bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomy Updates for Anaerobes
Authors: Shannon Samantha K. , Pence Morgan A. 
Published: December 2024

Abstract
The International Committee on Systematics of Prokaryotes (ICSP) and the International Code of Nomenclature of Bacteria (ICNB) are responsible for the naming of prokaryotes, including anaerobes. ICSP and ICNB maintain a strict set of rules for naming and renaming bacteria. Not all proposed taxonomic changes that are published are in compliance with the ICNB. Thus, it is imperative to consult reliable sources to prevent adoption of invalid taxonomy. Taxonomic changes are frequently proposed by evolutionary microbiologists, and new taxonomic name proposals may have detrimental effects for clinical laboratories and hospitals. The Clinical and Laboratory Standards Institute is currently developing a document to address taxonomy changes and guidance for updating organism names for laboratory reporting. Microbiology laboratory leadership should discuss taxonomy changes with infectious diseases and other key clinician groups to determine if changes should be incorporated into laboratory reporting.
Specimen Selection, Collection, and Transport for Anaerobic Culture
Authors: Harriott Melphine M. , Brown Kristen L. 
Published: December 2024

Abstract
Proper collection of specimens, to avoid contamination with organisms of the normal microbiota, and prompt transport to the laboratory for processing are essential. This is especially true for specimens sent to the laboratory for anaerobic culture. The laboratory director and staff must provide health care personnel with guidelines for the optimal type and amount of clinical specimens that are needed for anaerobic culture, including the appropriate methods for specimen collection. Patient care units, clinics, emergency rooms, and satellite facilities should be provided with appropriate collection and transport devices and complete instructions for their use. The ideal transport system should maintain the viability of the anaerobes during transport without allowing the overgrowth of members of the normal microbiota that are not a part of the pathogenic process. Good communication between the clinical microbiology laboratory and the clinical staff will ensure that collection and transport are optimal.
Culture Media for Anaerobes
Authors: Bard Jennifer Dien , Copsey‐Mawer Sarah , Precit Mimi 
Published: December 2024

Abstract

Selection of media is key to the recovery of anaerobic organisms from clinical specimens. Primary culture media are those onto which direct specimens are inoculated and may be enriched, nonselective, selective, or differential to allow for the initial recovery of clinically significant anaerobes and inhibition of facultative anaerobe overgrowth. Subculture of anaerobes from primary media to secondary media that are selective and/or differential aids in further identification of clinically significant anaerobes. Proper selection of the initial media used during specimen processing of anaerobic bacteriology aids in the overall accuracy of the workup and assists in recognition of key phenotypic characteristics including colonial morphology. As some anaerobes can be highly sensitive to oxygen exposure, it is recommended that prereduced, anaerobically sterilized media be used to inoculate clinical specimens. Anaerobes have a wide range of nutritional needs, but most strict anaerobes require hemin and vitamin K
1
.
Examination of Primary Culture Plates for Anaerobic Bacteria
Authors: Morris Trefor E. 
Published: December 2024

Abstract
The goal of processing primary culture plates is to isolate significant anaerobic organisms from the original specimen for identification and susceptibility testing when it is indicated. Comparison of culture results with what was seen on the original Gram stain of the specimen is critical. When culture plates are evaluated, all morphotypes observed in the original Gram stain should match the aerobes and anaerobes recovered. It is important to remember that anaerobic culture media permit facultatively anaerobic bacteria to grow. All bacterial isolates must be subjected to aerotolerance testing before being designated as anaerobes. Special precautions must be taken to avoid exposure of culture plates to oxygen during examination. A maximum of 20 min of exposure is recommended, as beyond this, some oxygen‐sensitive anaerobes will be killed. In addition, reduced culture media may become oxidized when exposed to air beyond this period, making the media unsuitable for isolation of fastidious anaerobes.
Rapid Disk, Spot Tests, and Other Rapid or Primary Methods for the Identification of Anaerobes
Authors: Clark Andrew , de Danies Margaret Ordoñez‐Smith 
Published: December 2024

