bluuebunny/crossref_metadata_2025_split huggingface dataset:
PyPHLAWD: A python tool for phylogenetic dataset construction
Authors: Smith Stephen A. , Walker Joseph F. 
Published: September 2018

Abstract

Comprehensive phylogenetic trees are essential for many ecological and evolutionary studies. Researchers may use existing trees or construct their own. In order to infer new trees, researchers often rely on programmes that construct datasets from publicly available molecular data.

Here, we present PyPHLAWD, a phylogenetically guided tool written in python that creates molecular datasets for building trees. PyPHLAWD constructs clusters (putative orthologs) that may be used for downstream analyses and provides users with a set of easy to interpret results. PyPHLAWD can conduct both baited (analyses that require the identification of gene regions a priori) and clustering analyses (analyses that do not require a priori identification of gene regions).

PyPHLAWD is extensible, flexible, open source, and available at https://github.com/FePhyFoFum/PyPHLAWD, with a detailed website outlining instructions and functionality at https://fephyfofum.github.io/PyPHLAWD/.

The utility of PyPHLAWD is highlighted here with an example workflow for the plant clade Dipsacales and may be applied to any clade with publicly available data on GenBank.
Clozapine as a first‐ or second‐line treatment in schizophrenia: a systematic review and meta‐analysis
Authors: Okhuijsen‐Pfeifer C. , Huijsman E. A. H. , Hasan A. , Sommer I. E. C. , Leucht S. , Kahn R. S. , Luykx J. J. 
Published: September 2018

ObjectiveNo consensus exists on whether clozapine should be prescribed in early stages of psychosis. This systematic review and meta‐analysis therefore focus on the use of clozapine as first‐line or second‐line treatment in non‐treatment‐resistant patients.MethodsArticles were eligible if they investigated clozapine compared to another antipsychotic as a first‐ or second‐line treatment in non‐treatment‐resistant schizophrenia spectrum disorders (SCZ) patients and provided data on treatment response. We performed random‐effects meta‐analyses.ResultsFifteen articles were eligible for the systematic review (N = 314 subjects on clozapine and N = 800 on other antipsychotics). Our meta‐analysis comparing clozapine to a miscellaneous group of antipsychotics revealed a significant benefit of clozapine (Hedges’ g = 0.220, P = 0.026, 95% CI = 0.026–0.414), with no evidence of heterogeneity. In addition, a sensitivity analysis revealed a significant benefit of clozapine over risperidone (Hedges’ g = 0.274, P = 0.030, 95% CI = 0.027–0.521).ConclusionThe few eligible trials on this topic suggest that clozapine may be more effective than other antipsychotics when used as first‐ or second‐line treatment. Only large clinical trials may comprehensively probe disease stage‐dependent superiority of clozapine and investigate overall tolerability.
Carotid Artery Calcification on Orthopantomograms (CACO Study) – is it indicative of carotid stenosis?
Authors: Constantine S , Roach D , Liberali S , Kiermeier A , Sarkar P , Jannes J , Sambrook P , Anderson P , Beltrame J 
Published: September 2018

AbstractIt is unclear whether incidental carotid artery calcification (CAC) on radiographs has a defined relationship to clinically significant carotid artery stenosis, and therefore risk of stroke. The primary objective of this study was to ascertain the relationship between dental radiograph detected carotid calcification and carotid artery stenoses ≥50% on carotid duplex ultrasound. We carried out an observational study of patients undergoing routine dental orthopantomogram (OPG) examinations. Consecutive patients with CAC on OPG were prospectively matched to those without CAC based on age and gender. Ultrasound of the carotid arteries was performed to determine the presence of stenosis (≥50%) in either vessel. Of 5780 consecutive OPG examinations with suitable images for analysis, CAC was detected in 10.8%. A total of 233 patients underwent carotid ultrasound (130 with and 103 without CAC on OPG). The prevalence of a clinically significant (≥50%) carotid stenosis on ultrasound was 15.4% (20/130) in those with CAC and 5.8% (6/103) for those without CAC on OPG. Incidental CAC detected on routine OPG requires both radiological reporting and clinical follow‐up since 1 in 7 patients will have a clinically significant carotid artery stenosis as compared with 1 in 20 patients who do not have CAC.Trial Registration: Australian and New Zealand Clinical Trials Registry website (U1111‐1148‐1066). http://www.ANZCTR.org.au/ACTRN12613001038785.aspx
Diagnosis and management of NSAID‐Exacerbated Respiratory Disease (N‐ERD)—a EAACI position paper
Authors: Kowalski Marek L. , Agache Ioana , Bavbek Sevim , Bakirtas Arzu , Blanca Miguel , Bochenek Grażyna , Bonini Matteo , Heffler Enrico , Klimek Ludger , Laidlaw Tanya M. , Mullol Joaquim , Niżankowska‐Mogilnicka Ewa , Park Hae‐Sim , Sanak Marek , Sanchez‐Borges Mario , Sanchez‐Garcia Silvia , Scadding Glenis , Taniguchi Masami , Torres Maria J. , White Andrew A. , Wardzyńska Aleksandra 
Published: September 2018

