bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatolian Empires: Local Experiences from Hittites to Phrygians at Çadır Höyük
Authors: Ross Jennifer C. , McMahon Gregory , Heffron Yağmur , Adcock Sarah E. , Steadman Sharon R. , Arbuckle Benjamin S. , Smith Alexia , von Baeyer Madelynn 
Published: October 2019

Abstract
Çadır Höyük provides rich evidence for the endurance and transformation of specific cultural features and phenomena at a rural center on the Anatolian plateau as it experienced the waxing and waning of control by imperial political powers of the Bronze and Iron Ages. Especially evident during those periods of imperial power is the construction and maintenance of public architecture; certain economic activities also shift in their importance at those times. Simultaneously, continuity in economic and social organization is also a feature stretching across times of imperial control and its loss. Examination of the archaeological evidence from Çadır Höyük suggests that nothing is as continuous, nor as discontinuous, as it might seem.
Landscape Heritage at Çadir Höyük: From Cartography to Digital Imagery
Authors: Lauricella Anthony J. , Offutt Stephanie , Şerifoğlu Tevfik Emre 
Published: October 2019

Abstract
Studies of archaeological cultural heritage typically focus on sites and landscapes threatened by military conflict, while threats from development and urban expansion are often more common. Excavations at Çadır Höyük began as a salvage campaign in advance of the construction of the Gelingüllü Dam—a modern infrastructural project. While our team has been excavating since 1994, the mound of Çadır Höyük and our host village of Peyniryemez have been recorded in maps and historical documents stretching as far back as the fifteenth century CE. This article examines the history of archaeological engagement at the site with a particular focus on the cartographic and visual record.
Conserving 5,000 Years of Artifacts
Authors: Avcil Soran 
Published: October 2019

Abstract
The conservation of finds is an essential part of any archaeological project and must include the employment of all possible modern conservation techniques. Trenches at Çadır Höyük range from the Late Chalcolithic to Middle Byzantine periods, with a correspondingly wide range of different types of artifacts. In some cases the age of an artifact determines the method needed for its conservation. But factors such as soil chemistry, salinity, humidity, and production technique can require different approaches even to metal of the same age. In addition, techniques change depending on the conservation condition of an artifact, which is not directly or predictably linked to its age. Most challenging are composite artifacts because they require the application of a variety of conversation techniques to a single object.
Environmental factors do not contribute significantly to shell shape in the Sprite Elimia, Elimia Proxima (Gastropoda: Pleuroceridae)
Authors: Shepard Benjamin R. E. , Minton Russell 
Published: October 2019

Abstract
Pleurocerid snail diversity has historically been defined by morphological shell features, and these features are believed to be phenotypic responses to environmental factors. More recently, authors have shown the importance of genetics in shell variability, even to the exclusion of any environmental effect. Work by Dillon on Elimia proxima in the 1980s aimed to address this genetic versus environmental correlation of shell features, without reaching a solid conclusion. Using Dillon’s original data and specimens, geometric morphometric analysis was used in a phylogenetic context to show that E. proxima shell variation at the population level is correlated with genetics and not with the environment. This data is the latest example to find that shell variation as the result of environmental factors is too simplistic an explanation in pleurocerids.
Fecal pellet surveys and DNA analysis reveal that Appalachian cottontails (Sylvilagus obscurus) are more widespread than previously recorded in western Maryland
Authors: Petrick Kelly Russo , Seddon William L. , Lambert Thomas D. , Ammer Frank K. 
Published: October 2019

Abstract
Although the Appalachian cottontail (Sylvilagus obscurus) is believed to be declining throughout its range, there is a lack of information on its specific distribution, as existing studies are limited in range and based on a small number of live-trapped rabbits. To better determine the species’ range in western Maryland, mtDNA extracted from fecal pellets collected at sites likely to house Appalachian cottontail populations was used for species identification. The identification success rate for this method was 87%. This noninvasive method allowed many more sites to be surveyed than would have been possible with live-trapping methods and found Appalachian cottontail at 18 sites where they were not previously recorded, indicating that the species may be more widespread in western Maryland than previously thought. This study provides a noninvasive method of species identification that would be useful for more widespread surveys of elusive species.
Toward a Theory of the Mechanism of High-Velocity, Low-Amplitude Technique: A Literature Review
Authors: Hennenhoefer Kevin , Schmidt Deborah 
Published: October 2019

