bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithms for Detection and Identification of Viruses
Authors: Landry Marie Louise , Babady N. Esther , Binnicker Matthew J. , Pinsky Benjamin A. , Tang Yi‐Wei 
Published: December 2024

Abstract
Diagnostic virology was a distinct discipline that was practiced primarily in public health, research, and academic settings. Over the past 50 years, change has been driven by advances in medical care and diagnostics, the increased number of immunosuppressed hosts, recognition of sexually transmitted viruses, emergence of epidemics and pandemics, and importantly, the development of antiviral therapies. Early technological improvements in the laboratory included enzyme immunoassays, IgM class capture assays, monoclonal antibodies for identification, rapid centrifugation cultures, and direct detection of viral antigens in clinical specimens by immunofluorescence. The most transformative, however, was the introduction of nucleic acid amplification tests, which are both rapid and sensitive, can be automated, highthroughput, or random access, and can detect viruses not amenable to routine culture. With the arrival of the coronavirus disease 2019 pandemic, ongoing trends accelerated. The use of respiratory viral culture was eliminated by many laboratories.
Influenza Viruses
Authors: Atmar Robert L. 
Published: December 2024

Abstract

The influenza viruses are members of the family
Orthomyxoviridae
. The transmission of influenza viruses to people from avian and swine species highlights the need for vigilant surveillance for such events. Antigen detection assays are used in a variety of formats to rapidly detect influenza viruses in clinical specimens and to confirm the identity of isolates grown in culture. Influenza viruses have been detected in clinical specimens by direct and indirect visualization of their typical morphological appearance by electron microscopy. Influenza virus isolation procedures should be performed under biosafety level 2 conditions. Influenza virus infections are also identified by serologic methods. The pandemic strain may develop because of genetic reassortment following coinfection of a susceptible host with human and animal influenza viruses or through gradual adaptation of an avian strain to mammalian hosts.
Rhinoviruses
Authors: Landry Marie Louise , Lu Xiaoyan 
Published: December 2024

Abstract

Human rhinoviruses (RVs) are members of the family
Picornaviridae
. RVs derive their name from the predominant site of their replication and symptomatology, the nose. The wider use of molecular methods in viral diagnostics has led to the discovery of a novel group of RVs identified in patients with lower respiratory tract disease. Symptoms of RV infection parallel the rise and fall of chemical mediators of inflammation. Psychological stress and inadequate sleep appear to increase susceptibility and the development of clinical symptoms. A presumptive diagnosis of RV isolates in cell culture is made by the appearance and progression of characteristic cytopathic effects in the appropriate cell lines. Serotyping of RV isolates by neutralization with type‐specific antisera used to be the gold standard for RV identification. Molecular typing based on reverse transcription polymerase chain reaction and amplicon sequencing has essentially replaced serotyping for type‐specific identification of RVs.
Varicella‐Zoster Virus
Authors: Greninger Alexander L. , Koelle David M. 
Published: December 2024

Abstract

This chapter provides taxonomy, description of the agent, epidemiology and transmission, clinical significance, diagnosis overview, therapy overview, direct examination, isolation and identification, serologic tests, and antiviral therapy and susceptibility of Varicella‐zoster virus (VZV). VZV belongs to the family
Herpesviridae
, based on morphological criteria, and is one of the nine human‐pathogenic herpesvirus species identified so far. VZV may infect susceptible cells either by fusion at the cell surface or by endocytosis. VZV is ubiquitous and highly contagious, and therefore, primary infection with VZV usually occurs in early childhood. The clinical appearance of chicken pox is usually dominated by a generalized vesicular rash. VZV is responsible for some cases of vasculopathy in both immunocompetent and immunosuppressed persons. One of the oldest direct detection methods is the Tzanck test. Analysis of CSF using nucleic acid amplification has become the method of choice for diagnosis of neurological disease associated with VZV.
Human Cytomegalovirus
Authors: Hodinka Richard L. 
Published: December 2024

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 Papillomaviruses
Authors: Cuschieri Kate , Unger Elizabeth R. 
Published: December 2024