AbstractNSAID‐exacerbated respiratory disease (N‐ERD) is a chronic eosinophilic, inflammatory disorder of the respiratory tract occurring in patients with asthma and/or chronic rhinosinusitis with nasal polyps (CRSwNP), symptoms of which are exacerbated by NSAIDs, including aspirin. Despite some progress in understanding of the pathophysiology of the syndrome, which affects 1/10 of patients with asthma and rhinosinusitis, it remains a diagnostic and therapeutic challenge. In order to provide evidence‐based recommendations for the diagnosis and management of N‐ERD, a panel of international experts was called by the EAACI Asthma Section. The document summarizes current knowledge on the pathophysiology and clinical presentation of N‐ERD pointing at significant heterogeneity of this syndrome. Critically evaluating the usefulness of diagnostic tools available, the paper offers practical algorithm for the diagnosis of N‐ERD. Recommendations for the most effective management of a patient with N‐ERD stressing the potential high morbidity and severity of the underlying asthma and rhinosinusitis are discussed and proposed. Newly described sub‐phenotypes and emerging sub‐endotypes of N‐ERD are potentially relevant for new and more specific (eg, biological) treatment modalities. Finally, the document defines major gaps in our knowledge on N‐ERD and unmet needs, which should be addressed in the future.
The Ovicaprine Mystique: Livestock Commodification in Postindustrial Lesotho
Authors: Hoag Colin 
Published: September 2018

ABSTRACTEconomic anthropologists often look to goods that resist commodification to understand how culture determines what can be exchanged and on what terms. Livestock in Africa have served as prominent examples of such “recalcitrant commodities.” In this article, I argue that goods that do not resist commodification—what I call “clean‐break commodities”—also illuminate the culture of the economy. Drawing on fifteen months of fieldwork in Lesotho, I contrast the reticence to sell cattle in African societies, long the focus of anthropologists as well as experts in conservation and development, with the prodigious sale of sheep and goats (i.e., ovicaprids). Narrow focus on charismatic cattle cultures obscures both the historically shifting commodification of ovicaprids and the economic dreamworlds in which they become enrolled. Ovicaprid cultures morphed over time as rural Basotho navigated their country's structural transitions in the regional political economy—from recently colonized ethnostate to labor reserve for South African mining industries and to defunct labor reserve. Just as the resistance of cattle to commodification described by James Ferguson as the “bovine mystique” opened a window into social life in the labor reserve, the facile commodification of ovicaprids that I call the “ovicaprine mystique” does the same throughout Lesotho's history. [bovine mystique, livestock, commodification, postindustry, sub‐Saharan Africa]
RMI and ROMA are equally effective in discriminating between benign and malignant gynecological tumors: A prospective population‐based study
Authors: Liest Ann‐Lisbeth , Omran Ahmed Shaker , Mikiver Rasmus , Rosenberg Per , Uppugunduri Srinivas 
Published: September 2018

AbstractIntroductionOur primary objective was to test the hypothesis that human epididymal protein 4 (HE4) and risk of ovarian malignancy index outperform the CA 125 and risk of malignancy index tests in categorizing a pelvic mass into high or low risk of malignancy in a Swedish population. Furthermore, cut‐off values needed to be defined for HE4 and ROMA in premenopausal and postmenopausal women prior to their introduction to clinical practice. A third objective was to investigate the correlation between HE4 levels in serum and urine.Material and methodsWomen with a pelvic mass scheduled for surgery were recruited from nine hospitals in south‐east Sweden. Preoperative blood samples were taken for analyzing CA125 and HE4 as well as urine samples for analyzing HE4.ResultsWe enrolled a total of 901 women, of whom 784 were evaluable. In the premenopausal and postmenopausal groups, no significant differences were found for sensitivity, positive and negative predictive value, either for RMI vs ROMA or for CA125 vs HE4 using a fixed specificity of 75%. Cut‐off values indicating malignancy were established for HE4 and ROMA in premenopausal and postmenopausal women. We found no correlation between HE4 concentration in serum and urine.ConclusionsWe could not confirm that ROMA had diagnostic superiority over RMI in categorizing women with a pelvic mass into low‐risk or high‐risk groups for malignancy in a Swedish population. We have defined cut‐off values for HE4 and ROMA. The lack of correlation between serum and urine HE4 obviates the introduction of urine HE4 analysis in clinical diagnostics.
The human yolk sac size reflects involvement in embryonic and fetal growth regulation
Authors: Odland Karlsen Henriette , Johnsen Synnøve L. , Rasmussen Svein , Trae Gro , Reistad Hilde M. T. , Kiserud Torvid 
Published: September 2018

