bluuebunny/crossref_metadata_2025 huggingface dataset:
Exclusive Posterolateral Arthroscopic and Endoscopic Approaches Used in the Treatment of Lateral Epicondylitis
Authors: Colombi Romain , Bevand Adrien , Devillier Alexandre , Baulot Emmanuel , Ezzahoui Abdelilah , Martz Pierre
Published: October 2019

Complications following arthroscopy of the elbow for the treatment of lateral epicondylitis are essentially related to the anterior arthroscopic approach. The principal aims of this study were to describe and evaluate the mixed arthroscopic and endoscopic surgical technique using posterolateral approaches exclusively. This was a retrospective study of consecutive patients operated on between 2005 and 2014 for lateral epicondylitis following more than 6 months of ineffective medical treatment. The exploration was arthroscopic via a distal posterolateral portal. The extensor carpi radialis brevis was disinserted via a proximal extra-articular posterolateral endoscopic portal. The postoperative clinical follow-up included subjective (visual analog scale, Nirschl) and objective (Mayo Clinic Elbow Performance Score) evaluations of pain, the time to return to work, the level of satisfaction, complications, and failures. Thirty-seven patients underwent the procedure, including 3 lost to follow-up. Mean±SD follow-up was 32.8±24.7 months. Mean±SD visual analog scale scores were 0.8±0.8 at rest, 2.4±1.3 during everyday activities, and 3.1±1.5 during effort. Mean±SD Mayo Clinic Elbow Evaluation Score was 10.1±1.0 of 12 and mean±SD Mayo Clinic Elbow Performance Score was 91.9±12.5 of 100. Mean±SD Nirschl score was 67.5±9.6 of 80. Mean±SD time to return to work was 2.0±2.6 months. The level of satisfaction was 94.1%. The failure rate was 2.9%, with no neurological lesions. With equivalent or even better results than those already published, this surgical procedure enables the treatment of lateral epicondylitis via posterolateral portals alone, thus avoiding the complications inherent to anterior and medial arthroscopic approaches. [
Orthopedics
. 2019; 42(6):e521–e527.]
Day of the Week of Surgery Affects Time to Discharge for Patients With Adolescent Idiopathic Scoliosis
Authors: Tileston Kali R. , Uzosike Maechi , Segovia Nicole , Rinsky Lawrence A. , Imrie Meghan N.
Published: October 2019

Unnecessary delays in discharge are extraordinarily common in the current US health care system. These delays are even more protracted for patients undergoing orthopedic procedures. A traditional hospital staffing model is heavily weighted toward increased resources on weekdays and minimal coverage on the weekend. This study examined the effect of this traditional staffing model on time to discharge for patients undergoing posterior spinal instrumentation and fusion for adolescent idiopathic scoliosis. Patients undergoing surgery later in the week had a significantly longer hospital stay compared with patients undergoing surgery early in the week (5.5 days vs 4.9 days, respectively;
P
=.003). This discrepancy resulted in a mean cost increase of $7749.50 for patients undergoing surgery later in the week. A subsequent quality, safety, value initiative (QSVI) was undertaken to balance physical therapy resources alone. Following the QSVI, patients undergoing surgery later in the week had a decreased mean length of stay of 3.78 days (
P
=.002). Patients undergoing fusion early in the week also had a decreased mean length of stay of 3.66 days (
P
<.001). There was no longer a significant difference in length of stay between the “early” and the “late” groups (
P
=.84). This study demonstrates that simply having surgery later in the week in a hospital with a traditional staffing model adversely affects the timing of discharge, resulting in a significantly longer and more costly hospital course. By increasing physical therapy availability on the weekend, the length of stay and the cost of hospitalization decrease precipitously for these patients. [
Orthopedics
. 2020; 43(1);8–12.]
Prediction Capabilities for Cyber Physical Vehicles
Authors: Varga Laszlo Z.
Published: October 2019