Abstract

Papillomaviruses are in the family
Papillomaviridae
. Human papillomavirus (HPV) initiates infection in primitive basal‐like epithelial cells, accessed through minor trauma or at specialized sites of epithelial transition, particularly the squamocolumnar junction. The epidemiology and transmission of genital and nongenital infections differ significantly. Nongenital infections manifesting as hand and foot warts are most common in children and adolescents. The epidemiology and natural history of genital or mucosal HPV differ by anatomic site, by sex, and by age. Warts are more common in immunocompromised individuals, including organ transplant recipients, those infected with HIV, and pregnant women. Recurrent respiratory papillomatosis is a rare condition characterized by benign papillomatous lesions of the larynx and other parts of the upper respiratory tract that are characteristically resistant to treatment. Nucleic acid amplification technologies are the mainstay of clinical HPV tests, particularly those designed to inform screening and management of cervical disease.
Human Polyomaviruses
Authors: Leuzinger Karoline , Hirsch Hans H. 
Published: December 2024

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.
Hepatitis B and D Viruses
Authors: Powell Eleanor A. , Tang Yi‐Wei 
Published: December 2024

Abstract

Hepatitis B virus (HBV), which was discovered in blood specimens from Aboriginal Australians in 1965, is an enveloped DNA virus in the genus
Orthohepadnavirus
of the
Hepadnaviridae
family. The replication of HBV DNA by reverse transcription is unique for human DNA viruses. The most common modes of HBV transmission are vertical transmission, early childhood infections from close contact with infected individuals, sexual activity, and injection drug use or other physical contact with infected body fluids. HBV infects hepatocytes, leading to either an acute infection that resolves or a chronic infection that lasts for years. Hepatitis D virus (HDV) relies on host cell machinery for replication, and the viral genome serves as a ribozyme for self‐ligation and cleavage. The differential diagnosis can be achieved through testing a battery of HDV and HBV markers, which combine in patterns characteristic for each condition.
Antiviral Agents
Authors: Santos Carlos A.Q. , Reyna Quito Manuela Jannet 
Published: December 2024

Abstract
There are five classes of antiviral agents for the treatment of human immunodeficiency virus type 1 (HIV‐1): nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs), nonucleoside reverse transcriptase inhibitors, protease inhibitors (PIs), entry/fusion inhibitors, and integrase strand transfer inhibitors. PIs are commonly used in combined antiretroviral therapy regimens in combination with NRTI and/or NtRTIs for maximum antiretroviral activity and to minimize the development of resistance. Integrase Strand Transfer Inhibitors a class of antiretroviral drugs, target the HIV‐1 integrase enzyme that mediates transfer of the reverse‐transcribed HIV‐1 DNA into the host chromosome. The common target for antiviral drugs active against both viruses is the reverse transcriptase function of the HIV and hepatitis B virus (HBV) replication enzymes. Chronic HBV infection plays an important role in the morbidity and mortality of HIV‐infected patients. Most of the antiviral compounds that are approved to treat the eight human herpesviruses are nucleoside or nucleotide analogues, which inhibit DNA replication.
Lagenidium
,
Paralagenidium
,
Pythium
,
Rhinosporidium
, and Uncultivated
Paracoccidioides
Species (Formerly
Lacazia loboi
)
Authors: Vilela Raquel , Mendoza Leonel 
Published: December 2024

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.
Cryptosporidium
Authors: Xiao Lihua , Feng Yaoyu 
Published: December 2024

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.
Filarial Nematodes
Authors: Showler Adrienne J. , Nutman Thomas B. 
Published: December 2024

Abstract

Filarial worms are arthropod‐transmitted nematodes that dwell, as adults, in the subcutaneous tissues and the lymphatics. Although eight filarial species infect humans, four are responsible for most of the pathology associated with these infections:
Wuchereria bancrofti
,
Brugia malayi
,
Onchocerca volvulus
, and
Loa loa
. The taxonomy of these parasites follows a newly adopted molecular approach. All filariae go through a complex life cycle that includes an infective larval stage carried by the insects and an adult worm stage that resides in humans, either in the lymph nodes, the adjacent lymphatics, the subcutaneous tissue, or the pleural/peritoneal cavities. There are significant differences in the clinical manifestations of filarial infections, or at least in the period over which the manifestations present, between patients native to the areas of endemicity and those who are travelers or recent arrivals in these same areas.
Less Common Helminths
Authors: PROCOP GARY W. 
Published: December 2024