AbstractIntroductionThe human yolk sac provides the embryo with stem cells, nutrients, and gas exchange. We hypothesized that more maternal resources, reflected in body size and body composition, would condition a a larger yolk sac, ensuring resources for the growing embryo. Thus, we aimed to determine the relation between maternal size in early pregnancy and yolk sac size.Material and methodsThis subsidiary study was embedded in the multinational World Health Organization fetal growth project that included healthy women with a body mass index of 18‐30, reliable information of their regular last menstrual period and singleton pregnancies. Yolk sac diameter, crown‐rump length, and maternal height, weight, body mass index, and body composition were assessed before 13 weeks of gestation, and the fetal biometry was repeated during the pregnancy.ResultsOf 140 participants, 122 with a successful yolk sac measurement were entered in the present analysis. Maternal weight was negatively associated with the yolk sac diameter (P = 0.007) and so was maternal height (P = 0.011), fat mass (P = 0.037), and lean body mass (P = 0.018), but not body mass index (P = 0.121). Significant effects were predominantly due to the female embryos and could be traced at 24 weeks of gestation. That is, a small yolk sac : crown‐rump length ratio in early pregnancy was associated with a high fetal abdominal circumference (P < 0.001) and estimated fetal weight (P = 0.001).ConclusionsThe human yolk sac is involved in the regulation of embryonic growth, but contrary to our hypothesis, the yolk sac has a compensatory capacity, being larger when the mothers are smaller; and the effect can be traced on fetal size at 24 weeks of gestation.
Optic nerve head blood flow regulation during changes in arterial blood pressure in patients with primary open‐angle glaucoma
Authors: Bata Ahmed M. , Fondi Klemens , Witkowska Katarzyna J. , Werkmeister René M. , Hommer Anton , Vass Clemens , Resch Hemma , Schmidl Doreen , Popa‐Cherecheanu Alina , Chua Jacqueline , Garhöfer Gerhard , Schmetterer Leopold 
Published: September 2018

AbstractPurposeAbnormal autoregulation of optic nerve head blood flow (ONHBF) has been postulated to play an important role in primary open‐angle glaucoma (POAG). We used laser Doppler flowmetry (LDF) to estimate quantitatively the ONHBF and compared ONHBF autoregulation between glaucoma patients and healthy controls during isometric exercise.MethodsForty patients with POAG and 40 healthy age‐ and sex‐matched subjects underwent three periods of isometric exercise, each consisting of 2 min of handgripping. Optic nerve head blood flow (ONHBF) was measured continuously using LDF. Systemic blood pressure, intraocular pressure and ocular perfusion pressure were assessed in all participants.ResultsIsometric exercise was associated with an increase in ocular perfusion pressure during all handgripping periods in both groups (p < 0.001). However, there was no change in ONHBF in either group. Three of the glaucoma patients and two of the healthy subjects showed a consistent 10% decrease in blood flow during isometric exercise, in spite of an increase in their blood pressure. This difference between groups was not significant (p = 0.61). Four other glaucoma subjects showed a consistent increase in blood flow of more than 10% during isometric exercise, whereas this was not seen in healthy subjects (p = 0.035).ConclusionThis study suggests that abnormal ONHBF autoregulation is more often seen in patients with POAG than healthy control subjects. The relationship to the glaucoma disease process is currently unknown and requires further investigation.
Binocular vision alterations after refractive and cataract surgery: a review
Authors: García‐Montero María , Albarrán Diego César , Garzón‐Jiménez Nuria , Pérez‐Cambrodí Rafael J. , López‐Artero Esther , Ondategui‐Parra Juan Carlos 
Published: September 2018

