bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic specimen identification of Harpacticoids (Crustacea:Copepoda) using Random Forest and MALDI‐TOF mass spectra, including a post hoc test for false positive discovery
Authors: Rossel Sven , Martínez Arbizu Pedro 
Published: March 2018

Abstract

Ecological studies require accurate identification of specimens. This is very time consuming when processing plankton, meiobenthos or soil biota samples due to the presence of a high number of minute specimens. A solution to this problem may be MALDI‐TOF MS, an emerging technique for identification of metazoan species. As an alternative to factory delivered software or clustering approaches, Random Forest (RF) models can be trained to identify species, using MALDI‐TOF data. However, in a real‐world scenario, RF models will fail in detecting species which were not included in the training dataset as well, thus producing false positives (misidentifications).

We produced MALDI‐TOF MS spectra for meiofauna species and trained RF models, using MALDI‐TOF bins as predictors and species as multi‐level target class. We used the empirical beta distribution of the probability of class assignment in the model to design a post hoc test for false positive discovery. Two strategies increase the final accuracy of species identification: (1) “class smoothing” consisting of in silico observations of classes, created by bootstrapping the value of each predictor within each class and: (2) adding a “null class” to the training dataset by bootstrapping predictor values and shuffling predictor labels creating a class without multivariate signal.

We prove that RF is an excellent method for species identification, using MALDI‐TOF MS data. The models are flexible enough to correctly classify observations created in silico by smoothing the classes. Our post hoc test unmasks false positive classifications successfully. Smoothing the classes and adding a null class to the training model attracts assignment of false positives to this class. In our example, a 100% false positive discovery could be achieved, while maintaining very high overall prediction accuracy.

Combining MALDI‐TOF MS and RF models is a step towards a fully automatic species identification workflow that is particularly necessary for species‐rich communities of small organism for ecological studies but also for routine monitoring. The post hoc test for false positive discovery can be applied to any RF multilevel classification model, not only in a biological context.
Identification of immunohistochemical localization of irisin in the dwarf hamster (Phodopus roborovskii) tissues
Authors: Gür F. M. , Timurkaan S. , Gençer Tarakçi B. , Yalçin M. H. , Özkan Z. E. , Baygeldi S. B. , Yilmaz S. , Eröksüz H. 
Published: March 2018

SummaryIrisin is mainly secreted by heart and skeletal muscle cells. It is an exercise‐induced protein that converts white adipose tissue to brown. Increased irisin expression was lead to weight loss and improved glucose tolerance. We investigated irisin immunoreactivity in various tissues of the dwarf hamsters (Phodopus roborovskii). Tissues were processed, embedded in paraffin, sectioned at 5 μm and stained immunohistochemically for irisin. In the retina, irisin was found almost all layers, except outer nuclear layer. Also, irisin immunoreactivity was observed in the skin, cornea, striated muscle, parotid gland, tongue, oesophagus, stomach and small intestine. The findings from this study support the notion that skeletal muscle is not the primary source of irisin.
Stress, anxiety, and depression of both partners in infertile couples are associated with cytokine levels and adverse IVF outcome
Authors: Haimovici Florina , Anderson Janis L. , Bates Gordon W. , Racowsky Catherine , Ginsburg Elizabeth S. , Simovici Dan , Fichorova Raina N. 
Published: March 2018

ProblemPsychiatric disorders and stress in women have been associated with poor IVF outcome. We hypothesized that both partners in the infertile couples are emotionally affected, and cytokines in both may link psychological to reproductive outcome.Method of StudyForty‐five IVF couples completed questionnaires and visual analog scales for stress and psychiatric disorders and had cytokines measured in serum, semen, cervicovaginal, and follicular fluids. Multivariable analyses, t tests, maximum likelihood estimates, Spearman correlation, and data mining were applied.ResultsPsychopathology was found in 72% of the couples. Female and male stress were associated with stress, anxiety, and depression in the respective partner, and with a lower likelihood of clinical pregnancy and live birth. Lower serum TGF‐β and higher cervicovaginal IL‐6 and IL‐1β were associated with stress. In data decision trees, cytokines in relation to stress and depression in both partners were found indicative of IVF failure.ConclusionInfertile couples may benefit from psychiatric evaluation and treatment of both partners.
Sodium‐glucose co‐transporter type‐2 inhibitors: pharmacology and peri‐operative considerations
Authors: Milder D. A. , Milder T. Y. , Kam P. C. A. 
Published: March 2018