Cyber physical systems open new ground in the automotive domain. Autonomous vehicles will try to adapt to the changing environment, and decentralized adaptation is a new type of issue that needs to be studied. This article investigates the effects of adaptive route planning when real-time online traffic information is exploited. Simulation results show that if the agents selfishly optimize their actions, then in some situations, the cyber physical system may fluctuate and sometimes the agents may be worse off with real-time data than without real-time data. The proposed solution to this problem is to use anticipatory techniques, where the future state of the environment is predicted from the intentions of the agents. This article concludes with this conjecture: if simultaneous decision-making is prevented, then intention-aware prediction can limit the fluctuation and help the cyber physical system converge to the Nash equilibrium, assuming that the incoming traffic can be predicted.
Conceptualizing Small and Medium-Sized Smart Cities in the Mediterranean Region
Authors: Panagiotopoulou Maria , Kokla Margarita , Stratigea Anastasia
Published: October 2019

Despite the remarkable interest in smart cities, noticed during the last decade, a consistent comprehension of the concept is not yet fully realized. Various definitions, ranging from exclusively technology-oriented perceptions to broader views, have been introduced, establishing a definitional polyphony and causing lack of semantic interoperability. Empirical evidence witnesses the prevalence of technology-pushed smart city initiatives as well as their failure to meet expectations in several urban domains. When planning “smart,” the relevance of ICT and their applications should be in alignment with spatial and other urban peculiarities and sub-systems' interactions, implying the need for getting deep insight into the city's ontology. The paper focuses on the extension/enrichment of an existing smart city ontology, with concepts and relationships stemming from Mediterranean small and medium-sized cities, in an attempt to outline their main key drivers and their interrelationships and fully grasp the smart city concept in the particular spatial context.
Kernelised Rough Sets Based Clustering Algorithms Fused With Firefly Algorithm for Image Segmentation
Authors: Chinta Srujan Sai
Published: October 2019

Data clustering methods have been used extensively for image segmentation in the past decade. In one of the author's previous works, this paper has established that combining the traditional clustering algorithms with a meta-heuristic like the Firefly Algorithm improves the stability of the output as well as the speed of convergence. It is well known now that the Euclidean distance as a measure of similarity has certain drawbacks and so in this paper we replace it with kernel functions for the study. In fact, the authors combined Rough Fuzzy C-Means (RFCM) and Rough Intuitionistic Fuzzy C-Means (RIFCM) with Firefly algorithm and replaced Euclidean distance with either Gaussian or Hyper-tangent or Radial basis Kernels. This paper terms these algorithms as Gaussian Kernel based rough Fuzzy C-Means with Firefly Algorithm (GKRFCMFA), Hyper-tangent Kernel based rough Fuzzy C-Means with Firefly Algorithm (HKRFCMFA), Gaussian Kernel based rough Intuitionistic Fuzzy C-Means with Firefly Algorithm (GKRIFCMFA) and Hyper-tangent Kernel based rough Intuitionistic Fuzzy C-Means with Firefly Algorithm (HKRIFCMFA), Radial Basis Kernel based rough Fuzzy C-Means with Firefly Algorithm (RBKRFCMFA) and Radial Basis Kernel based rough Intuitionistic Fuzzy C-Means with Firefly Algorithm (RBKRIFCMFA). In order to establish that these algorithms perform better than the corresponding Euclidean distance-based algorithms, this paper uses measures such as DB and Dunn indices. The input data comprises of three different types of images. Also, this experimentation varies over different number of clusters.
Students' Perceptions in Software Modelling Using UML in Undergraduate Software Engineering Projects
Authors: Matyokurehwa Kanos , Makoni Kendra Tafadzwa
Published: October 2019

The article establishes student perceptions in software modelling using UML in their final undergraduate projects. The research was done at a University in Botswana. The research used a mixed methods approach, an open-ended questionnaire was administered to the participants. A sample size of 140 participants that met the inclusion criteria was used in the research. The key findings from the research were that students find modelling using UML to be challenging. Some of the project supervisors were assigned to assist students with their projects were not knowledgeable with the student's project topic.
Why Design Thinking in IT Business Management Program?
Authors: Vijayakumar Bharathi S.  , Pande Mandaar
Published: October 2019

