bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the INNO-LIA Syphilis Kit as a Confirmatory Assay forTreponema pallidumAntibodies
Authors: Ebel Anne , Vanneste Lies , Cardinaels Martine , Sablon Erwin , Samson Isabelle , De Bosschere Katrien , Hulstaert Frank , Zrein Maan
Published: May 2021

The commercially available diagnostic tests for syphilis are mostly based on the use of extracted antigens ofTreponema pallidum. Pronounced cross-reactivities with other spirochete antigens are often reported. The aim of this study was to validate a novel multiparametric assay (the assay performed with the kit) INNO-LIA Syphilis for the confirmation of syphilis antibodies in a set of 840 documented human serum samples. All serum samples were previously tested at the French World Health Organization reference center for venereal diseases (Institute Alfred Fournier, Paris, France), with a consensus result provided for each sample. The study was conducted in two phases, with each phase involving a validation set (500 well-documented serum samples) and an exploratory set (340 serum samples) of serum samples, respectively. By measuring the sensitivity and specificity, we compared the result of the new assay with the consensus result on the basis of the results of a variable number of classical serological methods and clinical information when available. A sensitivity of 99.6% (95% confidence internal [CI], 98.5 to 99.9%) and a specificity of 99.5% (95% CI, 98.1 to 99.9%) were found for the new line immunoassay. Six of seven samples with indeterminate results by classical serology tested positive with the INNO-LIA Syphilis kit. This single multiparametric assay provides reliable confirmatory diagnostic information that must currently be obtained by the performance and interpretation of results of a combination of serological assays.
Optimized PCR Using Patient Blood Samples For Diagnosis and Follow-Up of Visceral Leishmaniasis, with Special Reference to AIDS Patients
Authors: Lachaud Laurence , Dereure Jacques , Chabbert Elisabeth , Reynes Jacques , Mauboussin Jean-Marc , Oziol Eric , Dedet Jean-Pierre , Bastien Patrick
Published: May 2021

We developed a highly sensitive PCR method that enables the diagnosis and posttherapeutic follow-up of visceral leishmaniasis with patient blood. The PCR assay was thoroughly optimized by successive procedural refinements to increase its sensitivity and specificity. It was compared to in vitro cultivation as well as to direct examination of bone marrow and to serology. Two hundred thirty-seven patients presenting with clinical signs compatible with visceral leishmaniasis were included in the study. Thirty-six were diagnosed as having Mediterranean visceral leishmaniasis (MVL). Twenty-three of them, including 19 AIDS patients, were monitored during and after treatment over a period from 2 weeks to 3 years. Our PCR assay proved more sensitive than in vitro cultivation, direct examination, and serology for all patients. It is simple and can be adapted to routine hospital diagnostic procedures. For the primary diagnosis of MVL, the sensitivity of PCR versus that of cultivation was 97 versus 55% with peripheral blood and 100 versus 81% with bone marrow samples. Regarding posttherapeutic follow-up, overall, 48% of positive samples were detected by PCR only. Seven patients presented with a clinical relapse during the study; six relapses were detected at first by PCR only, sometimes a few weeks before the reappearance of signs or symptoms. We conclude that an optimized and well-mastered PCR assay with a peripheral blood sample is sufficient to provide a secure diagnosis for all immunocompromised patients and most immunocompetent patients. We also suggest systematic posttherapeutic monitoring by PCR with peripheral blood for immunocompromised patients.
Species-Specific PCR as a Tool for the Identification of
Burkholderia gladioli
Authors: Whitby Paul W. , Pope Lauren C. , Carter Karen B. , LiPuma John J. , Stull Terrence L.
Published: May 2021