SummarySodium‐glucose co‐transporter 2 (SGLT2) inhibitors are an emerging class of oral hypoglycaemic agents with therapeutic benefits beyond better glycaemic control. A major concern of the sodium‐glucose co‐transporter 2 inhibitors is their propensity to cause euglycaemic ketoacidosis in the peri‐operative period and the potential for this critical diagnosis to be delayed or missed entirely. This review attempts to collate the case reports of sodium‐glucose co‐transporter 2 inhibitor ketoacidosis associated with surgery to highlight and put a perspective on this peri‐operative issue. Preventive strategies and the management of the ketoacidosis are discussed.
Prognostic Factors in Acute Aluminium Phosphide Poisoning: A Risk‐Prediction Nomogram Approach
Authors: Farzaneh Esmaeil , Ghobadi Hassan , Akbarifard Mahdieh , Nakhaee Samaneh , Amirabadizadeh Alireza , Akhavanakbari Ghodrat , Keyler Daniel E. , Mehrpour Omid 
Published: March 2018

AbstractAluminium phosphide (AlP) is a toxic agent associated with a high mortality rate following acute exposure from various routes. The aim of this study was to determine the clinical and laboratory findings useful for predicting the medical outcome of AlP‐poisoned patients using established scoring systems. This is a prospective study of AlP‐poisoned patients from 2010 to 2015 in Ardabil, Iran. All patients that presented with a confirmed diagnosis of acute AlP poisoning in the study interval were included in the study. Clinical and laboratory data, using Acute Physiology and Chronic Health Evaluation II (APACHE II), Sequential Organ Failure Assessment (SOFA) and Simplified Acute Physiology Score II (SAPS II) scoring systems, were compared for their predictive value in determining differences between survived and non‐survived patients. Univariate analysis (Mann–Whitney or t‐test), multiple logistic regression analysis, receiver operating characteristic (ROC) curve analysis and the Pearson correlation test were performed using STATA/SE 13.0 and the Nomolog Software. A total of 68 AlP‐poisoned patients with confirmed acute AlP poisoning were included for evaluation. Of these, 36 were non‐survived. Multiple logistic regression analysis was performed using parameters and values derived from patient clinical and laboratory data, and revealed that four factors were significant for predicting mortality: Glasgow coma score (GCS); systolic blood pressure (SBP); urinary output (UOP); and serum HCO3. A four‐variable, risk‐prediction nomogram was developed for identifying high‐risk patients and predicting the risk of mortality. Study results showed that SBP of <92.5 mmHg (p = 0.006); HCO3‐ < 12.9 mEq/L (p = 0.01), UOP < 1725 mL/day (p = 0.04); and GCS < 14.5 (p = 0.003) were significant predictors of AlP mortality. Scoring systems analysis showed SAPS II score >24.5, APACHE II score >8.5 and SOFA score >7.5 were predictive of non‐survival patients. The results of our study showed that SBP, GCS, UOP and serum HCO3 levels are the best prognostic factors for predicting mortality in AlP‐poisoned patients. According to the area under the ROC curve of the APACHE II score, when compared with SOFA and SAPS II scores, the APACHE II score can more effectively discriminate between non‐survivors and survived patients.
Randomized trial comparing caregiver‐only family‐focused treatment to standard health education on the 6‐month outcome of bipolar disorder
Authors: Perlick Deborah A , Jackson Carlos , Grier Savannah , Huntington Brittney , Aronson Andrew , Luo Xiaodong , Miklowitz David J 
Published: March 2018