Abstract

This chapter describes rapid disk tests, biochemical spot tests, and other methods that provide a cost‐effective and efficient mechanism for the characterization and identification of anaerobes isolated from clinical specimens. The indole test is helpful in obtaining an identification for certain anaerobic bacteria. Nitrate can be reduced to nitrite and other reduction products by anaerobic organisms possessing the enzyme nitrate reductase. Some anaerobic bacteria produce catalase, an enzyme that breaks down hydrogen peroxide (H
2
O
2
) into oxygen and water. Special‐potency disks can aid in confirming phenotypic characteristics and providing presumptive identification of anaerobic bacteria. Observing the color of fluorescence when anaerobic bacterial growth is exposed to long‐wavelength ultraviolet light can aid in the rapid detection and presumptive identification of certain anaerobic species. Anaerobic bacteria that produce enzymatic lipases can hydrolyze fats contained in egg yolk agar to produce glycerol and free fatty acids.
Use of Matrix‐Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for the Identification of Anaerobic Bacteria
Authors: Paulick Ashley L. , Copsey‐Mawer Sarah 
Published: December 2024

Abstract
Identification of clinically significant anaerobes is gaining in importance. This is due to both better understanding of clinically relevant organisms and the unpredictability of inter‐ and intraspecies variation in antimicrobial susceptibility testing along with increasing antimicrobial resistance. The use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for the identification of clinically relevant bacteria is now part of the routine workflow in many laboratories. This procedure provides guidance regarding the use of MALDI‐TOF MS specifically for the identification of anaerobes. Pure cultures following a plate‐to‐plate passage on anaerobic blood agar or Brucella agar plates should be used for MALDI‐TOF MS, since mixed inocula may lead to inaccurate results or no identification being rendered following MALDI‐TOF MS analysis.
Introduction
Authors: Harrington Amanda T. , McElvania Erin 
Published: December 2024

Abstract
Blood culture remains one of the most critical functions of the clinical microbiology laboratory, aiding in the diagnosis of bloodstream infection and therapy management for patients. Culture of blood specimens is largely accomplished using commercial, continuously monitored blood culture systems, and aerobic and anaerobic bacteria, fungi, and mycobacteria can be recovered using these methods. Postanalytical communication and coordination with clinical care teams, especially those who prescribe antibiotics, result in improved patient care, such as reducing the interval of time to effective treatment. Gram staining remains a cornerstone of clinical microbiology practice and is a useful and rapid tool for preliminary identification of organisms from blood culture specimens. The procedure for quality control and quality assurance for blood culture provides guidance on verification of continuous‐monitoring blood culture systems as well as recommended strategies for monitoring quality of blood culture processes using standard metrics, such as contamination rates.
Lysis Centrifugation
Authors: McElvania Erin 
Published: December 2024

Abstract
The Isolator system consists of Vacutainer tubes for blood collection that contain lysing, antifoaming, and anticoagulating agents. The lysis of red blood cells followed by centrifugation results in concentration of microorganisms from the blood and bone marrow specimen. The lysis centrifugation method can be used to culture routine bacterial pathogens and yeast, but the concentration step makes it particularly suited to detection of slowly growing and fastidious microorganisms, including Bartonella, Malassezia, and Mycobacterium species as well as thermally dimorphic and filamentous fungi. The limitations of lysis centrifugation are the requirement of specialized equipment and the high degree of manual processing. Due to the use of agar plates and manual processing, the lysis centrifugation method is prone to high rates of contamination with environmental and cutaneous microorganisms. The Isolator system can be used for quantitative assessment of microorganisms in the blood or bone marrow.
Blood Cultures: Postanalytical Considerations
Authors: Kamboj Kamal , Balada‐Llasat Joan‐Miquel 
Published: December 2024

Abstract
Blood cultures represent a critical tool for health care professionals as a means of detecting the presence of microbial organisms in the bloodstream of an infected individual. The presence of microorganisms in the bloodstream constitutes a serious situation that warrants timely and accurate identification of the microorganism(s) present. The Gram stain result of a positive blood culture is the important initial information that helps the clinician optimize empiric antimicrobial treatment. Blood culture contaminants are a major source of frustration for the clinician and laboratory personnel alike. The increased use of central venous catheters and other indwelling devices puts patients at elevated risk for bacteremia, often due to contamination or colonization of the line or hardware with cutaneous microbiota or environmental organisms. Interpretation of culture results for patients with indwelling devices in place is challenging. This procedure will address postanalytical processing for blood cultures, including reporting of results, interpretation, limitations, report archiving, consultation, and specimen storage.
Identification of Highly Pathogenic Bacteria by MALDI‐TOF MS
Authors: Tran Anthony 
Published: December 2024

