bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA Pyrosequencing–Based Identification of Pathogenic Candida Species by Using the Internal Transcribed Spacer 2 Region
Authors: Boyanton, Jr Bobby L. , Luna Ruth Ann , Fasciano Lea R. , Menne Kyle G. , Versalovic James 
Published: February 2021

Abstract
Context.—The incidence of infections due to diverse Candida species is increasing, with correspondingly different antifungal susceptibility patterns. Routine yeast identification methods cause significant delays in appropriate patient management.
Objective.—A DNA pyrosequencing strategy was evaluated for identification of pathogenic Candida species associated with human infections.
Design.—Clinical (n = 51) and commercial (n = 9) Candida isolates were identified in a blinded, parallel study consisting of routine fungal cultures and biochemical analyses in comparison with DNA pyrosequencing.
Results.—DNA pyrosequencing yielded species-level identification of all 60 Candida isolates, and sequencing interpretations agreed in all cases with results of biochemical and morphologic testing. Different Candida species were identified, such as C albicans, C dubliniensis, C glabrata, C guilliermondii, C krusei, C lusitaniae, C parapsilosis, and C tropicalis. Automated and manual approaches to DNA sequence interpretation, each coupled with the Identifire identification software, demonstrated 100% agreement with respect to Candida species identification. Twenty-one isolates yielded intraspecies DNA sequence differences (90%–98% nucleic acid sequence identity) by automated interpretation. Sequence differences resulted from single-nucleotide polymorphisms or single-base additions/deletions, in addition to interpretative challenges in homopolymeric tracts.
Conclusion.—DNA pyrosequencing coupled with automated DNA sequence alignment provides a practical approach for accurate and timely identification of Candida pathogens. Relatively rapid and facile genotypic studies by DNA pyrosequencing matched the effectiveness of extensive biochemical/morphologic studies for yeast identification.
The Utility of p16Ink4a in Discriminating Between Cervical Intraepithelial Neoplasia 1 and Nonneoplastic Equivocal Lesions of the Cervix
Authors: Redman Rachel , Rufforny Irina , Liu Chen , Wilkinson Edward J. , Massoll Nicole A. 
Published: February 2021

AbstractContext.—The protein p16Ink4a is overexpressed in cervical lesions associated with high-risk human papillomavirus (HPV) subtypes 16 and 18, but not in low-risk HPV subtypes 6 and 11 or non–HPV-associated cervical lesions.Objective.—To determine whether p16Ink4a expression in equivocal cervical lesions helps distinguish atypical non-HPV changes from HPV-related changes.Design.—One hundred ninety-one cervical lesions, including 81 cervical intraepithelial neoplasia 1, 52 squamous metaplasia, 33 cellular features suggestive of HPV-related change, 9 reserve cell hyperplasia, 4 microglandular hyperplasia, and 12 inflammatory cervicitis, were randomly selected from archival cervical biopsy specimens. All 191 samples were studied with p16Ink4a (JC8 monoclonal antibody). Reactivity for p16Ink4a was scored on a 3-tier system as follows: negative, 0% to 5% cells reactive; focal/scattered positive, greater than 5% and less than or equal to 80% cells reactive; diffuse positive, greater than 80% cells reactive. Reactivity was based on normal/reactive cervical specimens where anti-p16 antibody was negative/weakly expressed in non–cervical epithelial cells. Cervical intraepithelial neoplasia 1 lesions not reactive for p16Ink4a were investigated for the presence of high-risk HPV by real-time polymerase chain reaction.Results.—No p16Ink4a reactivity was detected in the cervical lesions associated with atypical non-HPV change. Eleven of the cervical intraepithelial neoplasia 1 lesions showed focal/scattered reactivity expression for p16Ink4a, and 19 of the CIN 1 lesions had diffuse reactivity. Fifty of 51 of the CIN 1 lesions negative for p16Ink4a were real-time polymerase chain reaction negative for the presence of high-risk HPV; 1 was real-time polymerase chain reaction positive for high-risk HPV.Conclusions.—The data support the routine use of p16Ink4a immunohistochemical evaluation of cervical biopsy specimens for better discrimination of non–HPV-associated lesions from HPV-related lesions.
Pituicytoma: Characterization of a Unique Neoplasm by Histology, Immunohistochemistry, Ultrastructure, and Array-Based Comparative Genomic Hybridization
Authors: Phillips Joanna J. , Misra Anjan , Feuerstein Burt G. , Kunwar Sandeep , Tihan Tarik 
Published: February 2021