AbstractObjectivesCaregivers of people with bipolar disorder often have depression and health problems. This study aimed to evaluate the sustained effects of a 12‐15 week psychoeducational intervention on the health and mental health of caregivers of persons with bipolar disorder. We also evaluated the effects of the intervention on patients’ mood symptoms over 6 months post‐treatment.MethodsCaregivers of 46 persons with bipolar disorder were randomized to 12‐15 weeks of a caregiver‐only adaptation of family‐focused treatment (FFT), in which caregivers were instructed on self‐care strategies and ways to assist the patient in managing the illness, or to 8‐12 sessions of standard health education. Independent evaluators assessed caregivers’ depression and physical health and patients’ mood symptoms before treatment, immediately after the treatment, and at 6 months post‐treatment.ResultsRandomization to FFT was associated with greater decreases in depression for both caregivers and patients over a 6‐month follow‐up period post‐treatment. Reductions in patients’ depression scores over 6 months post‐treatment were mediated by reductions in caregivers’ depression scores (z = −2.74, P < .01).ConclusionsInterventions that are effective in reducing mood symptoms and improving health behavior in caregivers may have important health and mental health benefits for patients with bipolar disorder. Specifically, a treatment focused on caregiver education about bipolar disorder and the need for the caregiver to attend to his/her own health and mental health can benefit patients, even without their direct participation.
Racial disparities in bipolar disorder treatment and research: a call to action
Authors: Akinhanmi Margaret O , Biernacka Joanna M , Strakowski Stephen M , McElroy Susan L , Balls Berry Joyce E , Merikangas Kathleen R , Assari Shervin , McInnis Melvin G , Schulze Thomas G , LeBoyer Marion , Tamminga Carol , Patten Christi , Frye Mark A 
Published: March 2018

ObjectivesHealth disparities between individuals of African and European ancestry are well documented. The disparities in bipolar disorder may be driven by racial bias superimposed on established factors contributing to misdiagnosis, including: evolving empirically based diagnostic criteria (International Classification of Diseases [ICD], Research Diagnostic Criteria [RDC] and Diagnostic and Statistical Manual [DSM]), multiple symptom domains (i.e. mania, depression and psychosis), and multimodal medical and additional psychiatric comorbidity.MethodsFor this paper, we reviewed the phenomenological differences between bipolar individuals of African and European ancestry in the context of diagnostic criteria and clinical factors that may contribute to a potential racial bias.ResultsPublished data show that bipolar persons of African ancestry, compared with bipolar persons of non‐African ancestry, are more often misdiagnosed with a disease other than bipolar disorder (i.e. schizophrenia). Additionally, studies show that there are disparities in recruiting patients of African ancestry to participate in important genomic studies. This gap in biological research in this underrepresented minority may represent a missed opportunity to address potential racial differences in the risk and course of bipolar illness.ConclusionA concerted effort by the research community to increase inclusion of diverse persons in studies of bipolar disorder through community engagement may facilitate fully addressing these diagnostic and treatment disparities in bipolar individuals of African ancestry.
Relationship of systemic inflammation and cellular immunity with advancement of cognitive decline in patients with Alzheimer's disease
Authors: Kawai Ukichiro , Uchida Nobuaki , Oono Miki , Fujita‐Nakata Michiyo , Nakanishi Megumi , Sanada Mitsuru , Nagayama Shigemi , Matsui Makoto 
Published: March 2018

AbstractObjectiveSystemic inflammation is known to be associated with Alzheimer's disease (AD) advancement. The aim of the present study was to examine the relationships of cognitive function in AD patients with the presence of systemic inflammation and immunological alterations.MethodsEight patients with AD and nine elderly individuals as a control group were enrolled, none of whom had a history of autoimmune diseases or were suffering from an infection. C‐reactive protein, interleukin‐6 and tumor necrosis factor‐α levels in serum were measured, while lymphocyte subsets were also determined using a flow cytometry system. In addition, two of the AD patients received repeated cognitive function and blood testing on an outpatient basis.ResultsIn the AD group, the percentages of CD3−CD16+CD56+ (natural killer) and CD4+CCR5+ (type 1 helper T) cells, and CD8+CD11a+ (cytotoxic T) lymphocytes were increased, whereas the percentages of CD19+ (B lymphocytes) and CD4+CD25brightCD127dim (regulatory T) cells were decreased as compared with the controls. Systemic inflammation, represented by elevated C‐reactive protein and interleukin‐6, was shown to aggravate cognitive function in both patients who underwent follow‐up outpatient examinations. However, lymphocyte subsets did not change in parallel with cognitive function.ConclusionsInflammatory acute clinical events have the potential to reduce cognitive function in AD patients, which could be partially attributed to a decrease in regulatory T cells in the blood. Furthermore, increased numbers of natural killer cells, cytotoxic T lymphocytes and type 1 helper T cells in these patients might reflect the presence of chronic inflammation, thus forming an immunological background.
Selecting and applying indicators of ecosystem collapse for risk assessments
Authors: Rowland Jessica A. , Nicholson Emily , Murray Nicholas J. , Keith David A. , Lester Rebecca E. , Bland Lucie M. 
Published: March 2018