Burkholderia gladioli
colonizes the respiratory tracts of patients with cystic fibrosis and chronic granulomatous disease. However, due to the high degree of phenotypic similarity between this species and closely related species in the
Burkholderia cepacia
complex, accurate identification is difficult. Incorrect identification of these species may have serious repercussions for the management of patients with cystic fibrosis. To develop an accurate procedure for the identification of
B. gladioli
, a molecular method to discriminate between this species and other species commonly isolated from the sputa of patients with cystic fibrosis was investigated. The 23S ribosomal DNA was cloned from several clinical isolates of
B. gladioli
, and the nucleotide sequence was determined. Computer-assisted sequence comparisons indicated four regions of the 23S rRNA specific for this species; these regions were used to design three primer pairs for species-specific PCR. Two of the primer pairs showed 100% sensitivity and specificity for
B. gladioli
when tested against a panel of 47 isolates comprising 19
B. gladioli
isolates and 28 isolates of 16 other bacterial species. One of the primer pairs was further assessed for species specificity by using a panel of 102 isolates obtained from the
Burkholderia cepacia
Research Laboratory and Repository. The species-specific PCR was positive for 70 of 74 isolates of
B. gladioli
and was negative for all other bacterial species examined. Overall, this primer pair displayed a sensitivity and specificity of 96% (89 of 93) and 100%, respectively. These data demonstrate the potential of species-specific PCR for the identification of
B. gladioli
.
Simplified Protocol for Pulsed-Field Gel Electrophoresis Analysis of
Streptococcus pneumoniae
Authors: McEllistrem M. Catherine , Stout Janet E. , Harrison Lee H.
Published: May 2021

A variety of pulsed-field gel electrophoresis (PFGE) protocols for the molecular subtyping of
Streptococcus pneumoniae
have been reported; most are time-consuming and complex. We sought to modify reference PFGE protocols to reduce the time required while creating high-quality gels. Only protocol modifications that resulted in high-quality banding patterns were considered. The following protocol components were modified. Lysis enzymes (lysozyme, mutanolysin, and RNase A) were deleted in a stepwise fashion, and then the lysis buffer was deleted. Lysis and digestion were accomplished in a single step with EDTA and
N
-lauroyl sarcosine (ES; pH 8.5 to 9.3) incubation at 50°C in the absence of proteinase K. All enzymes except the restriction enzyme were omitted. A minimum incubation time of 6 h was required to achieve high-quality gels. All of the reactions were performed within 9 h, and the total protocol time from lysis to gel completion was reduced from 3 days to only 36 h. Combining lysis and digestion into a single step resulted in a substantial reduction in the time required to perform PFGE for
S. pneumoniae
. The ES solution may have caused cell lysis by activating
N
-acetylmuramyl-
l
-alanine amidase, the pneumococcal autolysin.
Evaluation of a Combination Rapid Immunoassay for Detection of
Giardia
and
Cryptosporidium
Antigens
Authors: Chan Raymond , Chen Jing , York Mary K. , Setijono Norman , Kaplan Raymond L. , Graham Fitzroy , Tanowitz Herbert B.
Published: May 2021

A combination cassette format nonenzymatic rapid immunoassay for detection of
Giardia
and
Cryptosporidium
antigens was evaluated by using 556 patient stool specimens from three clinical laboratories. This assay (Genzyme Diagnostics
Contrast Giardia/Cryptosporidium
), which can be used with fresh or formalin-fixed specimens, had unadjusted sensitivities and specificities of 96.1 and 98.5% for
Giardia
and 100 and 98.7% for
Cryptosporidium
, respectively, in this study.
Evaluation of the BACTEC MGIT 960 and the MB/BacT Systems for Recovery of Mycobacteria from Clinical Specimens and for Species Identification by DNA AccuProbe
Authors: Alcaide Fernando , Benítez Miguel Angel , Escribà Josep M. , Martín Rogelio
Published: May 2021

A total of 120 mycobacterial isolates were recovered from 1,068 clinical specimens. Of these, 82.5% were in MGIT 960, 83.3% were in MB/BacT, 80% were in BACTEC 460, and 70% were on Löwenstein-Jensen medium. Mean times to detection of
Mycobacterium tuberculosis
(
n
= 96) were significantly shorter with MGIT 960 (12.6 days,
P
= 0.003) and BACTEC 460 (11.8 days,
P
< 0.001) than with MB/BacT (15.9 days). Although, MGIT 960 showed the lowest rate of recovery of
M. kansasii
genotype I (64.3%), the earliest growth was detected with this system (8.9 days). Low and similar rates of contamination were obtained with MGIT 960 (3.3%) and MB/BacT (3%). The AccuProbe test for identification showed excellent sensitivities with MGIT 960 (96.8%) and MB/BacT (100%) cultures. In addition to being nonradiometric, both MGIT 960 and MB/BacT are accurate, rapid, and labor-saving detection systems which could replace the radiometric method.
Convenient Test for Screening Metallo-β-Lactamase-Producing Gram-Negative Bacteria by Using Thiol Compounds
Authors: Arakawa Yoshichika , Shibata Naohiro , Shibayama Keigo , Kurokawa Hiroshi , Yagi Tetsuya , Fujiwara Hiroshi , Goto Masafumi
Published: May 2021