The purpose of this research is to explain the goals and process of administering a design thinking course in management education with particular reference to MBA-Information Technology Business Management (ITBM) stream. The study is unique and contributes to the existing body of knowledge in two significant ways. First, from a qualitative perspective, it presents a detailed narration about the planning and execution of the design thinking course to techno-management students which is a rare find in the existing literature. Second, from a quantitative perspective, the design thinking learning experiences from multiple dimensions are presented through an empirical study administered to the students. We applied exploratory factor analysis to identify certain key influencers (constructs) for learning design thinking, namely adoption willingness, empathy, collaboration, ideation, holistic learning and problem-solving.
A Comprehensive Analysis of Congestion Control Models in Wireless Sensor Networks
Authors: Ganesan Sangeetha , Muthuswamy Vijayalakshmi , Sannasi Ganapathy , Arputharaj Kannan
Published: October 2019

Congestion control is an important factor for performance improvement in wireless sensor networks (WSNs). Congestion occurs due to various reasons including a variation in the data rate between incoming and outgoing links, buffer size, flooding attacks and multiple inputs and minimum output capability. Various outcomes of congestion in sensor networks include immense packet loss or packet drop, fast energy depletion, unfairness across the network, reduced node performance and increased delay in packet delivery. Hence, there is an extreme need to check channel congestion in order to enhance the performance with better congestion management. The job of choosing a suitable congestion control technique is a challenging task for the network designer. In this article, the authors traverse through the underlying conceptual ideas on congestion control schemes which come under six unique models. This article highlights a survey on the existing works done so far on congestion control domains in sensor networks. A comparative analysis based on Quality of Service parameters has been discussed.
Mutation-Induced Conformational Changes and Energetics for Binding of FMN Ligand in Flavin Mononucleotide Riboswitch by Molecular Dynamics Simulations
Authors: Wakchaure Padmaja D. , Ganguly Bishwajit
Published: October 2019

Riboswitches are the type of regulatory elements present in the untranslated region of mRNA and specifically bind to the natural ligand to regulate gene expression. This binding specificity can be affected by even single point mutation incorporated in the core of the riboswitch. In this work, we have examined the mutations at the binding site residue in Flavin Mononucleotide (FMN) riboswitch structure with 30ns molecular dynamics simulations. The interaction of ligand (FMN) with riboswitch has been characterized using root mean square deviation, hydrogen bonding analysis, and the calculated binding affinities. Mutation at A48G and G62U show the enhanced binding energy however, the mutation at A85G, are energetically unfavorable compared to the wild type. This work gives valuable insight into the structures and energetics of the mutated FMN riboswitch to design new hits for biological applications.
Organ building in Lithuania in the 19th century
Authors: Gučas Rimantas
Published: October 2019

For Lithuania, the 19th century was marked by the symbol of the Russian Empire – Lithuania became a province of a foreign empire. Farming suffered a severe general downturn. As the Church’s powers began to be restricted, there was almost no opportunity for new significant instruments to emerge. The monasteries, which until then had been the initiators of the best organ building, were closed. Eastern Catholic (Unitarian) churches, which also had organs in Lithuania, became part of the Russian Orthodox Church, and the organs were ordered to be liquidated. The Catholic Church itself, unlike evangelicals, also had little regard for music and especially for organ matters. From the beginning of the 15th century, the development of Lithuanian organ culture was closely associated with Königsberg. Once the import customs were imposed, significant contacts which had taken place almost disappeared. The industrial revolution in Lithuania was delayed, and for half a century small artisan workshops still prevailed. Almost exclusively small, single-manual organs without pedals or positives were built. A large three-manual organ at Vilnius University St John’s Church was rather an exception. It was built by the Tiedemanns. This family, which originated in East Prussia, worked in the Baltic States throughout the first half of the 19th century. Only in the middle of the century did the new European organ building trend, the so-called organ romanticism, reach Lithuania. A particularly important role in this period was played by the experience of organ building of the neighbouring Curonia. Very few impressive examples were created, and in this respect Lithuania is hardly able to compete with the major countries of Central Europe. Lithuania is characterized by the fact that in the 19th century local masters and companies ( J. Rudavičius, M. Masalskis, F. Ostromensky), as well as masters from neighbouring Curonia (Herrmann, Weissenborn) and Poland (Blomberg) worked there. In western Lithuania, then part of Prussia, Terletzki was active. Meanwhile, large factories (Walcker, Rieger) reached Lithuania only in the first half of the twentieth century and only in a few instances. At that time, more work started to be focusing on the construction of two-manual with pedal instruments. At the end of the century, J. Rudavicius built some three-manual organs. His 63-stop organ built in 1896 for a long time was the largest in Lithuania. Although the 19th century Lithuanian organs are relatively modest compared to other countries, they have the value that is only growing in the context of present-day Europe, since the “progressive ideology” of more economically powerful European countries affected the art of organ building and few small romantic instruments are left.
Julius Juzeliūnas’ creative work and teaching methods through the eyes of his students
Authors: Gaidamavičiūtė Rūta
Published: October 2019