AbstractOngoing ecosystem degradation and transformation are major threats to biodiversity. Measuring ecosystem change toward collapse relies on monitoring indicators that quantify key ecological processes. Yet little guidance is available on selection and use of indicators for ecosystem risk assessment. We reviewed indicator use in ecological studies of ecosystem collapse in marine pelagic and temperate forest ecosystems. We examined indicator‐selection methods, indicator types (geographic distribution, abiotic, biotic), methods of assessing multiple indicators, and temporal quality of time series. We compared how these factors were applied in the ecological studies with how they were applied in risk assessments by using the International Union for Conservation of Nature's Red List of Ecosystems (RLE), for which indicators are used to estimate risk of ecosystem collapse. Ecological studies and RLE assessments rarely reported how indicators were selected, particularly in terrestrial ecosystems. Few ecological studies and RLE assessments quantified ecosystem change based on all 3 indicator types, and indicators types used differed between marine and terrestrial ecosystems. Several studies used indices or multivariate analyses to assess multiple indicators simultaneously, but RLE assessments did not because as RLE guidelines advise against them. Most studies and RLE assessments used time‐series data that spanned at least 30 years, which increases the probability of reliably detecting change. Limited use of indicator‐selection protocols and infrequent use of all 3 indicator types may hamper accurate detection of change. To improve the value of risk assessments for informing policy and management, we recommend using explicit protocols, including conceptual models, to identify and select indicators; a range of indicators spanning distributional, abiotic, and biotic features; indices and multivariate analyses with extreme care until guidelines are developed; time series with sufficient data to increase ability to accurately diagnose directional change; data from multiple sources to support assessments; and explicitly reporting steps in the assessment process.
TNF receptor‐associated factor 1 as a biomarker for assessment of non‐small cell lung cancer metastasis and overall survival
Authors: Wen Xiaoxing , Wang Bingping , Feng Tao , Yuan Wei , Zhou Jian , Fang Tao 
Published: March 2018

AbstractBackground and aimNon‐small cell lung cancer (NSCLC), which comprises 80%‐85% of all lung cancer cases, is one of the most common human malignancies. Despite great improvements in diagnostic technology and the introduction of new therapeutic agents in recent years, the 5‐year survival rate of NSCLC is still low. Tumor necrosis factor (TNF) receptor‐associated factor 1 (TRAF1) plays an important role in the TNF‐related apoptosis‐inducing ligand (TRAIL) associated signal pathway.MethodsIn this study, we aim to illuminate the function of TRAF1 in NSCLC. Toward that end, TRAF1 expression was detected using immunohistochemistry (IHC) in specimens from 200 NSCLC patients. The function of TRAF1 in the A549 and H1299 cell lines was evaluated by colony formation and MTT assays.ResultsOur data showed that TRAF1 was significantly upregulated in NSCLC tissues. TRAF1 expression was positively associated with NSCLC lymphatic metastasis and clinical stage and was negatively associated with overall patient survival. TRAF1 promoted NSCLC cell proliferationConclusionTRAF1 expression was positively associated with NSCLC lymphatic metastasis and histological grade and was negatively associated with overall patient survival. TRAF1 may be an important therapeutic target for NSCLC.
FOSB immunoreactivity in endothelia of epithelioid hemangioma (angiolymphoid hyperplasia with eosinophilia)
Authors: Ortins‐Pina Ana , Llamas‐Velasco Mar , Turpin Sara , Soares‐de‐Almeida Luís , Filipe Paulo , Kutzner Heinz 
Published: March 2018

