea (15.3%), with most cases of diarrhea being mild. Drug survival analysis by the Kaplan–Meier method revealed a 1‐year continuation rate of 46.8% and a 2‐year continuation rate of 37.4%. Dermatology Life Quality Index (DLQI) scores during the observation period declined from 9.3 to 2.8 (P < 0.0001) on average, with the DLQI‐0/1 achievement rate being 28.6%. Based on our findings, we conclude that apremilast is suitable as a long‐lasting basic treatment that is easy to prescribe in small clinics and easy to use in everyday life.
Sex, senescence, sources and sinks
Authors: Galipaud Matthias , Kokko Hanna 
Published: October 2019

Abstract

Why do most organisms age, and why do most of them reproduce sexually? Does sex rejuvenate? We review progress that has been made linking theories of senescence with those of sexual reproduction.

We show that there is a dearth of theory against the numerous questions waiting to be answered theoretically or empirically: observed senescence patterns are a result of past selection acting on individuals of different age categories and abundances, modes of reproduction (asexual, sexual, facultatively sexual, via buds or zygotes). Modular organisms present their own challenges. Assigning offspring an unambiguous age of zero at birth is often too simplistic.

We also comment on germline mutations as a form of ageing over generations (Lansing effect) and ask whether there is value in reinvigorating an old metaphor (1988, Sex and death in the protozoa. New York, NY, USA: Cambridge University Press) of chairs and their chairmakers who both are subject to deterioration over time, since endogenous repair is never foolproof.

Future theory could usefully revisit a known mathematical analogy between selection on senescence across age classes and source–sink theory. Some modes of reproduction (particularly asexuality) may yield offspring that are, in a sense, already aged, with the problem increasing over generations (ultimately leading to a demographic sink). Insofar as sexuality ‘rejuvenates’, it does so through a gamble that, with some frequency, produces ‘exogenously repaired’ individuals that act as a source of genes to future generations. This gamble has been argued to be managed best when life cycles include a unicellular stage (zygote), an argument that could be usefully complemented with an analysis of the relevant economic trade‐offs between offspring size and number.

A free Plain Language Summary can be found within the Supporting Information of this article.
Navigating through therpackages for movement
Authors: Joo Rocío , Boone Matthew E. , Clay Thomas A. , Patrick Samantha C. , Clusella‐Trullas Susana , Basille Mathieu 
Published: October 2019

AbstractThe advent of miniaturized biologging devices has provided ecologists with unprecedented opportunities to record animal movement across scales, and led to the collection of ever‐increasing quantities of tracking data. In parallel, sophisticated tools have been developed to process, visualize and analyse tracking data; however, many of these tools have proliferated in isolation, making it challenging for users to select the most appropriate method for the question in hand. Indeed, within thersoftware alone, we listed 58 packages created to deal with tracking data or ‘tracking packages’.Here, we reviewed and described each tracking package based on a workflow centred around tracking data (i.e. spatio‐temporal locations (x,y,t)), broken down into three stages: pre‐processing, post‐processing and analysis, the latter consisting of data visualization, track description, path reconstruction, behavioural pattern identification, space use characterization, trajectory simulation and others.Supporting documentation is key to render a package accessible for users. Based on a user survey, we reviewed the quality of packages' documentation and identified 11 packages with good or excellent documentation.Links between packages were assessed through a network graph analysis. Although a large group of packages showed some degree of connectivity (either depending on functions or suggesting the use of another tracking package), one third of the packages worked in isolation, reflecting a fragmentation in thermovement‐ecology programming community.Finally, we provide recommendations for users when choosing packages, and for developers to maximize the usefulness of their contribution and strengthen the links within the programming community.
Re‐assessing microbiomes in the low‐biomass reproductive niche
Authors: O’Callaghan JL , Turner R , Dekker Nitert M , Barrett HL , Clifton V , Pelzer ES 
Published: October 2019

The female reproductive tract represents a continuum between the vagina and the upper genital tract. New evidence from cultivation‐independent studies suggests that the female upper genital tract is not sterile; however, the significance of this for reproductive health and disease remains to be elucidated fully. Further, diagnosis and treatment of infectious reproductive tract pathologies using cultivation‐independent technologies represents a largely unchartered area of modern medical science. The challenge now is to design well‐controlled experiments to account for the ease of contamination known to confound molecular‐based studies of low‐biomass niches, including the uterus and placenta. This will support robust assessment of the potential function of microorganisms, microbial metabolites, and cell‐free bacterial DNA on reproductive function in health and disease.Tweetable abstractMolecular microbial studies of low‐biomass niches require stringent experimental controls to reveal causal relations in reproductive health and disease.
G protein‐coupled receptor kinase‐2: A potential biomarker for early diabetic cardiomyopathy
Authors: Lai Shuiqing , Fu Xiaoying , Yang Shufen , Zhang Shuting , Lin Qiuxiong , Zhang Mengzhen , Chen Hongmei 
Published: October 2019