The goal of this article is to show the peculiarities of Julius Juzeliūnas’ teaching methods. The specificity of composition as a discipline and its creative character naturally calls for an individual attitude to it. The qualitative survey method was applied for research. The composer taught creative work between 1952 and 2001, and over fifty students who studied under him graduated from the Lithuanian conservatoire. Adding up the creative potential of all of his students, most of the Lithuanian musical events of the last decades are covered, and it can be seen how they have shaped and continue to shape our music and reaction to it in a wider environment. Some of their compositions also receive response on a wider scale. Juzeliūnas’ school was far from being dogmatic. The term “multivector” can aptly define the results of his teaching methods as many different forces have to be taken into account: the expression of the professor’s individuality and his aesthetic principles, the development of the language of Lithuanian music, students’ individualities, and finally the historic turning point in Lithuania that changed the social relations in the country, globalisation challenges etc. Juzeliūnas applied his teaching methods individually for every student and he was open to innovation. Evaluating the creative maturity and relevance of their earlier pedagogue today most of the respondents mentioned the same most popular works – the African sketches, the symphony “Lygumų giesmės” (Songs of the Plains), and the opera “Žaidimas” (The Game). Juzeliūnas’ theoretical book “Akordo sandaros klausimu” (On the Structure of the Chord) and his encouragement to others to pursue scientific research also had a great influence.
Respostas anatômicas de Eumachia kappleri em três áreas da Amazônia Mato-Grossense
Authors: Rocha Virgilia Aparecida Pegorini , Pereira Andréia Anjo , Bento Karla Bianca de Deus , Fagundes Odair de Souza , Ribeiro Junior Norberto Gomes , Silva Ivone Vieira da
Published: October 2019