A simple disk diffusion test was constructed for detection of IMP-1-type metallo-β-lactamase-producing gram-negative bacteria. Two Kirby-Bauer disks containing ceftazidime (CAZ) and a filter disk containing a metallo-β-lactamase inhibitor were used in this test. Several IMP-1 inhibitors such as thiol compounds including 2-mercaptopropionic acid, heavy metal salts, and EDTA were evaluated for this test. Two CAZ disks were placed on a Mueller-Hinton agar plate on which a bacterial suspension was spread according to the method recommended by the National Committee for Clinical Laboratory Standards. The distance between the disks was kept to about 4 to 5 cm, and a filter disk containing a metallo-β-lactamase inhibitor was placed near one of the CAZ disks within a center-to-center distance of 1.0 to 2.5 cm. For IMP-1-producing strains, the growth-inhibitory zone between the two disks expanded, while no evident change in the shape of the growth-inhibitory zone was observed for CAZ-resistant strains producing serine β-lactamases such as AmpC or SHV-12. As a result, 2 to 3 μl of undiluted 2-mercaptopropionic acid or mercaptoacetic acid able to block IMP-1 activity gave the most reproducible and clearest results, and CAZ-resistant strains producing AmpC or extended-spectrum β-lactamases were distinguishable from IMP-1 producers by this test. A similar observation was made with IMP-1-producing clinical isolates such as
Serratia marcescens
,
Klebsiella pneumoniae
,
Escherichia coli
,
Enterobacter cloacae
,
Enterobacter aerogenes
,
Citrobacter freundii
,
Proteus vulgaris
,
Pseudomonas aeruginosa
,
Pseudomonas putida
,
Acinetobacter
spp., and
Alcaligenes xylosoxidans
. The specificity and sensitivity of this test were comparable to those of PCR analysis using
bla
IMP
-specific primers. Therefore, this convenient test would be valuable for daily use in clinical laboratories.
Quantitation of Human Immunodeficiency Virus Type 1 Group O Load in Plasma by Measuring Reverse Transcriptase Activity
Authors: Lerma J. Gerardo García , Soriano Vincent , Mas Antonio , Quiñones-Mateu Miguel E. , Arts Eric J. , Heneine Walid
Published: May 2021

We have evaluated the use of an ultrasensitive reverse transcriptase (RT) activity assay to monitor plasma viremia in two human immunodeficiency virus type 1 (HIV-1) group O-infected patients treated with stavudine, lamivudine, and indinavir. After a initial decline in RT levels observed at 4 weeks of therapy, RT-based plasma viremia returned to baseline values at 28 or 44 weeks of treatment. The rebound in levels of RT activity was associated with the detection of phenotypic resistance to lamivudine and with the Met184Val mutation. Analysis of RT activity in plasma provides a sequence-independent means of monitoring virus loads in HIV-1 group O-infected patients.
Additional Human Papillomavirus Types Detected by the Hybrid Capture Tube Test among Samples from Women with Cytological and Colposcopical Atypia
Authors: Kónya József , Veress György , Juhász Attila , Szarka Krisztina , Sápy Tamás , Hernádi Zoltán , Gergely Lajos
Published: May 2021

The type specificity of the human papillomavirus (HPV) Hybrid Capture Tube (HCT) test was evaluated by using typing with PCR (MY09-MY11)-restriction fragment length polymorphism (RFLP) and sequencing. All samples HCT test positive for only low-risk HPV (
n
= 15) or only high-risk HPV (
n
= 102) were confirmed, whereas 9 of 12 HCT test double-positive samples contained only high-risk HPV types as determined by PCR-RFLP. Several high-risk HPV types (HPV-53, -58, -62, -66, -CP8304, and -MM4) not included in the HCT test were indeed detected, indicating a broader detection range with retained distinction between low-risk and high-risk HPV types.
Identification of a Major Cluster of
Klebsiella pneumoniae
Isolates from Patients with Liver Abscess in Taiwan
Authors: Lau Yeu-Jun , Hu Bor-Shen , Wu Wan-Ling , Lin Yu-Hui , Chang Hwan-You , Shi Zhi-Yuan
Published: May 2021