Abstract

There are a wide variety of less commonly encountered helminthic parasites, which may be nematodes, cestodes, or trematodes. The diseases caused by these parasites are interesting and demonstrate their highly evolved life cycles and the complex interactions with their hosts. This chapter covers the less common causes of helminthic parasitic infections, particularly those caused by the less common nematodes and cestodes.
Spirometra
species, the etiologic agent of sparganosis, is the only less common cestode. Descriptions of a few of the other less common cestodes that may infect humans are given. Dietary and folk‐medicine customs are also important in the prevalence of human disease, as many of these are associated with the ingestion or application of raw animal products. The treatment of these parasites varies depending on the infectious agent, but common preventive measures may significantly diminish the transmission of many of these parasitic diseases.
Antiparasitic Agents
Authors: LEDER KARIN , McGUINNESS SARAH L. 
Published: December 2024

Abstract
A number of effective antiparasitic drugs are currently available. These agents are important both for therapy of infected individual patients and for control of parasitic infections at the community level. This chapter focuses on the mechanisms of action, pharmacology, clinical utility, and adverse effects of common first‐line antiparasitic therapies and newer drug alternatives. Major anthelmintic drugs, namely, albendazole, mebendazole, praziquantel, ivermectin, and diethylcarbamazine, are reviewed in detail, as is the newly approved moxidectin. Nitazoxanide, an agent with both anthelmintic and antiprotozoal activity, is also discussed. Major antiprotozoal drugs, including those used for malaria, infections with gastrointestinal protozoa, leishmaniasis, and trypanosomiasis, are also reviewed. Nitazoxanide is a 5‐nitrothiazole derivative with broad‐spectrum activity against numerous intestinal protozoa, helminths, and anaerobic bacteria. Major indications for its use are also shown. It was initially developed as a veterinary anthelmintic with activity against intestinal nematodes, cestodes, and liver trematodes.
Aligning and Observing the Liquid Crystal Director in 3D Using Small Magnetic Fields and a Wedge‐Cell
Authors: Gulati Lovish , Sánchez‐Somolinos Carlos , Giesselmann Frank , Fischer Peer 
Published: December 2024

AbstractThe mechanical and optical properties of liquid crystalline materials are largely dependent on the director profile. More complex soft robotic functions and programmed optical properties require spatially varying director profiles, ideally in 3D. However, it is challenging to achieve arbitrary director orientation with most established alignment techniques, as one needs to overcome surface interactions, use high electric or magnetic field strengths and temperatures. Another experimental difficulty is that there is a lack of suitable techniques that can be used to characterize the director in 3D. Here, this study first shows that the addition of 5CB to reactive mesogens permits cross‐linked liquid crystalline materials to be fabricated with a spatially varying 3D director profile using weak magnetic fields (0.13 T). This study also shows, how these can be characterized with an optical technique that uses a wedge cell to visualize the programmed 3D director profile. Interestingly, the method also permits the real‐time observation of the director. This work shows that it is possible to precisely control the director in 3D with low magnetic fields and that the dynamics can be directly observed, which facilitates potential applications of soft liquid crystalline (LC) gels and potentially also elastomers.
Nanotherapy‐Engineered Stem Cells Alleviate Myocardial Reperfusion Injury by Normalizing the Pathological Microenvironment and Promoting Cardiac Repair
Authors: Pan Lina , Hu Xiankang , Yang Hao , Chen Liyuan , Tang Heng , Luo Suxin , Hu Houyuan , Zhang Jianxiang 
Published: December 2024