Abstract
This review seeks to integrate the current literature to create a more unified and inclusive theory regarding the therapeutic mechanism of high-velocity, low-amplitude (HVLA) technique. The authors review the literature currently available regarding the physiologic effects of HVLA. The progression from an articulatory model to a neuromuscular one is discussed, and the body of work demonstrating that HVLA has a centralized mechanism of action, rather than just a local one, is described.
The association of depression with lower urinary tract symptoms: data from the National Health and Nutrition Examination Survey, 2005–2008
Authors: Park Jee Soo , Ham Won Sik , Hong Chang Hee , Chung Byung Ha , Koo Kyo Chul 
Published: October 2019

Background
To identify the factors associated with lower urinary tract symptoms (LUTS), we investigated associations between psychological factors, including depression and sleep disorders, and LUTS using the National Health and Nutrition Examination Survey (NHANES) database.

Materials and Methods
The NHANES database was examined for the period of 2005 to 2008. Men older than 40 years, who had completed questionnaires surveying their kidney/urologic, prostate, mental health, and sleep conditions were included in this study. LUTS was defined as the presence of two or more of the following symptoms: incomplete emptying, urinary hesitancy, urinary frequency, and nocturia. Multivariable models using logistic regression were used to compare groups of men with or without LUTS.

Results
Of 1,820 participants, 110 (6.1%) men reported depression, and 235 (12.9%) presented with LUTS. Men with LUTS were older and had a significantly higher prevalence of depression and unemployment. Sleep disorder was not associated with LUTS. Multivariable logistic regression models demonstrated that men reporting moderate depression had the highest age-adjusted odds (odds ratio = 5.89, 95% CI [3.44–10.11]; p < 0.001) of reporting clinical LUTS.

Conclusions
A significant association was observed between LUTS and depression, and between LUTS and employment status. Although the pathophysiology of these relationships is unclear, physicians should consider multi-disciplinary evaluation and treatment approaches for LUTS.
Medical Devices: Pre‐ and Postimplant Testing
Authors: Oliva Alessandra , Teresa Mascellino Maria , Vullo Vincenzo , Mastroianni Claudio M. 
Published: December 2024

Abstract
Medical devices are increasingly used to enhance patients' quality of life and support the health care system in terms of prevention, diagnosis, and treatment of several diseases. The presence of a device is a significant risk factor for a subsequent infection. Implant‐associated infections, including prosthetic joint infections and infections of endovascular and cardiac implantable electronic devices, are associated with high morbidity and extensive costs for the health care system. Devices can be colonized by bacteria belonging to the normal skin flora or by microorganisms carried on the hands of medical and surgical personnel during implantation procedure. In addition, a device infection can occur as a result of bacteremic seeding from a distant focus of infection. The pathogenesis of a device infection is related to the formation of bacterial biofilm on the implant surface. This chapter focuses on the specimen collection, transport, and handling, quality control, procedure, interpretation and limitations of the procedure.
Genital Cultures
Authors: Filkins Laura M. , Garner Omai B. 
Published: December 2024

Abstract

Routine genital cultures enable detection of nonfastidious aerobic bacteria and are only indicated for some clinical presentations of genital infections. When a routine genital culture is ordered, potentially clinically significant bacteria should be evaluated using an indication specific approach but often include
Enterobacterales
,
Pseudomonas aeruginosa
,
S. aureus
, and
Streptococcus pyogenes
. For certain pathogens, such as
Chlamydia trachomatis
,
N. gonorrhoeae
,
Haemophilus ducreyi
, or
S. agalactiae
(group B
streptococcus
(GBS) for prenatal screening), cultures are ordered specifically for those pathogens, with proper collection and selection media or cell culture. For diagnosis of GBS disease in nonpregnant adults and in neonates, routine culture of the symptomatic body site and routine cultures collected based on clinical risk assessment will detect this pathogen, along with the other potential pathogens that can be isolated from those cultures.
Respiratory Tract Cultures
Authors: Alby Kevin , Smedberg Jason R. , Lindsay Diane S. J. , Ricci Maria L. , Yarbrough Melanie L. , Burnham Carey‐Ann D. , Leber Amy L. , Bateman Allen C. , Gonzalez Mark D. , Pence Morgan A. 
Published: December 2024