AbstractBackgroundG protein‐coupled receptor kinase‐2 (GRK2) has been shown as a key regulator of cardiac function, and the myocardial GRK2 levels are mirrored by the levels in peripheral blood mononuclear cells (PBMCs). In this study, we evaluated the myocardial and PBMCs GRK2 levels in early diabetic cardiomyopathy (DCM).MethodsC57BL/KS‐db/db male diabetic mice at 12 weeks of age, as the type 2 diabetes (T2DM) animal model of early DCM were evaluated. Forty‐four T2DM patients with left ventricular diastolic dysfunction (LVDD), without evidence of hypertension, coronary artery diseases, congestive heart failure, and diabetic complications and without evidence of ischemia in a maximal treadmill exercise test, were recruited as the DM + LVDD group; 30 age‐matched T2DM patients without LVDD were recruited as the DM control group. Left ventricular diastolic function was evaluated by cardiac tissue Doppler. The pseudonormal pattern of ventricular filling and E′/A′ < 1 were regarded as LVDD.ResultsCompared to 8‐week‐old diabetic mice and 12‐week‐old control mice, GRK2‐mRNA level and expression in myocardial tissues of 12‐week‐old diabetic mice were significantly increased, as well as the left ventricular wall thickness and systolic function. And the collagen volume fraction (CVF), collagen‐3 expression, P53 expression, and cell apoptotic rate in the myocardium of 12‐week‐old diabetic mice elevated as well. The GRK2‐mRNA level in PBMCs of DM with LVDD was significantly higher than in DM control without LVDD.ConclusionsGRK2 expression increased in the myocardial tissue and the PBMCs at the early stage of DCM. These data support further research on the role of GRK2 as the clinical biomarker for early DCM.
Magnetocardiography for identification of coronary ischemia in patients with chest pain and normal resting 12‐lead electrocardiogram
Authors: Ramesh Raja , Senthilnathan Sengottuvel , Satheesh Santhosh , Swain Pragyna Parimita , Patel Rajesh , Ananthakrishna Pillai Ajith , Katholil Gireesan , Selvaraj Raja J. 
Published: October 2019

AbstractBackgroundIdentification of coronary ischemia in patients presenting with chronic chest pain is difficult as resting ECG can be normal. Diagnosis of coronary ischemia requires evaluation during exercise or pharmacological stress. A noninvasive test to identify coronary ischemia at rest without the need for exercise is desirable. We studied the diagnostic accuracy of magnetocardiography (MCG) at rest to detect coronary ischemia in these patients.MethodsPatients with chronic chest pain and suspected coronary ischemia with a normal ECG were included. Patients underwent treadmill test (TMT) and were divided into TMT positive and TMT negative groups. MCG was recorded in a magnetically shielded room. Iso‐field contour maps generated at the T‐wave peak were compared between the groups. From the magnetic field map (MFM), the magnetic field angle at T‐wave peak was calculated and was also compared across the two groups.ResultsThere were a total of 29 patients, 12 with positive TMT and 17 with negative TMT. An abnormal magnetic field angle was more common in the TMT positive group (72% vs. 6%). Abnormal contour maps in the form of nondipole patterns or abnormal orientation were seen in 81.8% (9/11) patients in TMT positive group and 6.8% (1/17) patients in the TMT negative group (p < .001).ConclusionAbnormal magnetic field angle and abnormal magnetic field maps in MCG recorded at rest are able to identify the presence of coronary ischemia in patients with chronic chest pain and a normal resting ECG.
Cervico‐vaginal placental α‐macroglobulin‐1 combined with cervical length for the prediction of preterm birth in women with threatened preterm labor
Authors: Radan Anda‐Petronela , Aleksandra Polowy Justyna , Heverhagen Anneke , Simillion Cedric , Baumann Marc , Raio Luigi , Schleussner Ekkehard , Mueller Martin , Surbek Daniel 
Published: October 2019

