bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium
: General Characteristics, Laboratory Processing, Staining, Isolation, and Detection Procedures
Authors: Martin Isabella , Pfyffer Gaby E. , Parrish Nicole 
Published: January 2025

Abstract

The genus
Mycobacterium
encompasses several prominent pathogenic species, most notably the members of the
Mycobacterium tuberculosis
complex,
Mycobacterium leprae
, and
Mycobacterium ulcerans
. Continued use of the single genus and long‐standing taxonomy will provide laboratorians and clinicians with a standardized approach for assessment of patients with mycobacterial disease and/or colonization that will result in fewer errors while conserving often limited and valuable resources. The sensitivity and time to growth detection of the
Mycobacterium
Growth Indicator Tube system are superior to that of solid media in clinical evaluations. With the advent of molecular techniques designed for molecular epidemiology, cross‐contamination linked either to laboratory procedures or, more rarely, to contaminated bronchoscopes can easily be proven. Quality control (QC) is vital for monitoring a laboratory's effectiveness in detecting and isolating mycobacteria. This includes standard components of laboratory quality assurance, such as personnel competency, procedure manuals, external proficiency testing, and QC of media, tests, and reagents.
Morganellaceae
,
Erwiniaceae
,
Hafniaceae
, and Selected
Enterobacterales
Authors: Giffen Samantha R. , Alby Kevin 
Published: January 2025

Abstract

The reclassification of the order
Enterobacteriales
to
Enterobacterales
as well as the taxonomic shuffling of many members of the former family
Enterobacteriaceae
has increased the importance and awareness of a number of non‐
Enterobacteriaceae
families. These include commonly known families, such as
Morganellaceae
, and lesser–known families, such as
Budviciaceae
. The family
Erwiniaceae
contains many important plant‐associated pathogens.
Pantoea
species have been isolated from plants, humans, and the natural environment, although they are most commonly plant pathogens. While stand‐alone nucleic acid amplification testing is uncommon for detection of
Enterobacterales
in clinical specimens, syndromic panel testing by nucleic acid amplification has allowed for the rapid progression of clinical microbiology diagnostics. The
Morganellaceae
are the most familiar organisms for which antimicrobial susceptibility testing is routinely performed. There are several FDA‐cleared panels available for a variety of clinical presentations, including positive blood cultures, pneumonia, and gastrointestinal infections. The GenMark panel includes
Morganella morganii
and specific identification of
Proteus mirabilis
.
Brucella
Authors: Araj George F. 
Published: January 2025

Abstract

The taxonomy of the family
Brucellaceae
and its phylogenetic aspects have been an ongoing challenge over the years and are currently a matter of debate, especially as it relates to the proposed reclassification of members of the genus
Ochrobactrum
into the genus
Brucella
. Lipopolysaccharide is the major antigen that dominates the antibody response. The intracellular location and survival of the organism contribute to its virulence and pathogenesis. Clinical categories of human brucellosis are based on arbitrary criteria. Clinical microbiology laboratories may identify colonies suspected of being
Brucella spp
. on the basis of a few morphologic, biochemical, and serologic tests. Molecular assays have promising potential for diagnosis of human brucellosis in clinical practice. Appropriate antimicrobial therapy for treatment of human brucellosis reduces morbidity, prevents complications, and minimizes relapses.
Campylobacter
and
Arcobacter
Authors: Nachamkin Irving 
Published: January 2025

Abstract

Two closely related genera,
Campylobacter
and
Sulfurospirillum
, are currently included in the family
Campylobacteraceae
.
Arcobacter
, previously included in the family Campylobacteraceae, is now classified as the sole species in its own family,
Arcobacteraceae
.
C. jejuni
and
C. coli
have been recognized since the early 1970s as agents of gastrointestinal infection. Numerous commercially available fecal antigen detection systems for Campylobacter in stool samples are cleared by the Food and Drug Administration in the United States. Nucleic acid amplification tests are now commonly being used to directly detect
Campylobacter
and other enteric pathogens in stool samples. Typing systems for Campylobacter epidemiologic studies vary in complexity and in their ability to discriminate between strains. Serologic testing appears to be useful for epidemiologic investigations but is not recommended for routine diagnosis of campylobacter infection.
Molecular Detection of Antibacterial Drug Resistance
Authors: Uprety Priyanka , Kirn Thomas J. 
Published: January 2025