Klebsiella pneumoniae
has emerged as the leading liver abscess pathogen in Taiwan, with the percentage rising from 30% in the 1980s to over 80% in the 1990s. Most of the patients with
K. pneumoniae
liver abscess are diabetic and without biliary tract disease. Some patients develop serious extrahepatic complications such as endophthalmitis, meningitis, lung abscess, and necrotizing fasciitis. Pulsed-field gel electrophoresis (PFGE) was used for cluster analysis of 96 isolates from patients with liver abscess and 60 isolates from patients with other diseases. A total of 136 PFGE types were identified. Among the 96 liver abscess-associated isolates, 60 (62.5%) were classified in major cluster A. Cluster A included 41 PFGE types (types 1 to 41) which had a genetic similarity of at least 72.4% ± 9.4%. The PFGE patterns of cluster A strains are so similar that they could have originated from the same ancestor. This study demonstrates that cluster A plays an important role in the high incidence of
K. pneumoniae
liver abscess in Taiwan.
Sequencing the Gene Encoding Manganese-Dependent Superoxide Dismutase for Rapid Species Identification of Enterococci
Authors: Poyart Claire , Quesnes Gilles , Trieu-Cuot Patrick
Published: May 2021

Simple PCR and sequencing assays that utilize a single pair of degenerate primers were used to characterize a 438-bp-long DNA fragment internal (

sodA
int

) to the
sodA
gene encoding the manganese-dependent superoxide dismutase in 19 enterococcal type strains (
Enterococcus avium
,
Enterococcus casseliflavus
,
Enterococcus cecorum
,
Enterococcus columbae
,
Enterococcus dispar
,
Enterococcus durans
,
Enterococcus faecalis
,
Enterococcus faecium
,
Enterococcus flavescens
,
Enterococcus gallinarum
,
Enterococcus hirae
,
Enterococcus malodoratus
,
Enterococcus mundtii
,
Enterococcus pseudoavium
,
Enterococcus raffinosus
,
Enterococcus saccharolyticus
,
Enterococcus seriolicida
,
Enterococcus solitarius
, and
Enterococcus sulfureus
). Sequence analysis of the

sodA
int

fragments enabled reliable identification of 18 enterococcal species, including
E. casseliflavus-E. flavescens
and
E. gallinarum
. The

sodA
int

fragments of
E. casseliflavus
and
E. flavescens
were almost identical (99.5% sequence identity), which suggests that they should be associated in a single species. Our results confirm that the
sodA
gene constitutes a more discriminative target sequence than 16S rRNA gene in differentiating closely related bacterial species.
Impact of Sample Type on Rapid Detection of Influenza Virus A by Cytospin-Enhanced Immunofluorescence and Membrane Enzyme-Linked Immunosorbent Assay
Authors: Landry Marie L. , Cohen Sandra , Ferguson David
Published: May 2021

Cytospin-enhanced direct fluorescent-antibody assay (DFA) detected 49 (92.5%) and rapid membrane enzyme-linked immunosorbent assay (ELISA) detected 40 (75.5%) of 53 influenza virus A-positive samples. All 15 positive nasopharyngeal aspirates from children were detected by both tests. In contrast, 34 of 38 (89.5%) positive swabs from adults were detected by DFA, but only 25 (66%) were detected by ELISA.
Serological Detection of
Capillaria hepatica
by Indirect Immunofluorescence Assay
Authors: Juncker-Voss Martina , Prosl Heinrich , Lussy Helga , Enzenberg Ulrike , Auer Herbert , Nowotny Norbert
Published: May 2021

In this paper, a serological assay for the detection of antibodies to
Capillaria hepatica
, a zoonotic parasite, is described. In the past, the only way of detecting
Capillaria hepatica
was to perform a liver biopsy. The indirect immunofluorescence (IIF) assay, based on liver sections of naturally infected mice and human serum samples, is suitable for detecting early stages of human infections and for screening purposes. No cross-reactivity with other parasitic infections was detected. We have applied the IIF assay to serum samples of 60 employees of the Zoological Garden of Vienna, Schönbrunn, Austria, and found one positive and one questionable sample.
Confirmation of
psaA
in All 90 Serotypes of
Streptococcus pneumoniae
by PCR and Potential of This Assay for Identification and Diagnosis
Authors: Morrison Katherine E. , Lake Derrick , Crook Jennifer , Carlone George M. , Ades Edwin , Facklam Richard , Sampson Jacquelyn S.
Published: May 2021