Abstract
The use of matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) for identification of pathogenic bacteria and fungi has become popular in diagnostic microbiology and public health laboratories due to its accuracy and speed of microorganism identification. Based on the presence or absence of organisms in the MALDI‐TOF MS library, testing of select agents may yield no identification or misidentifications. A biological risk assessment should be conducted prior to implementation of MALDI‐TOF MS to mitigate the risks to the laboratorian conducting the test. The biological risk assessment should be reviewed periodically as well as any time changes to the instrument or the MALDI‐TOF MS. This chapter focuses on the specimen collection, reagents and equipment, calibration and quality control, reporting results and limitations of procedure.
MALDI‐TOF MS for Identification of Bacteria and Yeast from Positive Blood Culture Broth
Authors: McElvania Erin 
Published: December 2024

Abstract
Identification of bacteria and yeast from blood culture is one of the most important functions of the microbiology laboratory due to the morbidity and mortality bloodstream infections inflict among patients. Matrix‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI‐TOF MS) provides identification of bacteria and yeast in under an hour. MALDI‐TOF MS performed directly from other patient specimens has not been implemented for routine use in clinical microbiology laboratories because the method does not perform well on polymicrobial specimens or those with a low burden of organisms. Blood culture broth is a complex specimen type due to the presence of RBCs and other blood components which must be separated from the bacteria or yeast to achieve high‐quality MALDI‐TOF MS spectra for accurate organism identification.
Screening Tests for Detection of High‐Level Mupirocin Resistance in
Staphylococcus aureus
Authors: Hemarajata Peera 
Published: December 2024

Abstract

High‐level mupirocin resistance (HLMR) in
Staphylococcus aureus
is defined by a mupirocin MIC of ≥512 μg/ml and is associated with the presence of plasmidencoded
mupA
or, less commonly,
mupB
genes in these isolates. Screening methods for detection of HLMR include assessing growth at a high concentration of mupirocin by broth microdilution or by disk diffusion using a 200‐μg mupirocin disk. Mupirocin ointment use is associated with increased rate of HLMR in
S. aureus
and, in particular, methicillin‐resistant
S. aureus
(MRSA). Failure of attempted MRSA decolonization using mupirocin may result in selection for genetic elements conferring resistance to other classes of antimicrobials.
Screen Tests to Detect High‐Level Aminoglycoside Resistance in
Enterococcus
spp.
Authors: Maris Alexander S. , Tao Lili 
Published: December 2024

Abstract
High‐level aminoglycoside resistance (HLAR) in enterococci is most commonly detected by assessing growth at high concentrations of gentamicin and sometimes streptomycin. Strains that show HLAR to gentamicin will not be synergistically killed with combinations of cell wall‐active drugs plus gentamicin. HLAR to gentamicin also means HLAR to tobramycin, netilmicin, amikacin, and kanamycin. This chapter describes the agar screen test in detail, and presents the reference to use of standard disk diffusion and broth microdilution MIC test procedures for detecting HLAR. 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.
Agar Screen Test to Detect Vancomycin Resistance in
Enterococcus
spp.
Authors: Maris Alexander S. , Tao Lili 
Published: December 2024

Abstract
This chapter describes agar dilution screen test in detail. The vancomycin agar screen is used to detect vancomycin‐resistant enterococcal colonies that have been isolated from clinical or surveillance cultures. MIC and species identification tests are subsequently required to determine if the isolate is a true vancomycin‐resistant enterococcus (VRE). VRE isolates possess acquired vancomycin resistance determinants that may be horizontally transferred with infection prevention implications; such VRE isolates contrast with isolates possess chromosomally mediated intrinsic low‐level vancomycin resistance, which does not pose infection prevention concerns. 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.
Toxins: Botulinum Toxin (
Clostridium botulinum
) and Staphylococcal Enterotoxin B (
Staphylococcus aureus
)
Authors: Egan Christina , Perry Michael J. 
Published: December 2024