Abstract
The detection of antibiotic resistance is one of the most important responsibilities of the clinical microbiology laboratory. The molecular detection of resistance determinants poses significant challenges, perhaps foremost of which is the genetic complexity of antibiotic resistance. This chapter provides an overview of FDA‐cleared molecular assays for the detection of antibiotic resistance. It discusses some commercial assays in development. In theory, whole‐genome sequencing should be most comprehensive molecular method to detect antimicrobial resistance, because it allows the simultaneous detection of resistance to numerous antibiotic classes. There appears to be limited interest in the commercial development of molecular assays for other resistance determinants. The chapter considers aminoglycoside resistance, resistant anaerobic bacteria, daptomycin resistance, fluoroquinolone resistance, and so on. With a continuing urgent clinical need for the rapid detection of antimicrobial resistance, and with many novel technologies in development, the molecular diagnosis of antibacterial drug resistance is likely to see expanded application in coming years.
Algorithms for Detection and Identification of Viruses
Authors: Landry Marie Louise , Babady N. Esther , Binnicker Matthew J. , Pinsky Benjamin A. , Tang Yi‐Wei 
Published: January 2025

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.
Hantaviruses
Authors: Klena John D. , Chiang Cheng‐Feng , Whitmer Shannon M. , Wang Yun F. , Shieh Wun‐Ju 
Published: January 2025

Abstract

This chapter provides taxonomy, description of the agents, epidemiology and transmission, clinical significance, collection, transport, and storage of species, direct examination, and identification of Hantaviruses. Hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) are rodent‐borne zoonoses caused by several members of the virus family
Hantaviridae
, genus
Orthohantavirus
. Diagnosis early in the course of disease is critical to the successful management of HFRS and HPS. The clinical and pathological features of severe HFRS and HPS are associated with acute thrombocytopenia and a reversible increase in microvascular (capillary) permeability. Immunohistochemistry has been used to detect hantaviral antigens in tissues from fatal HFRS cases, biopsy materials from nephropathia epidemica cases, and tissues from fatal HPS cases. There are a number of reference diagnostic laboratories in United States that offer laboratory testing, such as serologic testing. Isolation of hantavirus from natural hosts is difficult yet necessary for analyzing biological properties of these viruses.
Epstein‐Barr Virus
Authors: Gärtner Barbara C. 
Published: January 2025

Abstract
Epstein‐Barr virus (EBV) is associated with a wide variety of disease states, ranging from infectious mononucleosis (IM) to autoimmune diseases and malignant disorders. Antibody assays are employed primarily for patients with suspected IM. EBV is associated with a variety of disease states in immunocompetent and immunosuppressed individuals. Latex agglutination tests or immunochromatographic assays using erythrocyte antigens are used for heterophile antibody detection. Nucleic acid amplification tests and especially quantitative methods are the most important routine techniques for the detection of EBV in clinical specimens. Serologic testing using EBV‐specific assays remains the routine method of choice for the diagnosis or exclusion of EBV infection. Routine posttransplantation monitoring of EBV viral load has been recommended for posttransplant lymphoproliferative disorders prevention only in high‐risk settings but not as a routine in all transplant recipients. EBV DNA load can be found in cerebrospinal fluid both in noninfectious and, even more, in infectious underlying disorders including mononucleosis.
Hepatitis B and D Viruses
Authors: Powell Eleanor A. , Tang Yi‐Wei 
Published: January 2025

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.
Prion Diseases
Authors: Appleby Brian S. , Safar Jiri G. 
Published: January 2025

Abstract
Prion diseases, originally called transmissible spongiform encephalopathies, are invariably fatal neurodegenerative diseases that affect humans and animals. The unusual biological and biochemical properties of the infectious agent causing the disease were first recognized in studies of scrapie in sheep, which is the prototypic prion disease. Most cases of prion disease in humans arise sporadically, but some are attributed to PRNP mutations, and still others are caused by zoonotic or iatrogenic transmission. The differential diagnosis of prion disease includes rapidly progressive variants of dementias that are usually chronic and slowly progressive, autoimmune diseases, vascular disease, metabolic diseases, vitamin deficiency, malignancy, and infection. Autopsy is currently the gold standard for the diagnosis and classification of prion diseases and the determination of disease origin. The diagnosis or exclusion of prion disease should be based on the whole clinical picture, including clinical and family history, symptomatology, neurological signs, radiographic findings, and laboratory results.
General Approaches for Direct and Indirect Detection and Identification of Fungi
Authors: Fida Madiha , Wengenack Nancy L. , Theel Elitza S. 
Published: January 2025