Eumachia DC. é um gênero de Rubiaceae que recentemente teve sua circunscrição ampliada devido a estudos baseados em dados moleculares e distribuição geográfica. Rubiaceae, representanda por 13.235 espécies distribuídas em 614 gêneros é uma das maiores famílias de Angiospermas. Diante dessa grande diversidade e presença em diferentes estratos vegetacionais, espécies da família Rubiaceae possuem grande importância para estudos relacionados a ecologia, conservação e preservação em regiões tropicais. A anatomia ecológica pode ser uma abordagem útil para compreender as mudanças estruturais e entender os processos de colonização e sobrevivência de espécies. O objetivo deste estudo foi comparar a anatomia foliar de Eumachia kappleri (Miq.) Delprete & J.H. Kirkbr., ocorrente em três diferentes áreas, buscando identificar caracteres-chave que mostrem estratégias adaptativas em seus ambientes naturais. Os indivíduos foram coletados em três áreas inseridas em uma região onde ocorrem duas estações climáticas definidas. Para o estudo dos caracteres anatômicos, em cada área foram identificados três indivíduos e, destes, coletadas cinco folhas adultas, antes totalmente expostas ao sol, que foram fixadas em FAA50 por 48 horas e depois conservadas em etanol 70%. Posteriormente, com técnicas usuais em anatomia vegetal e com uso de lâminas de aço, foram obtidas secções transversais e procedeu-se a dissociação de epidermes. Lâminas histológicas semi-permanentes foram montadas, para visualização e registro fotográfico em fotomicroscópio fotônico trinocular acoplado a um computador. Para o estudo quantitativo serviram onze atributos anatômicos, analisados com o auxílio do software de análise de imagem. Após normalizar os dados necessários, uma matriz de correlação foi construída e posteriormente uma MANOVA foi realizada. Após identificar quais variáveis colaboraram para a significância da MANOVA, foi aplicado o teste de Tukey. Através da MANOVA foi possível identificar diferença significativa entre as áreas. Na maioria das variáveis morfoanatômicas os indivíduos da área Reserva FA (Reserva do Floresta Amazônica Hotel Resort) apresentaram medidas significativamente maiores que as outras duas áreas. A análise da anatomia foliar mostrou que E. kappleri apresenta características anatômicas que são consideradas comuns à família, porém quando comparadas em ambientes distintos, diferem em alguns aspectos. Conclui-se que algumas das variações anatômicas entre as amostras analisadas como espessura de epiderme e mesofilo favorecem a aclimatação da espécie às clareiras florestais, tornando-a bem ajustada em ambientes abertos.
Bullets as Pathogen—The Need for Public Health and Policy Approaches
Authors: Fleegler Eric W. , Vargas Laura , Pulcini Christian D. , Hargarten Stephen
Published: December 2024

This JAMA Viewpoint explores how public health principles related to communicable diseases and bullet-specific regulations could be applied in the US to prevent further injury and death due to gun violence.
Weekly Cisplatin Cycles and Outcomes for Chemoradiation in Head and Neck Cancer
Authors: Ma Sung Jun , Zhu Simeng , Virk Jas , Koempel Andrew , Bhateja Priyanka , Gogineni Emile , Baliga Sujith , Konieczkowski David , Mitchell Darrion , Jhawar Sachin , Grecula John , Old Matthew , Rocco James , Bonomi Marcelo , Blakaj Dukagjin
Published: December 2024

Importance

National Comprehensive Cancer Network guidelines recommend weekly cisplatin as an alternative concurrent systemic therapy for definitive chemoradiation in patients with head and neck cancer. However, the impact of different levels of adherence to weekly cisplatin on outcomes stratified by human papillomavirus p16 status remains unclear.

Objective

To evaluate the association between the number of weekly cisplatin cycles and outcomes.

Design, Setting, and Participants

This retrospective, observational, single-institution cohort study at The Ohio State Comprehensive Cancer Center included patients with a diagnosis of nonmetastatic head and neck cancer between December 1, 2011, and March 30, 2020, who received chemoradiation. Data analysis was performed between March and May 2024.

Exposure

A total of 5, 6, or 7 to 8 weekly cisplatin cycles.

Main Outcomes and Measures

The primary outcomes were overall survival (OS), progression-free survival (PFS), locoregional failure (LRF), and distant failure (DF). Cox multivariable analysis was performed for variables associated with OS and PFS, and Fine-Gray multivariable analysis was performed for variables associated with LRF and DF.

Results

A total of 142 patients met the criteria (119 men [83.8%]; median [IQR] age, 59 [54-63] years). Median (IQR) follow-up was 46.8 (40.8-55.6) months. Among 92 patients with reasons for cisplatin interruption reported, the most common reason was low blood counts (42 patients [45.7%]). Those who missed weekly cisplatin cycles had worse OS (adjusted hazard ratio [aHR], 2.22; 95% CI, 1.19-4.17; P = .01) and PFS (aHR, 1.83; 95% CI, 1.06-3.15; P = .03) than those who received 7 to 8 cycles. Cancer control outcomes were comparable between these groups (LRF aHR, 0.53; 95% CI, 0.15-1.93; P = .34; DF aHR, 1.51; 95% CI, 0.60-3.82; P = .38). Patients with p16-negative tumors who missed weekly cisplatin cycles had worse OS (for every missing cisplatin cycle, aHR, 11.34, 1.51-84.94; P = .02) than those treated with 7 to 8 cycles. However, for those with p16-positive tumors, there were no statistically significant differences in OS between those who missed weekly cisplatin cycles vs others who received 7 to 8 cycles (aHR, 1.21; 95% CI, 0.47-3.14; P = .69).