Abstract

Specimens from the upper respiratory tract (throat specimens, nasopharyngeal swabs, and nasal discharges) can be easily obtained but are contaminated with resident microbiota. Infections of the lower respiratory tract are the sixth leading cause of mortality in the United States, with 2 to 3 million cases per year, resulting in 500,000 hospitalizations. The purpose of the culture of respiratory secretions from cystic fibrosis (CF) patients is to isolate organisms associated with CF pulmonary disease so that appropriate interventions may be taken. Tympanocentesis and culture of the middle ear fluid are valuable tools for definitive diagnosis, guiding therapy, and evaluating treatment failures. In many laboratories in areas of low endemicity, culture‐based testing specifically for
Corynebacterium diphtheriae
has been discontinued due to the lack of requests and limitations in media shelf life.
Bartonella
Culture
Authors: Clarridge Jill E. , Harrington Amanda T. 
Published: December 2024

Abstract

The genus
Bartonella
comprises Gram‐negative short rod‐shaped bacteria that belong to the α‐2 subgroup of
Proteobacteria
. Depending on the level of host adaptation,
Bartonella
infection in the reservoir host ranges from asymptomatic to clinical manifestations with low morbidity and limited mortality or, rarely, life‐threatening disease, such as endocarditis. There are several methods of diagnosing bartonellosis in clinical specimens: serology, direct visualization, molecular methods such as polymerase chain reaction, and culture. Collection in ethylenediaminetetraacetic acid tubes or an Isolator tube system is the preferred method for culturing
Bartonella
species from blood. Detection of
Bartonella
species from clinical specimens using molecular methods has been shown to be more sensitive than culture for all specimen types and especially useful for cases in which lymphadenectomy or biopsy is not feasible or serologic results are equivocal.
Incubation Techniques for Anaerobic Bacteriology Specimens
Authors: Morris Trefor E. 
Published: December 2024

Abstract
This chapter describes the various environmental methods and incubation conditions used for anaerobic bacteriology specimens once a properly selected, collected, and transported specimen arrives in the laboratory. Ideally, the specimen is processed immediately on arrival in the laboratory and incubated under anaerobic conditions to prevent further exposure to oxygen. In general, growing cultures must not be exposed to oxygen for examination of culture media until after 48 h of incubation, since anaerobes are most sensitive to oxygen during the log phase of growth. One of the obvious advantages of using an anaerobic chamber/workstation is that technologists can inspect inoculated media without removing them from the anaerobic environment. The choice of incubation systems is influenced by cost, the number of anaerobic cultures performed, and laboratory space limitations. The anaerobic environment is monitored with a methylene blue strip or resazurin indicator.
Anaerobic Gram‐Negative Bacilli
Authors: She Rosemary C. , Church Deirdre L. 
Published: December 2024

Abstract

The anaerobic Gram‐negative bacteria are part of the microbiota of the oral cavity, gastrointestinal tract, and urogenital tract. Many taxonomic changes have been instituted based on newer biochemical and molecular sequencing considerations. Many of the bile‐sensitive species of Gram‐negative bacilli, such as
Prevotella
and
Porphyromonas spp.
, make up a large percentage of the normal microbiota in the oral cavity and are involved in many different types of oral infections. The pigmented anaerobic Gram‐negative bacilli include members of the genera
Prevotella
,
Porphyromonas
, and
Alistipes
. The chapter includes a few additional Gram‐negative rods of human pathogenicity. It also helps the laboratory staff to perform all analyses, including appropriate quality control recommendations, from the receipt of the specimen (anaerobic Gram‐negative bacilli) through processing, testing, interpretation, presentation of the final report, and subsequent consultation.
Clostridioides
(
Clostridium
)
difficile
as a Pathogen Involved in Antimicrobial Agent‐Associated Diarrhea, Colitis, and Pseudomembranous Colitis
Authors: Carroll Karen C. , Paulick Ashley L. 
Published: December 2024