Abstract
The pituicytoma is a rare neoplasm whose histogenesis is debated partly because of the diversity of tissue types present in the sellar region. In this article we illustrate the characteristic histologic, immunohistologic, and ultrastructural features of this unique neoplasm. Furthermore, we use array-based comparative genomic hybridization to demonstrate a unique pattern of genomic copy number aberrations in pituicytomas. Tumors were composed of bipolar, spindle cells that were immunopositive for S100, vimentin, and Bcl-2 and immunonegative for synaptophysin, chromogranin, and glial fibrillary acidic protein. Ultrastructural analysis was remarkable for absence of secretory granules. Array comparative genomic hybridization demonstrated genomic copy number imbalances, including losses on chromosome arms 1p, 14q, and 22q and gains on 5p. This pattern of genetic changes only partially overlaps with the genomic alterations reported in pituitary adenomas. In summary, our data suggest that pituicytomas are a unique subset of tumors of the sellar region.
Adult Testicular Granulosa Cell Tumor: A Review of the Literature for Clinicopathologic Predictors of Malignancy
Authors: Hanson Joshua Anspach , Ambaye Abiy B. 
Published: February 2021

Abstract
Adult testicular granulosa cell tumors are rare sex cord–stromal tumors of which only 28 have been previously reported. As compared with their ovarian counterparts, these tumors may follow a more aggressive course because the proportion of malignant cases is higher. To date, there are no clinical or pathologic features that definitively predict malignancy. We reviewed all prior case reports for features that may predict their malignant potential. Tumor size greater than 5.0 cm is the only feature statistically associated with malignancy. Mitotic count, tumor necrosis, patient age, and the presence of gynecomastia do not, at present, predict benign versus malignant behavior.
Increased Levels of Nuclear Factor κB and Fos-Related Antigen 1 in Lung Tissues From Patients With Acute Respiratory Distress Syndrome
Authors: Fudala Rafal , Allen Timothy Craig , Krupa Agnieszka , Cagle Philip T. , Nash Sandra , Gryczynski Zygmunt , Gryczynski Ignacy , Kurdowska Anna K. 
Published: February 2021

Abstract
Context.—Both nuclear factor κB and Fos-related antigen 1 have been implicated in the pathogenesis of inflammatory lung diseases, including acute lung injury/acute respiratory distress syndrome.
Objective.—To evaluate lung tissues from patients with acute respiratory distress syndrome for presence of nuclear factor κB and Fos-related antigen 1.
Design.—Lung tissue sections from 5 patients with acute respiratory distress syndrome and sections of normal lung tissues of 4 patients were stained with antibodies against epithelial cell marker (surfactant protein B) and nuclear factor κB or Fos-related antigen 1. Samples were analyzed using confocal laser microscopy.
Results.—We have detected significantly increased levels of activated nuclear factor κB and Fos-related antigen 1 in lung tissues from patients with acute respiratory distress syndrome compared with control tissues, suggesting that these transcription factors undergo activation in lungs of patients suffering from acute respiratory distress syndrome.
Conclusions.—Our data demonstrate that activated nuclear factor κB and Fos-related antigen 1 are elevated in epithelial cells in lung tissues of patients with acute respiratory distress syndrome.
Four Years' Experience With an Interlaboratory Comparison Program Involving First-Trimester Markers of Down Syndrome
Authors: Palomaki Glenn E. , Knight George J. , Lambert-Messerlian Geralyn , Canick Jacob A. , Haddow James E. 
Published: February 2021