Conclusions and Relevance

In this cohort study of patients with head and neck cancer who received definitive chemoradiation, those with p16-negative tumors who missed weekly cisplatin cycles had lower OS than those who received 7 to 8 cycles, although OS was comparable between these groups for p16-positive tumors. Cytopenia represented the most common reason for cisplatin interruption.
The Patient Portal Messaging Crisis
Authors: Grouse Carrie K. , Esper Gregory J.
Published: December 2024

This Viewpoint proposes strategies for improving patient portal–based communication.
Morganellaceae
,
Erwiniaceae
,
Hafniaceae
, and Selected
Enterobacterales
Authors: Giffen Samantha R. , Alby Kevin
Published: December 2024

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
.
Aeromonas*
Authors: Lamy Brigitte
Published: December 2024

Members of the genus
Aeromonas
are Gram‐negative facultative anaerobes that are straight, coccobacillary to bacillary cells with rounded ends.
Aeromonas
species are environmental opportunistic pathogens, involved in numerous types of diseases, including gastroenteritis and infections at a variety of extraintestinal sites, of which blood and wounds are the most common. Most clinical infections with aeromonads are related to an exposure to some type of aquatic source, whether the clinical specimen is feces or extraintestinal, and to a lesser extent to the ingestion of foods. Aeromonads survive well in specimens, and any of the widely used transport media are acceptable for transport, with Cary‐Blair generally considered to be the best for feces transportation. Whole‐genome sequencing is the reference method to identify aeromonads or to describe a novel species. Strains show a propensity to acquire resistance genes and to disseminate them to other bacteria. Antimicrobial susceptibility testing of local isolates is necessary because of emerging resistance.
Burkholderia
,
Stenotrophomonas
,
Ralstonia
,
Cupriavidus
,
Pandoraea
,
Brevundimonas
,
Comamonas
,
Delftia
, and
Acidovorax
Authors: Lipuma John J. , Currie Bart J. , Baird Robert W. , Vandamme Peter A. R.
Published: December 2024

Many of the bacteria discussed in this chapter formerly belonged to the genus Pseudomonas; others were described and named after the taxonomic dissection of this genus to conform to a modern phylogeny‐based taxonomy.
Burkholderia
,
Ralstonia
,
Cupriavidus
,
Pandoraea
,
Brevundimonas
,
Comamonas
,
Delftia
, and
Acidovorax
species are aerobic, non‐spore‐forming, straight or slightly curved Gram‐negative rods. Several molecular genetic methods are available to assess the relatedness of isolates of these genera during nosocomial or community outbreak investigations. Of the organisms discussed in this chapter, serologic tests have been used clinically to diagnose only infections with
B. pseudomallei
. Given the uncertainty regarding the role(s)
Delftia
,
Acidovorax
, and
Brevundimonas
play in human infection, antimicrobial susceptibility testing of isolates from human specimens as a matter of routine may not be warranted.
Acinetobacter
,
Chryseobacterium
,
Moraxella
,
Branhamella
and Other Nonfermentative Gram‐Negative Rods
Authors: Cools Piet , Nemec Alexandr , Abeele Anne‐Marie van den , Kämpfer Peter
Published: December 2024