Abstract

Clostridioides (Clostridium) difficile
is a major cause of health care‐associated diarrhea and the primary pathogen responsible for pseudomembranous colitis. Recent epidemiological trends note decreases in health care‐acquired
C. difficile
as a possible consequence of decreased fluoroquinolone use and increases in cases in the community in individuals lacking traditional risk factors. While
C. difficile
colitis was originally dubbed “clindamycin‐associated pseudomembranous colitis”, any antimicrobial agent, including those used to treat the infection itself (i.e., metronidazole and vancomycin), can be a risk factor. Disease results from action of toxins produced by the bacteria.
C. difficile
produces two toxins: toxin A, a weakly cytopathic toxin, is predominantly responsible for the enterotoxic activity of the organism, and toxin B, a potent cytotoxin, appears to play a major role in human disease.
Supplementing Blood Cultures with Chromogenic Media to Expedite Microorganism Identification and/or Antimicrobial Resistance Detection
Authors: Faron Matthew L. 
Published: December 2024

Abstract

Chromogenic agar is medium containing specific combinations of antibiotics and/or other inhibitory substances and chromogen substrates. This allows selective growth of specific organisms and differentiation of various species through colony color and morphology. Chromogenic medium has also been developed for the identification of other types of microorganisms, such as
Candida
species. Chromogenic agar is commonly used for screening polymicrobial specimens to identify resistant organisms, such as carbapenem‐resistant
Enterobacterales
or vancomycin‐resistant
Enterococcus
from rectal swabs or surveillance cultures from the anterior nares to identify methicillin‐resistant
Staphylococcus aureus
. After a Gram stain is performed, chromogenic agar appropriate for the Gram stain morphology can be inoculated to reduce the time to identification of bacterial species and/or key resistance profiles. Differentiation of
Candida
spp. can be improved using chromogenic agar, which may be helpful for laboratories that use rapid molecular methods, as some smaller panels may lack species‐specific identification or identify only a few species.
Multiplex Molecular Panels for Positive Blood Cultures
Authors: She Rosemary C. , Van Tam T. 
Published: December 2024

Abstract
This chapter provides microbial analysis of multiplex molecular panels with procedures for the detection, identification, and characterization of microorganisms involved in human infections. This procedure summarizes the major FDA‐cleared methods available for rapid identification of common bloodstream pathogens and antimicrobial resistance markers from positive blood culture bottles. The chapter discusses general considerations for implementation and application of such panels in the clinical laboratory. It covers proper quality control principles for analytical tests. With postanalytical considerations, the chapter provides attention to common test limitations, interpretive challenges, and results reporting. It emphasizes the importance of correlating molecular results with Gram stain and culture to help avoid pitfalls and aid in troubleshooting. The chapter also provides guidance on basic interpretations of molecular panels that include antimicrobial resistance markers. It develops collaboration among laboratory, patient providers, and antimicrobial stewardship stakeholders in order to maximize the clinical benefits of these molecular panels.
MALDI‐TOF MS for Identification of Acid‐Fast Bacilli and Aerobic Actinomycetes
Authors: Zelazny Adrian M. , Balada‐Llasat Joan‐Miquel 
Published: December 2024

Abstract
This chapter describes the use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for the identification of mycobacteria, Nocardia, and other aerobic actinomycetes after growth in culture. It evaluates the MALDI‐TOF MS technique results in a spectral profile that relates to the mass‐to‐charge ratio of the organism. Direct spotting or on‐target extraction is not advised for myco‐bacteria due to safety concerns and the cell wall properties of this microorganism group. For these reasons, tube extraction protocols are recommended and typically involve mechanical disruption via bead beating, sonication, and/ or vortexing in ethanol, formic acid, and/or acetonitrile. The extracted proteins are then spotted onto the target plate for MALDI‐TOF MS analysis, where the microbial profile is then compared with a reference database; matching algorithms are used to determine the organism's identity.
MALDI‐TOF MS for Filamentous Fungi Identification
Authors: Hanson Kimberly E. , Sobczyk Juliana , Snavely Emily 
Published: December 2024

