bluuebunny/crossref_metadata_2025_split huggingface dataset:
Arenaviruses and Filoviruses
Authors: Raabe Vanessa N. , Gilchrist Alison , Kraft Colleen 
Published: January 2025

Abstract

This chapter focuses on the viruses capable of causing viral hemorrhagic fever (VHF) from two taxa, the families
Arenaviridae
and
Filoviridae
. Some members of these virus families can cause severe VHF with high mortality in localized areas of the world. Continuing detection and isolation of new arenavirus and filovirus species from new geographic locations remains important for public health. Human infection with filoviruses and arenaviruses can cause a wide spectrum of illness. For virus isolation, antigen detection, and RT‐PCR, serum, heparinized plasma, or whole blood should be collected during the acute, febrile stages of illness and frozen on dry ice or in liquid nitrogen vapor. Most arenavirus and filovirus species grow well in cell culture. Early diagnosis of arenavirus and filovirus infections is desirable since specific monoclonal antibody treatments and appropriately selected antiviral drugs are, in certain cases, effective when treatment is initiated soon after onset.
Human Cytomegalovirus
Authors: Hodinka Richard L. 
Published: January 2025

Abstract
This chapter emphasizes the fundamental characteristics and clinical importance of cytomegalovirus (CMV) and focuses on the laboratory tests that can be used to identify the virus and to monitor and predict disease and susceptibility to antiviral therapy, and on the philosophy behind the interpretation and reporting of test results in various defined patient populations. Molecular and immunologic techniques, including whole‐genome sequencing directly from clinical specimens, have been used to study variation among CMV strains. CMV infections are common and usually asymptomatic in otherwise healthy children and adults; however, the incidence and spectrum of disease in newborns and in immunocompromised hosts establish this virus as an important human pathogen. Histopathologic testing, antigenemia assays, and qualitative and quantitative molecular methods have been routinely used for the direct detection of CMV from clinical samples. In the immunocompromised host, the use of direct detection methods to diagnose CMV disease is most beneficial for patient care.
Human Polyomaviruses
Authors: Leuzinger Karoline , Hirsch Hans H. 
Published: January 2025

Abstract
Polyomaviruses (PyVs) were discovered in the 1950s as infectious agents that pass bacterium‐tight filters and form different tumors in rodents, hence their name. The multifunctional large tumor antigen protein successfully maintained the bidirectional gene expression, which is a hallmark of the circular PyV genomes. Biopsy‐proven BK polyomavirus nephropathy is characterized by cytopathic changes in renal tubular epithelial cells, showing enlarged nuclei with intranuclear inclusions, rounding up, and cell detachment. Nucleic acid testing (NAT) is the most widely used diagnostic approach to detect viral DNA genomes in specimens from patients with suspected human polyomavirus (HPyV) infection. The diagnostic value of qualitative NATs in the clinical routine resides primarily in the analysis of sterile or NAT‐negative human materials, which must be obtained by clean invasive procedures. The assessment of HPyV‐specific immune responses is of increasing interest for evaluating the risk of primary infection or reactivation as well as identifying predictors of insufficient or reconstituted immune control.
Pneumocystis Jirovecii
Authors: Cushion Melanie T. , Smulian A. George , Powers‐Fletcher Margaret V. 
Published: January 2025

Abstract

Fungi in the genus
Pneumocystis
are extracellular, hostobligate, mostly host‐specific, and typically restricted to the lung tissues of mammals, although extrapulmonary manifestations have been reported.
Pneumocystis
species all appear to contain similar life cycle stages, although the clusters of organisms removed from the lungs of the different host species can vary in presentation and size. There is no consensus for a typing system for
P. jirovecii
. Serological assays to detect anti‐
P. jirovecii
antibodies are useful for epidemiological studies, but not for diagnosis of
Pneumocystis pneumonia
. The microscopic demonstration of
P. jirovecii
in tissue and fluids by staining with Gomori methenamine silver or a rapid variant of the Wright‐Giemsa stain, by immunofluorescent assay, or by other stains such as Papanicolaou stain should be considered sufficient for diagnosis.
Histoplasma
,
Blastomyces
,
Coccidioides
,
Paracoccidioides
and Other Dimorphic Fungi Causing Systemic Mycoses
Authors: Thompson George R. , Gomez Beatriz L. 
Published: January 2025