Abstract

Pathogenic microorganisms can contain genes that allow toxin production. Two toxin‐producing organisms are
Clostridium botulinum
and
Staphylococcus aureus
.
C. botulinum
is a group of anaerobic organisms, commonly found in soil and aquatic habitats throughout the world. Staphylococcal enterotoxin B (SEB) is one of several exotoxins that may be produced by
S. aureus
. Depending on the strain,
S. aureus
can produce a variety of extracellular proteins that act as virulence factors, including toxic shock syndrome toxin 1, exfoliative toxins A and B, and a family of structurally related proteins classified as enterotoxins. Testing for SEB may be performed by clinical laboratories with appropriate protocols and safety mitigation. The chapter covers safety considerations, specimen collection, and specimen processing, incubation and examination of cultures for preanalytical considerations. For analytical considerations, it provides quality control and identification. With postanalytical considerations, the chapter provides attention to summary/special considerations.
Eastern Equine Encephalitis Virus
Authors: Vetter Sara M. 
Published: December 2024

Abstract

Eastern equine encephalitis virus (EEEV) is a member of the Alphavirus group in the family
Togaviridae
. It is an enveloped, positive‐sense RNA virus and is part of a group of other important arthropod‐borne viruses such as chikungunya virus and Ross River virus. EEEV is the etiological agent of eastern equine encephalitis (EEE) disease in humans and equines. The main mosquito vector is
Culiseta melanura
, which is found in the southeastern United States, Central America, and northern South America, but other “bridge vectors”, such as
Aedes
,
Culex
, and
Coquillettidia
, which feed on both birds and mammals, are responsible for infections in equines and humans. EEEV has been detected only in the Western Hemisphere, being found in eastern Canada and all U.S. states east of the Mississippi as well as several other states, including Arkansas, Minnesota, South Dakota, and Texas. Clinical manifestations of EEE infection vary from low‐grade fever to severe encephalitis, including death.
Leveraging AI to improve health information access in the World's largest maternal mobile health program
Authors: Verma Shresth , Lalan Arshika , Diaz Paula Rodriguez , Danassis Panayiotis , Mahale Amrita , Sudan Kumar Madhu , Hegde Aparna , Tambe Milind , Taneja Aparna 
Published: December 2024

AbstractHarnessing the wide‐spread availability of cell phones, many nonprofits have launched mobile health (mHealth) programs to deliver information via voice or text to beneficiaries in underserved communities, with maternal and infant health being a key area of such mHealth programs. Unfortunately, dwindling listenership is a major challenge, requiring targeted interventions using limited resources. This paper focuses on Kilkari, the world's largest mHealth program for maternal and child care – with over 3 million active subscribers at a time – launched by India's Ministry of Health and Family Welfare (MoHFW) and run by the non‐profit ARMMAN. We present a system called CHAHAK that aims to reduce automated dropouts as well as boost engagement with the program through the strategic allocation of interventions to beneficiaries. Past work in a similar domain has focused on a much smaller scale mHealth program and used markovian restless multiarmed bandits to optimize a single limited intervention resource. However, this paper demonstrates the challenges in adopting a markovian approach in Kilkari; therefore, CHAHAK instead relies on non‐markovian time‐series restless bandits and optimizes multiple interventions to improve listenership. We use real Kilkari data from the Odisha state in India to show CHAHAK's effectiveness in harnessing multiple interventions to boost listenership, benefiting marginalized communities. When deployed CHAHAK will assist the largest maternal mHealth program to date.
Breaking the Trade‐Off Between Mobility and On–Off Ratio in Oxide Transistors
Authors: Chang Yu‐Cheng , Wang Sung‐Tsun , Lee Yung‐Ting , Huang Ching‐Shuan , Hsu Chu‐Hsiu , Weng Tzu‐Ting , Huang Chang‐Chang , Chen Chien‐Wei , Chou Tsung‐Te , Chang Chan‐Yuen , Woon Wei‐Yen , Lin Chun‐Liang , Sun Jack Yuan‐Chen , Lien Der‐Hsien 
Published: December 2024