The gene encoding the pneumococcal surface adhesin A (PsaA) protein,
psaA
, was confirmed in all
Streptococcus pneumoniae
serotypes by a newly developed PCR (
psaA
PCR) assay. Eighty-nine of the 90 serotypes amplified produced an 838-bp fragment; the exception was a serotype 16F strain acquired from the American Type Culture Collection (ATCC). Analysis of 20 additional 16F strains from the United States and Brazil showed that the gene was amplified in all 16F strains, implying that the serotype 16F ATCC strain must be a variant. The specificity of the assay was verified by the lack of signal from analysis of heterologous bacterial species (
n
= 30) and genera (
n
= 14), including viridans group streptococci. The potential of the assay for clinical application was shown by its ability to detect pneumococci in culture-positive nasopharyngeal specimens. Demonstration of
psaA
in all 90 serotypes and lack of amplification of heterologous organisms suggest that this assay could be a useful tool for detection of pneumococci and diagnosis of disease.
Development and Evaluation of a Phage Typing Scheme for
Vibrio cholerae
O139
Authors: Chakrabarti A. K. , Ghosh A. N. , Nair G. Balakrish , Niyogi S. K. , Bhattacharya S. K. , Sarkar B. L.
Published: May 2021

The scenario of cholera that existed previously changed in 1992 and 1993 with the emergence of toxigenic
Vibrio cholerae
O139 in India. The genesis of the new serogroup formed the impetus to search for O139 phages in and around the country. A total of five newly isolated phages lytic to
V. cholerae
O139 strains were used for the development of this phage typing scheme. These phages differed from each other and also differed from the existing O1 phages in their lytic patterns, morphologies, restriction endonuclease digestion profiles, and immunological criteria. With this scheme, 500
V. cholerae
O139 strains were evaluated for their phage types, and almost all strains were found to be typeable. The strains clustered into 10 different phage types, of which type 1 (38.2%) was the dominant type, followed by type 2 (22.4%) and type 3 (18%). Additionally, a comparative study of phage types in 1993 and 1994 versus those from 1996 to 1998 for O139 strains showed a higher percentage of phage type 1 (40.5%), followed by type 3 (18.8%) during the period between 1993 and 1994, whereas phage type 2 (32.1%) was the next major type during the period from 1996 to 1998. This scheme comprising five newly isolated phages would be another useful tool in the study of the epidemiology of cholera caused by
V. cholerae
O139.
Differentiation of
Mycobacterium tuberculosis
Complex and Nontuberculous Mycobacterial Liquid Cultures by Using Peptide Nucleic Acid-Fluorescence In Situ Hybridization Probes
Authors: Drobniewski F. A. , More P. G. , Harris G. S.
Published: May 2021

A blinded comparison of peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) with routine identification methods was performed on 74 consecutively positive mycobacterial liquid cultures. All
Mycobacterium tuberculosis
cultures (48 of 48) and 22 of 27 (81.5%) nontuberculous cultures were correctly identified (including one mixed culture). Five isolates yielded no reaction with either probe and were identified as
Mycobacterium xenopi
,
Mycobacterium fortuitum
, or
Mycobacterium flavescens
.
Quality Control Guidelines for Disk Diffusion and Broth Microdilution Antimicrobial Susceptibility Tests with Seven Drugs for Veterinary Applications
Authors: Odland Brant A. , Erwin Meredith E. , Jones Ronald N.
Published: May 2021