Abstract

The dimorphic fungi causing systemic disease belong to the class
Eurotiomycetes
, order
Onygenales
. This chapter covers the dimorphic members of the families
Onygenaceae
and
Ajellomycetaceae
.
Ajellomycetaceae
contains the species
Ajellomyces dermatitidis
,
A. capsulatum
,
A. duboisii
, and
A. crescens
, the anamorphs of which have been placed in the genera
Blastomyces
and
Histoplasma
. DNA sequence data place
Paracoccidioides
in the family
Ajellomycetaceae
as well. However, it is important to appreciate that tissue‐form cells of
Histoplasma
and
Blastomyces
can appear similar to each other as well as to yeast cells of various Candida species,
Cryptococcus neoformans
,
Cryptococcus gattii
, and
Talaromyces marneffei
and to endospores of
Coccidioides
species.
Lagenidium
,
Paralagenidium
,
Pythium
,
Rhinosporidium
, and Uncultivated
Paracoccidioides
Species (Formerly
Lacazia loboi
)
Authors: Vilela Raquel , Mendoza Leonel 
Published: January 2025

Abstract

The identification of
Lagenidum
and
Paralagenidium
species is only possible using molecular methodologies, such as PCR and sequencing. Based on taxonomic and other morphological characteristics, these four anomalous species,
Lagenidium
,
Pythium
,
Rhinosporidium
, and the uncultivated fungus previously known as
Lacazia loboi
, were not well understood. Vilela recently reported that the uncultivated fungus developing skin granulomas in dolphin and humans, long believed to be
Lacazia loboi
, comprised two different
Paracoccidioides
species:
P. ceti
and
P. loboi
. Because few DNA sequences from dolphins with the disease were used in phylogenetic analysis, the separation of the dolphin DNA from the cultivated
Paracoccidioides
species remained a puzzle. Deep skin scrapings and tissue biopsies from human and dolphins suspected of skin disease due to uncultivated
Paracoccidioides
species should be submitted to the laboratory.
Mechanisms of Resistance to Antifungal Agents
Authors: Perlin David S. 
Published: January 2025

Abstract
This chapter focuses on the epidemiologic, biological, and molecular nature of antifungal drug resistance. Antifungal drug action and the host immune system often must work synergistically to control and clear an infection. “Microbiological resistance” refers to decreased susceptibility of a fungal strain to an antifungal agent, which is reflected in standardized antifungal in vitro susceptibility testing relative to susceptible standard reference strains, as defined by the Clinical Laboratory Standards Institute and the European Committee on Antimicrobial Susceptibility Testing. The azole antifungal agents are the most prominent example of drug selection for less susceptible species. The polyene drug amphotericin is fungicidal, and resistance rarely occurs. Fungi encode numerous putative drug efflux transporters that have the potential to influence susceptibility to azole antifungal agents by reducing the effective cellular concentration of drugs below their inhibitory threshold. Biofilms are among the most prevalent forms of microbial growth in nature.
Taxonomy and Classification of Human Eukaryotic Parasites
Authors: Adl Sina M. , Mathison Blaine A. 
Published: January 2025

Abstract
The eukaryotic parasites of medical importance are classically known as protozoan, arthropod, and helminthic parasites; the last includes nematodes, cestodes, trematodes, and acanthocephalans. The modern classification of biological species intends to reflect an evolutionary history of living organisms. Eukaryotes are divided into five monophyletic lineages called supergroups, of which four include human parasites: SAR, Excavata, Amoebozoa, and Opisthokonta. These supergroups replace the previous kingdoms that encompassed the eukaryotes. The chapter outlines basic characters of the parasitic protists by clade and the state of their classification at the level of family and genus. Species are identified by sequencing of the 18S small rRNA gene regions and phylogenetic analysis, and the species identification is verified against reference sequences. Modern specimen analysis is discovering new opportunistic pathogens related to known pathogenic groups, but others unrelated to known pathogenic genera will continue to be encountered.
Reagents, Stains, and Media: Parasitology
Authors: Potters Idzi , Linscott Andrea J. 
Published: January 2025