Abstract
Context.—We initiated a voluntary, self-funded interlaboratory comparison program in the fall of 2005 because no proficiency testing program was available to laboratories in North America offering first-trimester, combined serum and ultrasound, Down syndrome screening.
Objectives.—To evaluate the first 4 years of the interlaboratory comparison program against stated goals, to identify areas of concern, and to create new initiatives as indicated.
Design.—Five serum samples are distributed 3 times a year to be tested for pregnancy-associated plasma protein A, human chorionic gonadotropin or its β subunit, and dimeric inhibin-A; participants convert these results into multiples of the median. Patient histories include nuchal translucency information that enables the calculation of the risk of Down syndrome. Also included are educational components linked to interlaboratory comparison program results. Assessment of integrated (first- and second-trimester markers) risks is accomplished by having participants combine interlaboratory comparison program results with their results from a second-trimester proficiency testing program administered by the College of American Pathologists.
Results.—The precision profile for pregnancy-associated plasma protein A shows decreasing coefficients of variation with increasing pregnancy-associated plasma protein A concentrations and multiples of the median (25% to 11% and 30% to 15%, respectively). In contrast, coefficients of variation are a relatively constant 12% throughout the entire range of human chorionic gonadotropin results. On a logarithmic scale, the median coefficient of variation of the risk of Down syndrome is 9%.
Conclusions.—Participants in the interlaboratory comparison program reliably measure analytes, compute multiples of the median, and calculate consistent Down syndrome risks. Assays for the measurement of pregnancy-associated plasma protein A are not standardized and are less precise than those for human chorionic gonadotropin. Participants calculate reliable median equations given sonographer-specific sets of paired crown-rump length and nuchal translucency measurements.
Ultrasound Physics and Instrumentation for Pathologists
Authors: Lieu David 
Published: February 2021

Abstract
Context.—Interest in pathologist-performed ultrasound-guided fine-needle aspiration is increasing. Educational courses discuss clinical ultrasound and biopsy techniques but not ultrasound physics and instrumentation.
Objective.—To review modern ultrasound physics and instrumentation to help pathologists understand the basis of modern ultrasound.
Data Sources.—A review of recent literature and textbooks was performed.
Conclusions.—Ultrasound physics and instrumentation are the foundations of clinical ultrasound. The key physical principle is the piezoelectric effect. When stimulated by an electric current, certain crystals vibrate and produce ultrasound. A hand-held transducer converts electricity into ultrasound, transmits it into tissue, and listens for reflected ultrasound to return. The returning echoes are converted into electrical signals and used to create a 2-dimensional gray-scale image. Scanning at a high frequency improves axial resolution but has low tissue penetration. Electronic focusing moves the long-axis focus to depth of the object of interest and improves lateral resolution. The short-axis focus in 1-dimensional transducers is fixed, which results in poor elevational resolution away from the focal zone. Using multiple foci improves lateral resolution but degrades temporal resolution. The sonographer can adjust the dynamic range to change contrast and bring out subtle masses. Contrast resolution is limited by processing speed, monitor resolution, and gray-scale perception of the human eye. Ultrasound is an evolving field. New technologies include miniaturization, spatial compound imaging, tissue harmonics, and multidimensional transducers. Clinical cytopathologists who understand ultrasound physics, instrumentation, and clinical ultrasound are ready for the challenges of cytopathologist-performed ultrasound-guided fine-needle aspiration and core-needle biopsy in the 21st century.
An Update on Reporting Histopathologic Prognostic Factors in Melanoma
Authors: Ivan Doina , Prieto Victor G. 
Published: February 2021