AbstractTo review binocular and accommodative disorders documented after corneal or intraocular refractive surgery, in normal healthy prepresbyopic patients. A bibliographic revision was performed; it included works published before 1st July 2017 where accommodation and/or binocularity was assessed following any type of refractive surgical procedure. The search in Pubmed yielded 1273 papers, 95 of which fulfilled the inclusion criteria. Few publications reporting binocular vision and/or accommodative changes after refractive surgery in normal subjects were found. The reduction in fusional vergence is the most frequently reported alteration. Anisometropia is an important risk factor for postoperative binocular vision‐related complaints. Most diplopia‐related visual complaints, irrespective of the surgical procedure, were in fact misdiagnosed preoperative disorders. The preoperative evaluation of patients seeking spectacle/contact lens independence should include a complete binocular and accommodation assessment where parameters such as the phoric posture, accommodative amplitude and facility, near point of convergence, fusional reserves and accommodative convergence/accommodation coefficient are measured. This would allow the identification of risk factors that could compromise the success of the refractive surgery and cause clinical symptoms.
Electroretinogram abnormalities in nonanterior childhood uveitis
Authors: Brouwer Anna H. , van Genderen Maria. M. , de Wit Gerard C. , de Boer Joke H. 
Published: September 2018

AbstractPurposeA major point of concern in uveitis is the development of irreversible retinal changes after inflammation. In this study, we assess how nonanterior childhood uveitis affects retinal function using full‐field electroretinography (ERG).MethodsCross‐sectional study. ERGs of 63 uveitis eyes (33 children) were measured according to extended International Society for Clinical Electrophysiology of Vision (ISCEV) protocols. ERG abnormalities were investigated in relation to the following clinical parameters: demographics, uveitis characteristics, including severity of inflammation, treatment, best corrected visual acuity (BCVA), cystoid macular oedema (CME) on optical coherence tomography and fluorescein angiography score.ResultsThe ERG showed abnormalities in 34 eyes (54%). The most frequent ERG abnormalities were prolonged implicit times of the cone b‐wave (37%; n = 23/63) and an abnormal 30‐Hz flicker response (implicit time and/or amplitude) (33%; n = 21/63). Factors associated with these ERG abnormalities were CME (p = 0.021) and 3+ vitreous cells (p = 0.021). BCVA in eyes with and without these ERG abnormalities did not statistically differ and was relatively good (median: 0.05 LogMAR, IQR: 0.00–0.15 LogMAR).ConclusionThe ERG is frequently affected in childhood uveitis indicating a global retinal dysfunction. ERG abnormalities seem to be associated with a more severe posterior segment inflammation and a younger age. If an association between ERG abnormalities and long‐term visual outcome can be made in the future, these early ERG findings during the course of childhood uveitis have significance for treatment strategies.
Pharmacokinetics and safety of single and multiple doses of rasagiline in healthy Japanese and caucasian subjects
Authors: Elgart Anna , Rabinovich‐Guilatt Laura , Eyal Eli , Gross Aviva , Spiegelstein Ofer 
Published: September 2018

AbstractAs of March 2018, rasagiline is approved for the treatment of Parkinson disease in 55 countries including Japan. The present study evaluated the pharmacokinetics (PK) and safety of rasagiline in healthy Japanese and Caucasian subjects following single and multiple administrations of three rasagiline doses. In this double‐blind, placebo‐controlled study, 64 healthy subjects (32 Japanese and 32 Caucasian) received either rasagiline (0.5, 1.0, or 2.0 mg) or placebo for 10 days with PK sampling for single‐dose administration on day 1 and for multiple administration on day 10. Regardless of administration schedule, rasagiline plasma concentrations and dose‐related increases in exposure parameters were similar between Japanese and Caucasians. Rasagiline accumulation (2‐fold for 0.5 mg and 3‐fold for 1.0 mg and 2.0 mg doses) following multiple administration was similar across the ethnic groups. Geometric mean ratios (GMR) comparing Japanese to Caucasians for AUC0‐24, Cmax and AUCinf following single administration were 1.38, 1.17 and 1.38 for 0.5 mg; 1.22, 1.20 and 1.22 at 1.0 mg; and 1.02, 1.00 and 1.02 at for 2.0 mg. GMR for AUCtau and Cmax,ss following multiple administration were 1.43 and 1.06 at 0.5 mg, 1.06 and 1.00 at 1.0 mg, and 1.09 and 1.07 at 2.0 mg. Safety measures were unremarkable and similar between Caucasian and Japanese subjects. Comparable systemic exposure and safety parameters were demonstrated for rasagiline administered to healthy Japanese and Caucasian subjects.
Gestational diabetes incidence and delivery outcomes in Western China: A prospective cohort study
Authors: Mak Jonathan K. L. , Lee Andy H. , Pham Ngoc Minh , Pan Xiong‐Fei , Tang Li , Binns Colin W. , Sun Xin 
Published: September 2018