Abstract
The frequency with which invasive fungal infections (IFIs) occur has markedly increased over the past decade. The ability to rapidly detect and identify the causative fungal agents is essential for the successful management of IFIs. The ability to detect fungi in clinical material depends on several factors, including the quality of the specimen that is received into the laboratory. Microscopic examination of specimens can be carried out with either unfixed specimens or fixed, stained specimens. The use of unfixed specimens has the advantages of being quick and relatively simple to carry out; the use of fixed, stained specimens may highlight features specific to certain fungi and also the host response in tissue, but they take longer to process and hence may delay reporting. Detection of antibodies targeting fungal pathogens may be useful in a range of IFIs, particularly when they occur in immunocompetent patients; however, these assays may have limited use in significantly immunocompromised patients.
Candida
,
Cryptococcus
, and Other Yeasts of Medical Importance
Authors: Borman Andrew M. , Johnson Elizabeth M. 
Published: January 2025

Abstract

Unicellular fungi which typically divide by budding have traditionally been referred to as yeasts. The rapidly expanding use of molecular identification strategies has permitted detailed phylogenetic analyses, allowing more accurate delineation of taxonomic boundaries and the reclassification of many yeast species and genera. Molecular identification approaches have also further added to the taxonomic complexity via the delineation of a number of cryptic species and species complexes in many traditional
Candida
species that can be separated only based on DNA sequencing analysis. The heterogeneous genus
Candida
belongs to the order Saccharomycetales within the ascomycetes.
Rhodotorula
spp. and species in the allied genus
Cystobasidium
share many similar physiologic and morphologic properties with
Cryptococcus
spp., as they are round to oval‐shaped, multilateral budding yeasts with capsules, although capsules, when present, are typically small. Carbohydrate antigens have provided useful targets for several commercial kits for the detection of disseminated candidiasis.
Scalable δ$$ \delta $$‐Level Coherent State Synchronization of Multi‐Agent Systems with Adaptive Protocols and Bounded Disturbances
Authors: Nojavanzadeh Donya , Liu Zhenwei , Saberi Ali , Stoorvogel Anton A. 
Published: January 2025

ABSTRACTIn this paper, we study scalable ‐level coherent state synchronization for multi‐agent systems (MAS) where the agents are subject to bounded disturbances/noises. We propose a scale‐free framework designed solely based on the knowledge of agent models and agnostic to the communication graph and the size of the network. We define the level of coherency for each agent as the norm of the weighted sum of the disagreement dynamics with its neighbors. The objective is to restrict the network's coherency level to without a‐priori information about the disturbance.
Ferroelectric Polarization‐Induced Performance Enhancements in BiFeO3/BiVO4 Photoanodes for Photoelectrochemical Water Splitting
Authors: Gunawan Michael , Bowdler Owen , Zhou Shujie , Fang Xueqing , Zhang Qi , Sakamoto Yasuhiro , Sun Kaiwen , Gunawan Denny , Chang Shery L.Y. , Amal Rose , Valanoor Nagarajan , Scott Jason , Hart Judy N. , Toe Cui Ying 
Published: January 2025

AbstractPhotoelectrochemical (PEC) processes will play a crucial role in future clean energy systems, however severe charge recombination and sluggish charge transfer kinetics have hindered their practical adoption. Exploiting ferroelectric polarization‐controlled charge dynamics promises an additional lever that can potentially enable the performance limits of traditional static photoelectrodes to be surpassed. Here one of the most notable ferroelectric polarization‐induced photocurrent enhancements is reported, using a heterostructure of the multiferroic bismuth ferrite (BFO) and the photoactive bismuth vanadate (BVO) in a neutral pH electrolyte. In contrast to previous works, enhancements for both poling directions are reported, of 136% for down‐poled BFO/BVO and 70% for up‐poled BFO/BVO at 1.23 VRHE in comparison to the unpoled sample, delivering a Faradaic efficiency of >95% for prolonged oxygen evolution reaction. Extensive PEC and surface analyses complemented by density functional theory (DFT) calculations reveal the improvements are attributed to the modulation of gradients in the BFO band energies, as well as changes in band‐bending and offsets at the interfaces. Given the scalability of the employed sol–gel synthesis method and the use of environmentally benign materials and PEC conditions, these findings pave the way for multifunctional materials as new‐generation agile and dynamic catalysts and photoelectrode systems.
Polymerized Small‐Molecule Acceptors with Linker Length‐Dependent Photocatalytic Activity for High‐Performance Solar Hydrogen Evolution
Authors: Zhao Jingcheng , Liu Yulu , An Ruiqi , Fu Yingying , Wang Panpan , Wu Xiaofu , Tong Hui , Wang Lixiang 
Published: January 2025