AbstractMyocardial infarction, the most severe manifestation of coronary artery disease, is a leading cause of mortality worldwide. Here, a novel nanotherapy engineering approach is reported for enhancing therapeutic effects of mesenchymal stem cells (MSCs) on myocardial ischemia‐reperfusion (MI/R) injury. An anti‐oxidative and anti‐inflammatory nanotherapy (TPCD NP) is first fabricated. MSCs are successfully engineered with TPCD NP by endocytosis, and TPCD NP engineering does not affect stemness of MSCs. TPCD NP‐internalized MSCs (tn‐MSCs) are resistant to oxidative stress, cytotoxicity, and apoptosis induced by reactive oxygen species (ROS). Under oxidative distress, tn‐MSCs show stronger paracrine activity compared to MSCs. Consistently, tn‐MSCs effectively enhance angiogenesis of endothelial cells under pathological conditions. Also, tn‐MSCs protect cardiomyocytes from ROS‐induced cytotoxicity and apoptosis by improving mitochondrial membrane potential and regulating the p53 signaling pathway. In mice with MI/R injury, the survival time of tn‐MSCs in the injured heart is prolonged, compared to pristine MSCs. Correspondingly, tn‐MSCs more significantly reduce the infarct size, improve cardiac function, and promote cardiac remodeling in MI/R injury mice. Mechanistically, tn‐MSCs alleviate MI/R injury by attenuating oxidative stress and inflammation, inhibiting cardiomyocyte apoptosis, and promoting cardiac repair. Consequently, tn‐MSCs are promising for treating cardiovascular diseases linked to oxidative distress and inflammation.
Improving Energy Storage and Nickel Manganese Cobalt Oxide Cathode Lifetime via a Tannic Acid/Iron (III) Metal Phenolic Network Coating
Authors: Park Donghyuck , Shin Subin , Sherrell Peter C. , Roy Binayak , Callaghan Kimberley L. , Caruso Frank , Ellis Amanda V. 
Published: December 2024

AbstractSurface coating lithium‐ion battery cathodes is a promising strategy to improve performance and mitigate cathode degradation. The coatings studied to date focus on either electronically or ionically conducting layers, which have been introduced to enhance the redox reactions of cathode particles, or oxide‐based physical protection layers limiting surface degradation. Such coatings require high‐temperature, time‐consuming synthesis processes, along with uncertainty in the specific interactions between these coatings and lithium ions. Here, metal‐phenolic network coated LiNi0.6Mn0.2Co0.2O2 (NMC) cathodes are, produced using naturally occurring polyphenols via a rapid one‐step assembly, improve cathode electrochemical performance. The performance improvement arises from the interaction between lithium ions and the coated layer, which enhances the lithium‐ion transport to the cathode. In half‐cell 1C rate cycling conditions, the modified cathode displays a 20% reduction in overpotential and a 54% decrease in interfacial resistance compared to the uncoated cathode. In a full‐cell format, the modified cathode exhibits a 10% increase in capacity and a 54% increase in lifespan for constant current cycling; in addition to a 5% increase in capacity and a 25% increase in lifespan for constant current‐constant voltage (CCCV) cycling. This work paves the way for improving cathode materials via eco‐friendly lithium‐ion attraction strategies.
Regulating Charge Transfer in a Heterojunction Photoanode for Efficient Photo‐Charging of Zn‐Air/Sulfion Hybrid Batteries
Authors: Kong Lingqiao , Qiao Jingyuan , Li Wang , Xia Linhong , Yan Bingzhen , Zhang Shuai , Ruan Qiushi , Sun Zheng Ming 
Published: December 2024

AbstractIntegrating sulfion‐rich wastewater purification with photo‐charging Zn‐Air batteries enables dual benefits for solar energy storage and environmental protection. However, photo‐charging efficiency is hindered by charge transfer issues. Here, the study synthesizes a CdS@CdIn2S4 core–shell photoelectrode and uses Kelvin Probe Force Microscopy (KPFM) to probe surface potential changes and photo‐charge transfer under illumination. The outer shell (CdIn2S4) exhibits upward band bending and a Conduction Band (CB) more negative than bulk CdS, leading to the accumulation of photoelectrons on the surface, which is detrimental to sulfion oxidation. Vacancy engineering aligns the Fermi energy of two materials, creating an optimal type‐II configuration that accumulates holes on the surface, thereby boosting the photo‐charging current density in Zn‐Air/Sulfion hybrid batteries by 18‐fold. A benchmark photo‐charging current density of 1.26 mA cm−2 is therefore achieved for Zn‐Air/Sulfion hybrid batteries. This work demonstrates the effectiveness of regulating charge transfer pathways in photo‐charging Zn‐Air/Sulfion hybrid batteries, showing potential applications in various photo‐assisted batteries.