AbstractIntroductionPreterm birth is a major cause of neonatal morbidity and mortality. There is an urgent need to accurately predict imminent delivery to enable necessary interventions such as tocolytic, glucocorticoid, and magnesium sulfate administration. We aimed to evaluate placental α‐macroglobulin‐1 as a new diagnostic marker in the prediction of preterm birth.Material and methodsWe performed a prospective observational trial in women with intact membranes between 24+0 and 36+6 weeks of gestation. We included both women with and without threatened preterm labor symptoms. We evaluated the test performance of placental α‐macroglobulin‐1 measurements in cervicovaginal fluid regarding three different presentation‐to‐delivery intervals: ≤2, ≤7, ≤14 days. In addition, we calculated placental α‐macroglobulin‐1 performance in combination with other prognostic factors such as ultrasonographic cervical length measurements.ResultsWe included 126 women in the study. We detected high specificity (97%‐98%) and negative predictive value (89%‐97%) for placental α‐macroglobulin‐1 at all time intervals. We assessed placental α‐macroglobulin‐1 in combination with cervical length measurements (≤15 mm) in the sub‐group of women presenting with threatened preterm labor symptoms (n = 63) and detected high positive predictive values (100%) for 7‐ and 14‐day presentation‐to‐delivery intervals.ConclusionsOur study provides evidence that placental α‐macroglobulin‐1 testing in cervicovaginal fluid, in combination with cervical length measurements, accurately predicts preterm birth in women with preterm labor symptoms. This novel test combination may be used clinically to triage women presenting with threatened preterm labor, avoiding overtreatment and unnecessary hospitalizations.
High‐throughput sequencing of T‐cell receptor alpha chain clonal rearrangements at the DNA level in lymphoid malignancies
Authors: Komkov Alexander , Miroshnichenkova Anna , Nugmanov Gaiaz , Popov Alexander , Pogorelyy Mikhail , Zapletalova Eva , Jelinkova Hana , Pospisilova Sarka , Lebedev Yuri , Chudakov Dmitriy , Olshanskaya Yulia , Plevova Karla , Maschan Michael , Mamedov Ilgar 
Published: October 2019

SummaryRearrangements of T‐ and B‐cell receptor (TCR and BCR) genes are useful markers for clonality assessment as well as for minimal residual disease (MRD) monitoring during the treatment of haematological malignancies. Currently, rearrangements of three out of four TCR and all BCR loci are used for this purpose. The fourth TCR gene, TRA, has not been used so far due to the lack of a method for its rearrangement detection in genomic DNA. Here we propose the first high‐throughput sequencing based method for the identification of clonal TRA gene rearrangements at the DNA level. The method is based on target amplification of the rearranged TRA locus using an advanced multiplex polymerase chain reaction system and high‐throughput sequencing, and has been tested on DNA samples from peripheral blood of healthy donors. Combinations of all functional V‐ and J‐segments were detected, indicating the high sensitivity of the method. Additionally, we identified clonal TRA rearrangements in 57 out of 112 tested DNA samples of patients with various T‐lineage lymphoproliferative disorders. The method fills the existing gap in utilizing the TRA gene for a wide range of studies, including clonality assessment, MRD monitoring and clonal evolution analysis in different lymphoid malignancies.
Mycobacterium tuberculosis does not show evidence of molecular DNA in human cadaveric ocular tissues in an endemic setting
Authors: Chauhan Harish , Bansal Reema , Kumar Aman , Sharma Surya P. , Gude Geethanjali , Nahar Uma , Singh Ramandeep , Jain Arun K. , Gupta Vishali 
Published: October 2019

AbstractBackgroundMycobacterium tuberculosis (MTB) in latent infection has been demonstrated in pulmonary/extra‐pulmonary locations (lung, spleen, liver, kidney, adipose tissue) in autopsy studies, but its presence in ocular tissues in the latent state is not known.MethodsWe conducted molecular and histopathological study of 100 cadaver eyes (50 humans) who died from causes other than tuberculosis (TB) (and were potential candidates for corneal transplantation) to detect MTB in ocular tissues in an endemic setting. After removal of the corneal button, an 8 to 10 mm block of tissue (choroid, retina and part of the vitreous) was excised from the remaining globe for DNA isolation. Gel‐based IS6110 and devR3 polymerase chain reaction (PCR) assays were done, followed by real‐time PCR using beta actin gene as an internal control. Sixteen randomly selected DNA samples were double checked using a commercial kit for MTB and non‐tuberculous mycobacteria (NTM) DNA. The remaining larger part of the globe was subjected to histopathology.ResultsThe mean age was 65.14 ± 18 years. All 100 samples were negative for both IS6110 and devR, and all 16 samples were negative with NTM MTB commercial kit. All samples were negative with Ziehl‐Neelsen stain for acid fast bacilli and none showed any inflammation or granulomatous pathology.ConclusionsMTB could not be detected in human ocular tissues in latent state in India, a TB‐endemic country. This may suggest the inability of MTB to seed ocular tissues in the latent state, unlike other organs which serve as reservoirs for the bacilli in the absence of manifest disease.
Combined soil and foliar ZnSO4 application improves wheat grain Zn concentration and Zn fractions in a calcareous soil
Authors: Zhao Aiqing , Wang Bini , Tian Xiaohong , Yang Xingbin 
Published: October 2019