AbstractBackgroundFew studies have examined the age‐standardized incidence of gestational diabetes mellitus (GDM) for comparison between populations. Information on delivery outcomes is also lacking for Chinese women with GDM. Therefore, the present study aimed to determine age‐standardized GDM incidence and assess its association with maternal and neonatal outcomes.MethodsA total of 1901 pregnant women were recruited in Chengdu, Sichuan Province. GDM was diagnosed between 24 and 28 weeks’ gestation using oral glucose tolerance tests. Age‐standardized incidence rates of GDM were calculated using the direct method. Delivery outcomes were extracted from medical records and compared between the GDM and non‐GDM groups.ResultsThe age‐standardized GDM incidence was 18.3% (95% CI 15.6‐21.1) and increased with maternal age and prepregnancy body mass index (BMI). Women with GDM experienced longer length of stay in hospital, shorter gestation at delivery, and a higher risk of cesarean delivery. Their newborns were more likely to be macrosomic or small for gestational age, and to require neonatal intensive care.ConclusionsThe incidence of GDM was high in Western China, especially among older and overweight women. Moreover, women with GDM had higher rates of adverse delivery outcomes. The findings lend further support for the screening, prevention, and management of GDM in Chinese women.
Direct role of FLT3 in regulation of early lymphoid progenitors
Authors: Zriwil Alya , Böiers Charlotta , Kristiansen Trine A. , Wittmann Lilian , Yuan Joan , Nerlov Claus , Sitnicka Ewa , Jacobsen Sten E. W. 
Published: September 2018

SummaryGiven that FLT3 expression is highly restricted on lymphoid progenitors, it is possible that the established role of FLT3 in the regulation of B and T lymphopoiesis reflects its high expression and role in regulation of lymphoid‐primed multipotent progenitors (LMPPs) or common lymphoid progenitors (CLPs). We generated a Flt3 conditional knock‐out (Flt3fl/fl) mouse model to address the direct role of FLT3 in regulation of lymphoid‐restricted progenitors, subsequent to turning on Rag1 expression, as well as potentially ontogeny‐specific roles in B and T lymphopoiesis. Our studies establish a prominent and direct role of FLT3, independently of the established role of FLT3 in regulation of LMPPs and CLPs, in regulation of fetal as well as adult early B cell progenitors, and the early thymic progenitors (ETPs) in adult mice but not in the fetus. Our findings highlight the potential benefit of targeting poor prognosis acute B‐cell progenitor leukaemia and ETP leukaemia with recurrent FLT3 mutations using clinical FLT3 inhibitors.
Occupation and risk of cancer of the renal pelvis in Nordic countries
Authors: Michalek Irmina Maria , Martinsen Jan Ivar , Weiderpass Elisabete , Kjaerheim Kristina , Lynge Elsebeth , Sparen Pär , Tryggvadottir Laufey , Pukkala Eero 
Published: September 2018

ObjectivesTo evaluate occupational variation in the incidence of the malignant neoplasm of the renal pelvis in the population of the Nordic countries: Denmark, Iceland, Finland, Norway and Sweden.Materials and MethodsThe study cohort comprised 14.9 million individuals. Data on occupational history were obtained from national censuses. Standardized incidence ratios (SIRs) were calculated for each occupation.ResultsThe highest SIRs were found in seamen (1.51, 95% confidence interval [CI] 1.23–1.82), printers (1.39, 95% CI 1.11–1.71), welders (1.37, 95% CI 1.03–1.78), and public safety workers (1.35, 95% CI 1.12–1.62). The lowest SIRs were observed in forestry workers (0.47, 95% CI 0.35–0.62), gardeners (0.72, 95% CI 0.62–0.83) and woodworkers (0.81, 95% CI 0.72–0.91).ConclusionsThe study suggests that there is an association between profession and risk of malignancy of the renal pelvis. The possible associations between exposure to asbestos, heavy metals and welding fumes, and risk of developing the disease should be studied further.