Abstract

The evaluation of clinical specimens for ova and parasites in the clinical laboratory can involve the use of direct macroscopic examination of the specimen and microscopic examination of fresh and fixed specimens, as well as culture for some parasitic organisms. Formalin has been used in parasitology as an all‐purpose fixative for concentration procedures. A solution of iodine can be used for preparing direct or concentrated wet mounts for parasitological examination. Iodine stains can be purchased commercially for use in routine parasitology. Examination of blood films for parasites includes the use of two common stains, the Giemsa stain and Wright's stain, both derivatives of the original Romanowsky stain. Cultures can be performed for only a few parasitic organisms, including
Acanthamoeba
species,
Naegleria fowleri
,
Plasmodium
species, intestinal amebae,
Trichomonas vaginalis
,
Leishmania
species, and
Trypanosoma
species. Culture media used for parasite recovery are sometimes referred to as being either defined or undefined.
Plasmodium
and
Babesia
Authors: Pritt Bobbi S. 
Published: January 2025

Abstract

Plasmodium
and
Babesia
are intraerythrocytic protozoan parasites that cause malaria and babesiosis, respectively. Both are transmitted through the bite of an infected arthropod and cause significant human morbidity and mortality worldwide. The
Plasmodium
parasite is transmitted primarily through the bite of an infected
Anopheles
mosquito, and competent mosquito vectors are found throughout the world. The antigens most commonly detected by the commercially available rapid diagnostic tests are pan‐ or species‐specific
Plasmodium
lactate dehydrogenase,
Plasmodium falciparum
histidine‐rich protein 2, and panspecific
Plasmodium
aldolase. Serologic testing plays only a small role in diagnosis of acute malaria, given that antibodies are frequently absent at the time of patient presentation. Members of the genus
Babesia
infect a wide range of wild and domestic animals worldwide using primarily ixodid tick vectors. Babesiosis due to
Babesia microti
and
Babesia duncani
/
B. duncani
‐like parasites can manifest as asymptomatic or mild infection to life‐threatening illness.
Toxoplasma
Authors: Robert‐Gangneux Florence 
Published: January 2025

Abstract

Toxoplasmosis is a worldwide zoonosis caused by infection with the parasite
Toxoplasma gondii
. It is one of the most common parasitic infections in humans and is most typically asymptomatic.
T. gondii
is a protozoan parasite classified in the Apicomplexa: Conoidasida: Coccidia: Eimeriorina, genus Toxoplasma. Serologic prevalence data indicate that toxoplasmosis is one of the most common infections of humans throughout the world. Serologic screening of organ donors and recipients allows the identification of patients at risk of donor‐derived primary infection. Toxoplasmosis can be categorized into four clinical groups: infection acquired in the immunocompetent patient; infection acquired or reactivated in the immunodeficient patient; congenital infection; and ocular infection. Diagnosis of toxoplasmosis is critical in four clinical settings: pregnant women with infection during gestation, newborns with suspected congenital toxoplasmosis, patients with retinochoroiditis, and immunocompromised patients.
Pathogenic and Opportunistic Free‐Living Amebae
Authors: Cope Jennifer R. , Ali Ibne Karim M. , Visvesvara Govinda S. 
Published: January 2025

Abstract

Free‐living amebae belonging to the genera
Naegleria
,
Acanthamoeba
, and
Balamuthia
can infect humans and other animals and cause potentially severe, life threatening disease. This chapter presents a list of clinical syndromes caused by free‐living amebae infections. Free‐living amebae can be cultivated in axenic conditions or in the presence of a mammalian cell culture for research purposes. The real‐time multiplex PCR assay is a fast, sensitive, and robust assay that detects all three pathogenic free‐living amebae,
Acanthamoeba
spp.,
B. mandrillaris
, and
N. fowleri
, simultaneously in a single specimen and has many advantages over conventional PCR. All clinical specimens should first be examined microscopically, and if amebae are visualized, then the clinician should be immediately notified.
Cryptosporidium
Authors: Xiao Lihua , Feng Yaoyu 
Published: January 2025

Abstract

Cryptosporidium
spp. are protozoan parasites that inhabit the brush borders of the gastrointestinal and respiratory epithelium of various vertebrates, causing enterocolitis, diarrhea, and cholangiopathy in humans.
Cryptosporidium
spp. are well‐recognized water and foodborne pathogens in industrialized nations, having caused many outbreaks of human illness.
Cryptosporidium
spp. are intracellular protozoan parasites that primarily infect epithelial cells of the intestine and biliary ducts, especially the ileum and colon. The distribution of
Cryptosporidium parvum
and
Cryptosporidium hominis
in humans is a reflection of the role of different transmission routes in cryptosporidiosis epidemiology. Cryptosporidiosis in immunocompromised persons, including patients with HIV, is frequently associated with chronic, life‐threatening diarrhea. In clinical laboratories,
Cryptosporidium
spp. in stool specimens are commonly detected by microscopic examinations of oocysts, immunologic detection of antigens, and nucleic acid amplification testing. Genotyping and subtyping have been used in characterizations of
Cryptosporidium
infections, especially in cryptosporidiosis surveillance and outbreak investigations.
Cestodes
Authors: Cabada Miguel M. , Jimenez Juan , Garcia Hector H. 
Published: January 2025