AbstractDietary zinc (Zn) deficiency is a common micronutrient deficiency in humans. Zinc fertilization has been proved to be an effective approach to improve grain Zn concentration in wheat and alleviate Zn deficiency in humans. To maximize the potential of Zn fertilization, it is necessary to select appropriate Zn fertilizer forms and application methods. Here, combined soil and foliar application of ZnSO4, rather than Zn‐EDTA, effectively increased grain Zn concentration in winter wheat (Triticum aestivum L. cv. “Xiaoyan 22”) grown in a calcareous soil. However, neither ZnSO4 nor Zn‐EDTA, when applied to the soil or the foliage alone, had any significant effect on grain Zn concentration. The fractions of Zn loosely bound to organic matter, carbonate‐bound Zn and manganese oxide‐bound Zn in the rhizosphere soil changed dynamically over the course of the wheat growth period, with the highest levels found at the jointing stage. The residual ZnSO4 fertilizer had a positive effect on grain Zn concentration in the subsequent wheat crop due to increased storage of phytic acid in wheat grains and high concentrations of Zn loosely bound to organic matter and carbonate‐bound Zn in the soil. In comparison, Zn‐EDTA applied to the soil only increased the exchangeable‐Zn fraction, and had little residual effect on any other Zn fraction. Repeated soil applications of Zn‐EDTA would be effective to improve grain Zn concentration in wheat plants in subsequent years.Highlights
Effects of Zn fertilization in a calcareous soil were tested by a 3‐year field experiment.
Combined soil and foliar application of ZnSO4 improved grain Zn concentration in wheat.
Foliar ZnSO4 or Zn‐EDTA application alone had no significant effects on grain Zn concentration.
Soil ZnSO4 application had a long‐term positive effect on grain Zn concentration in the subsequent wheat crop.
Genetic attribution and perceived impact of epilepsy in multiplex epilepsy families
Authors: Garofalo Diana C. , Sorge Shawn T. , Hesdorffer Dale C. , Winawer Melodie R. , Phelan Jo C. , Chung Wendy K. , Ottman Ruth 
Published: October 2019

AbstractObjectiveStudies have found that affected individuals who believe the cause of their disorder is genetic may react in various ways, including optimism for improved treatments and pessimism due to perceived permanence of the condition. This study assessed the psychosocial impact of genetic attribution among people with epilepsy.MethodsStudy participants were 165 persons with epilepsy from multiplex epilepsy families who completed a self‐administered survey. Psychosocial impact of epilepsy was assessed with the Impact of Epilepsy Scale, containing items about relationships, employment, overall health, self‐esteem, and standard of living. Genetic attribution was assessed using a scale derived from three items asking about the role of genetics in causing epilepsy in the family, the chance of having an epilepsy‐related mutation, and the influence of genetics in causing the participant's epilepsy. We estimated prevalence ratios (PRs) for impact of epilepsy above the median using Poisson regression with robust standard errors, adjusting for number of lifetime seizures and time since last seizure.ResultsParticipants’ age averaged 51 years; 87% were non‐Hispanic white, 63% were women, and 54% were college graduates. The genetic attribution scale was significantly associated with having a high impact of epilepsy (adjusted PR = 1.4, 95% confidence interval = 1.07‐1.91, P = .02). One of the three genetic attribution questions was also significantly associated with a high impact of epilepsy (belief that genetics had a big role in causing epilepsy in the family, adjusted PR = 1.8).SignificanceThese findings reflect an association between the psychosocial impact of epilepsy and the belief that epilepsy has a genetic cause, among people with epilepsy in families containing multiple affected individuals. This association could arise either because belief in a genetic cause leads to increased psychosocial impacts, or because a greater psychosocial impact of epilepsy leads some to believe their epilepsy is genetic.