AbstractDeveloping organic semiconductor photocatalysts with alterable optical properties and excitonic behaviors for photocatalytic hydrogen evolution has received significant attention recently. Herein, three polymerized small‐molecule acceptors (PSMAs) with different linker lengths, namely PY‐1T, PY‐2T and PY‐3T, are designed and synthesized to construct nano‐photocatalysts. In comparison with small‐molecule YDT, these PSMAs exhibit broader absorption in both visible and near‐infrared (NIR) light region as well as enlarged exciton diffusion length. In the meanwhile, the intramolecular charge transfer and separation in PSMAs is promoted by varying the linker length, leading to enhanced light harvesting and charge utilization. As a result, the single‐component nano‐photocatalyst based on PY‐3T achieves an impressive average hydrogen evolution rate (HER) of 400.3 mmol h−1 g−1 under AM 1.5G sunlight (100 mW cm−2), which is ≈48 times greater than that of YDT NPs (8.3 mmol g−1 h−1). These results not only prove the potential that developing polymerized small‐molecule acceptors with extended chain length as efficient photocatalysts, but also elucidate the importance of regulating linker length in designing high‐performance photocatalysts.
Van der Waals Gap Enabled Robust Retention of MoS2 Floating‐Gate Memory for Logic‐In‐Memory Operations
Authors: Niu Wencheng , Zou Xuming , Tang Lin , Bu Tong , Zhang Sen , Jiang Bei , Dang Mengli , Hong Xitong , Ma Chao , He Penghui , Zhou Peng , Liu Xingqiang , Liao Lei 
Published: January 2025

AbstractFloating gate (FG) memory can store data for decades without a power supply. Herein, high‐performance MoS2 FG transistors with stable operations are demonstrated, in which a van der Waals (vdW) gap is constructed between tunnelling oxide layer and channel to prevent the leakage. The atomic FG structure is one‐step formed from HfS2 flake by ozone treatment while the supersaturated oxygen at the interface affords to the vdW gap. The vdW gap MoS2 FG transistors exhibit stable operations after 21 days, ultralow leakage current (0.1 fA µm−1), excellent retention capability >105 s, high on/off ratio of 107, and desirable cycling endurance performance (>1000 cycles). Configurable logic‐in‐memory devices are accomplished with multi‐gated structures through multi‐level programming operations, which is modulated by different electrostatic potential on the FG stack. NAND and NOR output logic sequences are generated. The designed FG memory is promising for developing in‐memory computing systems.
Smart Flow Micro‐Reaction Device Integrated with Oxygen Reduction Catalysts for Gaseous Electrochemiluminescence Sensing
Authors: Geng Yuqian , Cao Yue , Wu Ru , Zhang Yiteng , Zhang Min , Zhou Yang , Zhu Jun‐Jie 
Published: January 2025

AbstractThe sensitive detection of low‐concentration gases has significant implications for environmental monitoring, clinical diagnosis, and other fields of scientific inquiry. Electrochemiluminescence (ECL) is a widely accepted analytical technique known for its high sensitivity, precision, and minimal background interference. Nevertheless, it has rarely been documented in the context of gas‐oriented sensing. This study presents an innovative paradigm for gas sensing, which integrates oxygen reduction reactions (ORR) and a gas diffusion electrode (GDE) into a gas flow micro‐reaction device. The integration aims to optimize mass transfer, ensure adequate electrochemical contact, facilitate efficient electron transfer, and ultimately enhance ECL emission. The viability of this effective in situ gas sensing strategy under mild conditions without pre‐treatments is substantiated by experimental and model calculation evidence. This homemade micro‐reaction device enables the efficient quantification of formaldehyde with a limit of determination (LOD) as low as 12.7 ppb and paves the way for universal gaseous ECL sensing.
Tissue‐Engineered Therapeutics for Lymphatic Regeneration: Solutions for Myocardial Infarction and Secondary Lymphedema
Authors: Chiu Alvis , Rutkowski Joseph M. , Zhang Qixu , Zhao Feng 
Published: January 2025

AbstractThe lymphatic system, which regulates inflammation and fluid homeostasis, is damaged in various diseases including myocardial infarction (MI) and breast‐cancer‐related lymphedema (BCRL). Mounting evidence suggests that restoring tissue fluid drainage and clearing excess immune cells by regenerating damaged lymphatic vessels can aid in cardiac repair and lymphedema amelioration. Current treatments primarily address symptoms rather than underlying causes due to a lack of regenerative therapies, highlighting the importance of the lymphatic system as a promising novel therapeutic target. Here cutting‐edge research on engineered lymphatic tissues, growth factor therapies, and cell‐based approaches designed to enhance lymphangiogenesis and restore lymphatic function is explored. Special focus is placed on how therapies with potential for immediate lymphatic reconstruction, originally designed for treating BCRL, can be applied to MI to augment cardiac repair and reduce heart failure risk. The integration of these novel treatments can significantly improve patient outcomes by promoting lymphatic repair, preventing pathological remodeling, and offering new avenues for managing lymphatic‐associated diseases.