Abstract
Context.—Accurate diagnosis of melanocytic lesions is essential for the adequate clinical management of patients. Thus, thorough reporting of histopathologic parameters, especially in the initial biopsies, is a critical component of both diagnosis and staging.
Objective.—o review current data on histopathologic prognostic factors for melanoma, with special emphasis on their use and applicability to clinical practice. Special attention is focused on the criteria highlighted by the new 2009 version of The American Joint Committee on Cancer (AJCC) system of melanoma staging and classification.
Data Sources.—Published peer-reviewed literature and personal experience of the authors.
Conclusions.—When reporting melanoma, we recommend that a template be provided, including all the histologic parameters that have been proved significant in determining the tumor staging and prognosis of a patient. The template may also include other details that may be helpful in further analysis of potential complete excisional biopsies or metastatic lesions, such as predominant type of tumor cells, presence or absence of desmoplastic component, or associated benign melanocytic lesions. Although there are several drawbacks in reporting some of these histopathologic parameters (interobserver variability, occasional lack of a perfectly reproducible method for quantifying these criteria), we suggest that at least the essential histopathologic parameters highlighted by the newest version of the AJCC system for melanoma staging and classification should be included in the report.
Update on Fluorescence In Situ Hybridization in Melanoma: State of the Art
Authors: Gerami Pedram , Zembowicz Artur 
Published: February 2021

Abstract
Context.—Recent advances in understanding the molecular basis of melanoma have resulted in development of fluorescence in situ hybridization (FISH) protocols designed to detect genetic abnormalities discriminating melanoma from nevi. The most extensively studied is a 4-probe multicolor FISH probe panel targeting chromosomes 6 and 11. Validation studies showed promising sensitivity and specificity for distinguishing benign nevi and malignant melanoma by FISH. Recent studies show that a melanoma FISH assay has great potential for becoming an important diagnostic adjunct in classification of melanocytic lesions and in diagnosis of melanoma.
Objective.—To present a comprehensive review of the science and practical aspects of FISH in melanoma for pathologists considering the use of melanoma FISH in their practice.
Data Sources.—Review of the literature and personal experience of the authors.
Conclusions.—Judicious use of a 4-probe multicolor melanoma FISH procedure can enhance accuracy for diagnosis of melanoma and improve classification of melanocytic proliferations.
Linnaean natural history: An eighteenth-century ecology of knowledges
Authors: Burnett Linda Andersson 
Published: February 2021

Keynote lecture at the conference "Nature and the Natural in the Eighteenth Century" organized by the Norwegian Society for Eighteenth-Century Studies, 3 February 2021.
RECORDED LECTURE: https://septentrio.uit.no/media/AnderssonBurnett_0.mp4
The lecture is in English. Abstract (in Norwegian): Linda Andersson Burnett leder et større forskningsprosjekt som tar for seg Carl von Linnés nettverk av korrespondenter og innsamlere som et eksempel på citizen science, eller «folkeforskning». Linné reiste selv omkring i riket og samlet observasjoner og artseksemplarer, mest berømt er hans Lappländska resa i 1732. Men som professor og anerkjent botaniker ble han mer og mer avhengig av bidrag fra samlere. Dels var det studenter, «linnélärjungar», som reiste rundt i hele verden. Dels var det lekfolk, lokale kontaktpersoner rundt omkring i det svenske riket. Hvem var disse lekfolkene, og hva var det slags natursyn som lå til grunn for deres samleraktivitet? Og ikke minst: Hvordan forholdt de seg til naturfolket lengst nord i det svenske riket, samene? Dette er spørsmål som Andersson Burnett vil belyse i sitt foredrag, «Linnaean natural history: An eighteenth-century ecology of knowledge».
COVID-19 incidence and mortality in Nigeria: gender based analysis
Authors: Olusola-Makinde Olubukola O. , Makinde Olusola S. 
Published: February 2021

Background
Coronavirus Disease 2019 (COVID-19) has been surging globally. Risk strata in medical attention are of dynamic significance for apposite assessment and supply distribution. Presently, no known cultured contrivance is available to fill this gap of this pandemic. The aim of this study is to develop a predictive model based on vector autoregressive moving average (VARMA) model of various orders for gender based daily COVID-19 incidence in Nigeria. This study also aims to proffer empirical evidence that compares incidence between male and female for COVID-19 risk factors.