Abstract

Adult cestode tapeworms have a flattened body composed of the scolex, bearing the fixation organs such as suckers, hooks, and bothria; the neck, where the cellular reproduction occurs; and the strobila, formed by numerous segments called proglottids. The fish tapeworm,
Dibiothriocephalus latus
, is the largest intestinal parasite of humans.
Taenia saginata
, the beef tapeworm, is endemic to most of the world. Humans are the only definitive host for this tapeworm, and infection carries minimal health risks.
Taenia solium
, the pork tapeworm, has an extensive geographic distribution and a large impact on human health due to its association with seizure disorders.
T. solium
neurocysticercosis is the most common cause of acquired epilepsy in developing countries.
Hymenolepis nana
is the smallest of the intestinal tapeworms of humans and the most common tapeworm infection throughout the world. In its zoonotic cycle,
H. nana
is a parasite of mice, and beetles act as intermediate hosts.
Arthropods of Medical Importance
Authors: Mathison Blaine A. 
Published: January 2025

Abstract

Arthropods comprise a diverse group of invertebrate animals, united by a common body plan of a jointed, chitinous exoskeleton. Four major extant groups of arthropods have members of medical importance: hexapods (insects), arachnids, crustaceans, and myriapods (e.g., millipedes and centipedes). Arthropods are thought of by many in clinical settings with respect to their role as vectors, transmitters of infectious agents, including viruses, bacteria, protozoans, helminths, and, in the case of
Dermatobia hominis
(the “human” botfly), other arthropods. There are five major groups of vectors: the Diptera (flies and mosquitoes), Hemiptera (kissing bugs), Siphonaptera (fleas), Psocodea (lice), and the order Acarina (ticks and mites). Arthropods that invade a host's body and cause disease include mites (scabies), fleas (tungiasis), fly larvae (myiasis), and pentastomes. Delusion of parasitosis can be a serious illness which can be treated by experienced mental health professionals.
Anisotropic Shape‐Memory Cryogel with Oriented Macroporous Channel for Hemorrhage Control and Tissue Generation
Authors: Pan Zheng , He Gang , Xian Yiwen , Huang Qiqi , Li Shuqi , Li Huangting , Zhang Chong , Wu Decheng 
Published: January 2025

AbstractInjectable shape‐memory materials represent a promising solution for managing severe bleeding from deep, inaccessible wounds. However, many existing expandable hemostats consist of randomly porous networks and often exhibit inadequate liquid absorption, non‐degradability, and potential cytotoxicity, which limits their effectiveness in hemostasis and wound repair. To overcome these challenges, this study introduces an anisotropic hemostatic cryogel, SALC, featuring oriented macroporous channels made from biocompatible polymers (poly(ethylene glycol), gelatin, and lignin) through a simple one‐step cryo‐structuration process. This structural alignment provides the cryogel with low water flow resistance, efficient fluid transport, and rapid shape recovery. SALC demonstrates superior liquid adsorption and retention, in vitro tamponade sealing, and pro‐coagulant properties compared to commercial gelatin sponges and XSTAT, along with favorable biocompatibility and biodegradability. The hemostatic efficacy of SALC surpasses clinically used counterparts in rat models of liver perforation and femoral artery transection. Remarkably, SALC achieves effective hemostasis in porcine models of severe hepatic, femoral artery, and cardiac injuries. Additionally, this anisotropic cryogel supports liver tissue regeneration by promoting cell migration and angiogenesis while mitigating inflammatory responses. The cryogel is also lightweight and easy to carry and implement. Overall, SALC shows promising clinical applications for treating severe hemorrhages and improving wound healing.
Multiplexed Bio‐detection on an Interferometric Optical Waveguide Assembly
Authors: Bratash Oleksii , Courson Rémi , Malaquin Laurent , Leichle Thierry , Buhot Arnaud , Leroy Loïc , Engel Elodie 
Published: January 2025