AbstractAmorphous oxide semiconductors (AOS) are pivotal for next‐generation electronics due to their high electron mobility and excellent optical properties. However, In2O3, a key material in this family, encounters significant challenges in balancing high mobility and effective switching as its thickness is scaled down to nanometer dimensions. The high electron density in ultra‐thin In2O3 hinders its ability to turn off effectively, leading to a critical trade‐off between mobility and the on‐current (Ion)/off‐current (Ioff) ratio. This study introduces a mild CF4 plasma doping technique that effectively reduces electron density in 10 nm In2O3 at a low processing temperature of 70 °C, achieving a high mobility of 104 cm2 V⁻¹ s⁻¹ and an Ion/Ioff ratio exceeding 10⁸. A subsequent low‐temperature post‐annealing further improves the critical reliability and stability of CF4‐doped In2O3 without raising the thermal budget, making this technique suitable for monolithic three‐dimensional (3D) integration. Additionally, its application is demonstrated in In2O3 depletion‐load inverters, highlighting its potential for advanced logic circuits and broader electronic and optoelectronic applications.
High External Quantum Efficiency and Ultra‐Narrowband Organic Photodiodes Using Single‐Component Photoabsorber With Multiple‐Resonance Effect
Authors: Yao Xiang , Li Yanru , Sun Yajing , Li Yao , Li Ting , Tang Zheng , Wu Jiaying , Fei Zhuping 
Published: December 2024

AbstractOrganic photodiodes (OPDs) that utilize wavelength‐selective absorbing molecules offer a direct approach to capturing specific wavelengths of light in multispectral sensors/imaging systems without filters. However, they exhibit broad response bandwidths, low external quantum efficiency (EQE), and often require compromises in two‐component photoactive materials. Herein, the first utility of boron‐nitrogen (BN) single‐component photoabsorbers, leveraging a multi‐resonance effect are introduced to attain OPDs with both record‐high EQE of 33.77% and ultra‐small full‐width half‐maximum (FWHM) of 36 nm in the reported narrowband OPDs using single‐component photoabsorbers. It is found that the outstanding performance of these narrowband OPDs can be attributed to the ultra‐small FWHM, slow charge recombination, low activation energy, and balanced bipolar charge transport within the para‐tert‐butyl substituted B,N‐embedded rigid polycyclic molecule (BNCz) film. Furthermore, BN derivatives such as BN(p)SCH3, BN(p)SO2CH3, and pyBN‐m‐H have also shown high EQE, minimal FWHM, and tunable photoresponse peaks ranging from blue‐violet to blue‐turquoise, highlighting the potential of BN molecules and molecular engineering in the development of novel narrowband absorbers for advanced wavelength‐selective OPDs. Such pioneering working can provide a class of novel narrowband absorbers to propel the advancement of high‐performance wavelength‐selective OPDs.
Photocatalytic C−I Bond Borylation and Phosphorylation of Diaryliodonium Salts with Excellent Atom‐Economy
Authors: Ding Tian‐Yu , Guo Xiao‐Ning , Chen Bin , Tung Chen‐Ho , Wu Li‐Zhu 
Published: December 2024

AbstractHighly atom‐economic conversion of diaryliodonium salts represents an underdeveloped but highly desirable domain. Most reactions involving these species only utilize single aryl group of the diaryliodonium salts and produce an equivalent of aryl iodide as waste. Herein, by further transforming the side‐product aryl iodide, we report an overall new two‐step one‐pot strategy that allows photocatalytic C−I bond borylation of diaryliodonium salts and ensures effective conversion of both aryl groups of the diaryliodonium into the relevant arylboronic esters. Mechanistic investigations suggest that electron‐donor‐acceptor complex is formed between the photocatalyst phenothiazine and diaryliodonium salt substrate. Upon visible light irradiation, this complex produces aryl radical and aryl iodide. With addition of a base in the second step, the reducing ability of the photocatalyst is enhanced via proton‐coupled electron transfer process, thereby aryl iodide produced in the first step is reduced to yield aryl radical again. Both aryl radicals generated in the two steps react with B2(OR)4 to produce the corresponding monoarylation product in a quantitative yield. The strategy is also applicable for C−I bond phosphorylation of diaryliodonium salts, ensuring that both aryl moieties can be phosphorylated with high efficiency.