Methods
Wilcoxon signed-rank test is employed to investigate the significance of the difference in the gender distributions of the daily incidence. A VARMA model of various orders is formulated for the gender based daily COVID-19 incidence in Nigeria. The optimal VARMA model is identified using Bayesian information criterion. Also, a predictive model based on univariate autoregressive moving average model is formulated for the daily death cases in Nigeria. Fold change is estimated based on crude case-fatality risk to investigate whether there is massive underreporting and under-testing of COVID-19 cases in Nigeria.

Results
Daily incidence is higher in males on most days from 11 April 2020 to 12 September 2020. Result of Wilcoxon signed-rank test shows that incidence among male is significantly higher than female (p-value < 2.22 × 10−16). White neural network test shows that daily female incidence is not linear in mean (p-value = 0.00058746) while daily male incidence is linear in mean (p-value = 0.4257). McLeod-Li test shows that there is autoregressive conditional heteroscedasticity in the female incidence (Maximum p-value = 1.4277 × 10−5) and male incidence (Maximum p-value = 9.0816 × 10−14) at 5% level of significance. Ljung-Box test (Tsay, 2014) shows that the daily incidence cases are not random (p-value=0.0000). The optimal VARMA model for male and female daily incidence is VARMA (0,1). The optimal model for the Nigeria’s daily COVID-19 death cases is identified to be ARIMA (0,1,1). There is no evidence of massive underreporting and under-testing of COVID-19 cases in Nigeria.

Conclusions
Comparison of the observed incidence with fitted data by gender shows that the optimal VARMA and ARIMA models fit the data well. Findings highlight the significant roles of gender on daily COVID-19 incidence in Nigeria.
Characterization and Classification of Soils of Harve-1 Microwatershed of Chamarajanagar District, Karnataka, India
Authors: Hegde Rajendra , Kumar M. B. Mahendra , Niranjana K. V. , Seema K. V. , Dhanorkar B. A. 
Published: February 2021

Aims: The detailed survey of the microwatershed was carried out by using digitized cadastral map as a base. The objective of the investigation was undertaken to characterize and classify the soils of Harve-1 microwatershed of Chamarajanagar district, Karnataka.
Place and Duration of Study: soil survey was done and soil samples were collected from Harve-1 microwatershed of Chamarajanagar district in the year 2016. The laboratory characterization and soil classification work was done at National Bureau of soil survey and land use planning, Regional centre Hebbal, Bangalore, Karnataka.
Methodology: Using Cartosat-1 and LISS-IV merged satellite data at the scale of 1:7920 were used in conjunction with the cadastral map as a base. Soil profiles were exposed and location of soil profiles was recorded using GPS and studied from each landform for describing morphological characteristic as per the guidelines given in USDA soil survey manual (Soil Survey Staff 2014). Based on the soil-site characteristics, ten soil series were identified using the method employed by Reddy (2006). Horizon wise soil samples were collected, processed and analysed for various properties by adopting standard procedure.
Results: The study showed that, the soils were moderately shallow to moderately deep in depth. The colour of the soils varied from dark red to dark reddish brown. Texture of the soil varied from sandy loam to sandy clay loam in surface and sandy clay loam to sandy clay in subsurface. The structure was weak medium sub-angular blocky to moderate medium sub-angular blocky throughout the profile in all series. The consistency of majority of the soils were friable, slightly sticky and slightly plastic in surface and friable, moderately sticky and moderately plastic in subsurface. Soil reaction varied from slightly acidic to alkaline (5.70 to 8.18) in nature. Organic carbon content of the soils was low to high (0.20 to 1.24 per cent). Calcium and magnesium are dominant exchangeable cations followed by sodium and potassium. The CEC of the soils ranged from 3.17 to 25.76 cmol (p+) kg-1. Major proportion of soil series in the microwatershed belonged to the order of Alfisols (Paralitic Rhodustalfs, Typic Rhodustalfs, Typic Haplustalfs and Rhodic Paleustalfs) except Honnenahalli (HNH) series belong to the order of Inceptisols (Typic Haplustepts).
Conclusion: The soils of the microwatershed were comes under the order of alfisols and inceptisols. This generated information can help the researchers, farmers and planners to manage the natural resources for future planning and also to achieve sustainable productivity.