AbstractMultiplexed remote bio‐detection is demonstrated through an optical waveguide assembly coated with interferometric layers. Image conduits (IC)s, composed of 3012 individual cores, are coated with interferometric layers of tantalum pentoxide (Ta2O5) and silica (SiO2) to transform each core into a sensitive sensor. The spectral response of the IC as a function of refractive index (RI) changes is obtained and compared with the simulated one. The experimental sensitivities and resolutions of individual cores of the waveguide are assessed in remote detection mode by imaging through the optical assembly. For 75% of the cores, a sensitivity better than 510%. RIU−1 (RI Unit) is obtained, corresponding to a resolution better than 7 × 10−4 RIU. Furthermore, the coated face of IC is functionalized with two localized arrays of hundred‐micrometer droplets containing two different oligonucleotide (ODN) probes using a polymeric 3D‐printed microcantilever. Hybridization of complementary ODN strands is detected for one of the probes, the second being a negative control. Interaction kinetics are monitored in functionalized areas by grouping several cores or on individual cores. Thus, multiplexed bio‐detection on the surface of an interferometric waveguide is demonstrated for the first time paving the way for applications in multiplex in situ biosensing, and, ultimately, in vivo endoscopic diagnosis.
High‐Performance Droplet‐Based Triboelectric Nanogenerators: A Comparison of Device Configuration and Operating Parameters
Authors: Chaithaweep Kanokwan , Pharino Utchawadee , Pongampai Satana , Hajra Sugato , Kim Hoe Joon , Charoonsuk Thitirat , Maluangnont Tosapol , Sriphan Saichon , Vittayakorn Naratip 
Published: January 2025

AbstractDroplet‐based electricity generators (DEGs) harness liquid‐solid electrification to convert water droplets impacts into electrical energy. This study systematically examines how droplet height, droplet volume, flow rate, and substrate tilt angle influence DEG performance using polytetrafluoroethylene (PTFE) as a triboelectric layer and deionized water. Three electrode designs (double, top, bottom) are evaluated, revealing that the double‐electrode configuration delivers the highest output. This enhanced performance arises from synergistic droplet motion, electrical double‐layer formation, and charge discharge, as validated by an equivalent circuit model. By varying droplet heights from 1–20 cm, volumes of 7.7–50 µL, flow rates of 50–300 drops/min, and tilt angles of 0–90°, an optimized setup yields −70 V and 22 mA, translating to a power density of 0.28 µW cm−2. High‐speed imaging correlates these outputs with droplet impact dynamics and the resulting charge transfer. Additionally, the optimized DEG can power small electronic devices, charge capacitors, and monitor artificial acid rain in real‐time, displaying distinct electrical signals compared to typical rainwater. These findings underscore the potential of DEGs as renewable energy harvesters and smart environmental sensors, paving the way for advanced on‐demand power generation in diverse settings.
Mannose Promotes β‐Amyloid Pathology by Regulating BACE1 Glycosylation in Alzheimer's Disease
Authors: Liang Chensi , Yuan Ziqi , Yang Shangchen , Zhu Yufei , Chen Zhenlei , Can Dan , Lei Aiyu , Li Huifang , Leng Lige , Zhang Jie 
Published: January 2025

AbstractHyperglycemia accelerates Alzheimer's disease (AD) progression, yet the role of monosaccharides remains unclear. Here, it is demonstrated that mannose, a hexose, closely correlates with the pathological characteristics of AD, as confirmed by measuring mannose levels in the brains and serum of AD mice, as well as in the serum of AD patients. AD mice are given mannose by intra‐cerebroventricular injection (ICV) or in drinking water to investigate the effects of mannose on cognition and AD pathological progression. Chronic mannose overload increases β‐amyloid (Aβ) burdens and exacerbates cognitive impairments, which are reversed by a mannose‐free diet or mannose transporter antagonists. Mechanistically, single‐cell RNA sequencing and metabolomics suggested that mannose‐mediated N‐glycosylation of BACE1 and Nicastrin enhances their protein stability, promoting Aβ production. Additionally, reduced mannose intake decreased BACE1 and Nicastrin stability, ultimately lowering Aβ production and mitigating AD pathology. this results highlight that high‐dose mannose consumption may exacerbate AD pathogenesis. Restricting dietary mannose may have therapeutic benefits.