Abstract
Identification of fungi in the clinical microbiology laboratory has traditionally relied on a combination of phenotypic characteristics, including colony morphology, microscopic examination, growth characteristics, and biochemical reactions. Sequencing‐based approaches require specialized molecular expertise, can be costly, and are relatively slow. Matrix‐assisted laser desorption ionization‐time of flight (MALDI‐TOF) mass spectrometry (MS) is a more rapid and inexpensive methodology that has been used for the identification of microorganisms, including molds, in the microbiology laboratory. Organisms are identified by using intact cells or cell protein extracts which are ionized into charged molecules using a laser. By measuring the mass to charge ratio of the ionized molecules, a spectral fingerprint is generated. These spectral fingerprints are then compared with a database of known spectra from reference organisms to generate an accurate, species‐level identification. This chapter describes protocols for application of MALDI‐TOF MS to identify filamentous fungi in the clinical microbiology laboratory.
Beta‐Lactamase Tests
Authors: Campeau Shelley , Deak Eszter 
Published: December 2024

Abstract

Beta‐lactamases are important mediators of bacterial resistance to beta‐lactam agents. The beta‐lactamase tests detect penicillinases where detection predicts resistance to the penicillinase‐labile penicillins. Routine beta‐lactamase tests are performed directly from bacterial colonies and are based on visual detection of the end products of beta‐lactamase hydrolysis, demonstrated with a colorimetric reaction. Direct beta‐lactamase testing can be performed on Gram‐negative and Grampositive anaerobes other than the
Bacteroides fragilis
group, as organisms in the
B. fragilis
group are beta‐lactamase producers and predictably resistant to penicillin, amoxicillin, and ampicillin. For direct beta‐lactamase tests, coagulase‐negative staphylococci may require induction to demonstrate a positive beta‐lactamase reaction.
Extended‐Spectrum Beta‐Lactamase Testing for
Enterobacterales
Authors: Pitout Johan J. 
Published: December 2024

Abstract
The extended‐spectrum β‐lactamases (ESBLs) are enzymes that cause resistance to the oxyimino‐cephalosporins and the monobactams but not the cephamycins or the carbapenems. The detection of ESBLs involves a screening step followed by confirmation tests. ESBLs are inhibited by “classical“ β‐lactamase inhibitors such as clavulanic acid, sulbactam, and tazobactam. Laboratory tests for confirming ESBL‐producing bacteria are based on this property. The phenotypic ESBL confirmatory test can be performed by disk diffusion or by the broth microdilution MIC method. Commercially available ESBL gradient diffusion strips may also be used for ESBL confirmatory testing. The chapter covers proper quality control principles for analytical tests. With postanalytical considerations, it provides attention to common test limitations, interpretive challenges, and results reporting.
Solid Media Used for Isolation
Authors: Wengenack Nancy L. 
Published: December 2024

Abstract

Both liquid and solid media are recommended for optimal recovery of mycobacteria in culture. Pure cultures of mycobacteria, particularly
Mycobacterium tuberculosis
, are still required, despite the availability of molecular technology, to obtain phenotypic antimicrobial susceptibility test results and for strain typing. The advantage of solid medium is that it enables the detection of mixed cultures and contaminants. Egg‐based or agar‐based media may be used. The main advantage of an egg‐based medium is that it best supports the growth of
M. tuberculosis
and permits niacin testing, if needed. The advantages of agar‐based media include less contamination and earlier and easier visibility of colonial morphology. Colonial morphology can aid in the identification of mycobacteria. Use of both nonselective and selective media is needed for optimal mycobacterial isolation, the latter containing one or more antimicrobial agents to prevent overgrowth by contaminating bacteria or fungi.