This chapter covers the organisms which belong to a group of taxonomically and phylogenetically diverse, Gram‐negative, non‐fermentative rods and coccobacilli. Most of the organisms are found in the environment, that is, soil and water. For each group of closely related species, the chapter presents their taxonomic history, addresses the clinical importance of the species, and describes the phenotypic data that are useful to differentiate this group from other groups and to differentiate the species within this group. It discusses antibiotic susceptibility characteristics and treatment options. Decisions regarding the significance of GNF in a clinical specimen must consider the clinical condition of the patient and the source of the specimen submitted for culture. Identification of GNF may be important to document health care‐related outbreaks linked to hospital environments or medical devices.
Bordetella
and Related Genera
Authors: Kilgore Paul E. , Coenye Tom
Published: December 2024

Bordetellae are catalase positive and oxidize amino acids, but no carbohydrates are fermented.
Achromobacter
species are Gram‐negative, nonsporulating, small bacilli.
Alcaligenes
species are Gram‐negative, strictly aerobic rods or coccobacilli that possess oxidase and catalase activity. Cells of
Kerstersia
and
Advenella
species are Gram‐negative, small, and rod‐shaped or coccoid and occur alone, in pairs, or in short chains. Motility is strain dependent. Cells from
Paenalcaligenes
species are Gram‐negative, small rods. Many
Achromobacter
species have been recovered from clinical samples or from the hospital environment. Direct fluorescent‐antibody staining (DFA) on nasopharyngeal swabs or aspirates to detect
B. pertussis
or
B. parapertussis
is rapid and simple but lacks adequate sensitivity and specificity; for this reason, DFA is not recommended.
Brucella
Authors: Araj George F.
Published: December 2024

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.
Legionella
Authors: Lindsay Diane S. J. , Ricci Maria Luisa
Published: December 2024

The family
Legionellaceae
is composed of a single genus,
Legionella
, and comprises 66 validly named species and three subspecies.
Legionella pneumophila
,
Legionella micdadei
,
Legionella bozemanii
, and
Legionella longbeachae
are the most important species from a clinical standpoint, with
L. pneumophila
causing more than 90% of Legionnaires' disease (LD) globally, apart from Australia and New Zealand, where
L. longbeachae
predominates. LD is a type of bacterial pneumonia caused by
L. pneumophila
and other
Legionella spp
. Identification of
Legionella spp
. in a clinical laboratory is optimally performed by observation of visual morphology, agglutination methods, and matrix‐assisted laser desorption ionization–time of flight mass spectrometry. Antimicrobial agents regarded as effective for treatment of LD are macrolides, fluoroquinolones, and, rarely, rifampin, all achieving adequate intracellular concentrations.
Peptostreptococcus
,
Finegoldia
,
Anaerococcus
,
Peptoniphilus
,
Parvimonas
,
Murdochiella
,
Veillonella
, and Other Anaerobic Cocci
*
Authors: Veloo Alida C. M. , Johnson Crystal N.
Published: December 2024

Gram‐positive anaerobic cocci (GPAC) belong to the Firmicutes phylum and have been known to most bacteriologists as peptococci or peptostreptococci. The genera
Anaerococcus
,
Anaerosphaera
,
Fastidiophila
,
Finegoldia
,
Gallicola
,
Murdochiella
,
Parvimonas
,
Peptococcus
,
Peptoniphilus
, and
Peptostreptococcus
are Gram‐positive, coccobacillary or occasionally coccoid cells. The genera
Veillonella
, Acidaminococcus,
Megasphaera
,
Anaeroglobus
, and
Negativicoccus
are Gram‐negative cocci. The polymicrobial nature of GPAC infections, in addition to inadequate classification, has most likely contributed to neglect the clinical significance of individual species of GPAC. A variety of microscopic, immunologic, and molecular techniques have been developed for direct examination of GPAC. New information regarding the antimicrobial susceptibilities of individual GPAC is increasing due to the improvement in classification and identification.
Clostridium, Clostridioides
, and Other Clostridia
Authors: Kuijper Ed J. , Reubsaet Frans A. G. , Barbut Frédéric
Published: December 2024