BackgroundAccurate distinction of epithelioid hemangioma (EH) from its malignant mimics is paramount but remains challenging due to its wide morphological spectrum and lack of objective molecular markers. FOSB oncogenic activation was recently identified as a key event in endothelial proliferation. We sought to investigate the FOSB staining pattern in EH with angiolymphoid hyperplasia with eosinophilia (EH‐AHLE) morphology and to evaluate its value in differential diagnosis of epithelioid vascular tumors.MethodsFrom the authors' files, 15 representative cases of EH‐ALHE were selected and evaluated for their FOSB immunostaining pattern. Other vascular proliferations which can be morphological mimics were also tested: epithelioid hemangioendothelioma (EHE) (5 cases) and epithelioid angiosarcoma (EAS) (5 cases).ResultsAll 15 cases of EH‐ALHE showed strong and homogeneous FOSB nuclear expression in endothelial cells with ample cytoplasm and intracytoplasmic vacuoles. All cases of EHE and EAS lacked FOSB immunoreactivity or showed only incidental weak FOSB immunoreactivity in less than 5 nuclei per lesion.ConclusionsFOSB immunohistochemistry is sensitive in the diagnosis of EH‐ALHE, and allows differentiation from its histological mimics. An immunohistochemical panel including not only pan‐cytokeratin AE1/AE3 and endothelial markers, but also FOSB, helps in the diagnosis of epithelioid vascular tumors.
Effect of cDMEM media containing Ectoine on human periodontal ligament mesenchymal stem cell survival and differentiation
Authors: Tuncer Budanur Damla , Zibandeh Noushin , Genç Deniz , Gökalp Muazzez , Kaşali Kamber , Akkoç Tunç , Sepet Elif 
Published: March 2018

AbstractBackground/AimEctoine is an amino acid that can preserve osmotic balance and has more preservative activity than other osmoregulators. There are no published reports on the osmoregulators’ effects on viability or differentiation of dental stem cells. The aim of this study was to investigate the effect of Ectoine as a storage media on the viability and differentiation potential of human periodontal ligament mesenchymal stem cells (hPDLMSCs).Materials and MethodshPDLMSCs were obtained from impacted third molar teeth. The cells were isolated, submitted to trilineage differentiation, and characterized by flow cytometer (FC). hPDLMSCs were incubated with different media containing Ectoine, complete DMEM (cDMEM), Ectoine+cDMEM, milk, and tap water for 2, 6, 12, and 24 h. The cells were analyzed by FC for viability, early‐apoptosis, late apoptosis, and necrosis rates. Osteogenic and fibroblastic differentiation in hPDLMSCs were investigated by Alizarin red stain and vimentin expression.ResultsAll treated groups showed significant decreases in cell viability after 2 h. Significant increases were detected in the number of dead cells between 2 and 12 h in all groups except the Ectoine+cDMEM group. The deposition of mineral matrix nodules was significantly higher in cells cultured with Ectoine+cDMEM compared with the other media. Higher vimentin expressions were detected in cells cultured with cDMEM and Ectoine+cDMEM media, respectively.ConclusionsEctoine added to cDMEM media, promoted cell survival plus osteogenic and fibroblastic differentiation of hPDLMSCs.
Clinical response to Nabiximols correlates with the downregulation of immune pathways in multiple sclerosis
Authors: Sorosina M. , Clarelli F. , Ferrè L. , Osiceanu A. M. , Unal N. T. , Mascia E. , Martinelli V. , Comi G. , Benigni F. , Esposito F. , Martinelli Boneschi F. 
Published: March 2018

Background and purposeNabiximols (Sativex®) is a cannabinoid‐based compound used for the treatment of moderate to severe spasticity in multiple sclerosis (MS). The aim of the study was to investigate the effect of the administration of Nabiximols on blood transcriptome profile of patients with MS and to interpret it in the context of pathways and networks.MethodsWhole‐genome expression profiling was performed in whole blood of 33 subjects with MS at baseline and after 4 weeks of drug treatment. Patients were classified as responders (n = 19) and non‐responders (n = 14). Pathway and network analyses on genes modulated by the drug were performed, followed by in vitro stimulation of peripheral blood mononuclear cells with pro‐inflammatory agents to support the immunomodulatory properties of the drug.ResultsIndividual effect size was modest; however, we observed a downregulation of several immune‐related pathways after 4 weeks of treatment, which was more pronounced when restricting analyses to responders. Interesting hub molecules functionally related to the immune system emerged from network analysis, including NFKB1, FYN, MAP14 and TP53. The immunomodulatory properties of the drug were confirmed through in vitro assays in peripheral blood mononuclear cells collected from patients with MS.ConclusionsOur findings support the immunomodulatory activity of cannabinoids in patients with MS. Further studies in more specific cell types are needed to refine these results.