The genus
Clostridium
comprises obligately anaerobic (or occasionally aerotolerant), Gram‐positive rods commonly found in soil, water, and gastrointestinal tracts of insects and animals, as well as humans. Accurate, definitive identification is needed to better define the role of clostridia in disease, to aid the clinician in selecting optimal treatment, and for public health purposes (e.g., hospital‐acquired
Clostridioides difficile disease
). The isolation of a
Clostridium
species from a clinical specimen, even a blood culture, may or may not be significant clinically, and culture results should be interpreted in relation to the clinical findings for the patient. Identification of clostridia in specimens from sites of infection due to mixed organisms can be time‐consuming and expensive. Typing of
Clostridioides difficile
fosters understanding of the epidemiology of infections and has become increasingly important with the emergence of outbreaks caused by hypervirulent strains.
Leptospira
Authors: Galloway Renee L. , Gulvik Christopher A.
Published: December 2024

The genus
Leptospira
comprises spiral‐shaped bacteria with hooked ends. This genus, along with the genera
Leptonema
and
Turneriella
, makes up the family
Leptospiraceae
in the order
Spirochaetales
and class
Spirochaetes
of the phylum
Spirochaetae
. Leptospires are divided into serovars defined by agglutination after cross‐absorption with homologous antigen. Leptospires are ubiquitous, either free‐living in water or wet soil, or associated with renal colonization of mammals. Knowledge of the prevalent serovars and their maintenance hosts is essential for understanding the epidemiology of the disease. The clinical presentation of leptospirosis is biphasic, with a septicemic phase lasting about a week, followed by the immune phase, characterized by antibody production and excretion of leptospires in the urine. Nucleic acid amplification tests, such as PCR, have been widely used for detection of leptospires. Leptospiral DNA has been amplified from blood, plasma, serum, urine, aqueous humor, cerebrospinal fluid, and tissues obtained at autopsy or biopsy.
Treponema
and
Brachyspira
Authors: Seña Arlene C. , Pillay Allan , Radolf Justin D.
Published: December 2024

Spirochetal phylotypes identified in the human mouth belong exclusively to the genus
Treponema
.
Brachyspira
spp. are oxygen‐tolerant anaerobes differentiated by phenotypic growth characteristics and degree of beta‐hemolysis. The epidemiologic importance of
Treponema denticola
and other oral treponemes arises to a great extent from their occurrence as members of the polymicrobial consortium that causes gingivitis and periodontitis. Two Brachyspira species,
Brachyspira aalborgi
and
Brachyspira pilosicoli
, have been associated definitively with human intestinal spirochetosis. The method used for direct detection of
Treponema pallidum
depends upon the stage of disease, the clinical presentation, and the type of specimen obtained.
T. pallidum
can be detected in lesion exudate by darkfield microscopy or nucleic acid amplification tests. Most infants with congenital syphilis are asymptomatic at birth. Serologic tests play an important role in syphilis diagnosis by supplementing direct detection methods for early syphilitic lesions, for diagnosing latent infection, and confirming suspected tertiary disease.
Chlamydia
Authors: Greub Gilbert , Munson Erik
Published: December 2024

This chapter focuses on the important human pathogens within the genus
Chlamydia
, as well as on
Parachlamydia acanthamoebae
,
Waddlia chondrophila
, and
Simkania negevensis
, for which evidence gathered over the past 20 years supports possible pathogenicity in humans. The taxonomy of
Chlamydiales
is rapidly evolving and progressively moving from a purely phenotypic taxonomy to a polyphasic taxonomy combining phenotypic, molecular, and phylogenetic characteristics.
Chlamydia
,
Parachlamydia
,
Waddlia
, and
Simkania
all present biphasic developmental stages with elementary body and reticulate body formation.
Chlamydia trachomatis
is the most common bacterial agent of sexually transmitted infection in the world.
Chlamydia psittaci
causes a wide variety of clinical conditions in humans, ranging from asymptomatic infection to severe, even fatal pneumonia and systemic infections. For
Chlamydia trachomatis
, one effective method for identification of the organism in cell culture is to stain the monolayers with species‐specific fluorescein‐conjugated monoclonal antibodies.
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

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

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

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

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

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

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

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

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

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

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.