This multicenter study proposes antimicrobial susceptibility (MIC and disk diffusion methods) quality control (QC) parameters for seven compounds utilized in veterinary health. Alexomycin, apramycin, tiamulin, tilmicosin, and tylosin were tested by broth microdilution against various National Committee for Clinical Laboratory Standards (NCCLS)-recommended QC organisms (
Staphylococcus aureus
ATCC 29213,
Enterococcus faecalis
ATCC 29212,
Streptococcus pneumoniae
ATCC 49619,
Escherichia coli
ATCC 25922, and
Pseudomonas aeruginosa
ATCC 27853). In addition, disk diffusion zone diameter QC limits were determined for apramycin, enrofloxacin, and premafloxacin by using
E. coli
ATCC 25922,
P. aeruginosa
ATCC 27853, and
S. aureus
ATCC 25923. The results from five or six participating laboratories produced ≥99.0% of MICs and ≥95.0% of the zone diameters within suggested guidelines. The NCCLS Subcommittee for Veterinary Antimicrobial Susceptibility Testing has recently approved these ranges for publication in the next M31 document.
Bacteremic Pneumonia Caused by a Single Clone of
Streptococcus pneumoniae
with Different Optochin Susceptibilities
Authors: Tsai Hsiu-Yuan , Hsueh Po-Ren , Teng Lee-Jene , Lee Ping-Ing , Huang Li-Min , Lee Chin-Yun , Luh Kwen-Tay
Published: May 2021

Two isolates of
Streptococcus pneumoniae
having different optochin susceptibilities were recovered from a blood sample of a 2-year-old boy with community-acquired pneumonia. The two isolates were documented to belong to a single clone on the basis of the isolates' identical serotype (23F), antibiograms by the E-test, random amplified polymorphic DNA patterns generated by arbitrarily primed PCR, pulsed-field gel electrophoresis, and restriction fragment length polymorphism of the penicillin-binding protein genes
pbp2b
and
pbp2x
.
Polymorphism in the Pertussis Toxin Promoter Region Affecting the DNA-Based Diagnosis ofBordetellaInfection
Authors: Nygren Malin , Reizenstein Elisabet , Ronaghi Mostafa , Lundeberg Joakim
Published: May 2021

The pertussis toxin (PT) promoter region is a frequently used target for DNA-based diagnosis of pertussis and parapertussis infections. The reported polymorphism in this region has also allowed discrimination of species in mixtures with severalBordetellaspecies by their specific PCR amplicon restriction patterns. In the present study, we investigated the degree of polymorphism in order to confirm the reliability of the assay. Five different sequence types of the amplified 239- or 249-bp region were found among the 33Bordetella pertussis,B. parapertussis, andB. bronchisepticaAmerican Type Culture Collection reference strains and patient isolates analyzed. According to the sequences that were obtained and according to the PT promoter sequences already available in the databases, restriction enzyme analysis withTaqI,BglI, andHaeII, which gave four different patterns, can be performed to reliably identifyB. pertussis,B. parapertussis, andB. bronchiseptica.
Characterization ofStreptococcus agalactiaeIsolates of Bovine and Human Origin by Randomly Amplified Polymorphic DNA Analysis
Authors: Martinez Gabriela , Harel Josee , Higgins Robert , Lacouture Sonia , Daignault Danielle , Gottschalk Marcelo
Published: May 2021

Streptococcus agalactiaeis considered one of the major causes of bovine intramammary infections. It is also found in the vaginas of women without any apparent clinical symptoms, but reports of neonatal infections, causing significant morbidity, are relatively frequent. The aim of this study was to evaluate the genetic diversity ofS. agalactiaestrains isolated from bovine milk and from asymptomatic women in Québec, Canada, by randomly amplified polymorphic DNA (RAPD) analysis. A total of 185 bovine isolates and 38 human isolates were first serotyped for capsular polysaccharide by double diffusion in agarose gel (bovine isolates) and coagglutination (human isolates). Strains were then studied by RAPD using 3 primers, designated OPS11, OPB17, and OPB18, which were selected from 12 primers. Thirty-eight percent of bovine isolates and 82% of human isolates could be serotyped. Prevalent serotypes were type III (28%) for bovine isolates and types V (26%) and III (24%) for human isolates. RAPD results showed that, taken together, all isolates (of bovine and human origin) shared 58% similarity. Ninety-four percent of these isolates were clustered in four groups (I, II, III, and IV) with 70% similarity among them. Three clusters, A (48 isolates), B (14 isolates), and C (32 isolates), with 79 to 80% similarity were identified within group IV, whereas the three other groups did not present any clusters. Despite some clustering of human isolates, relatively high diversity was seen among them. Relatively high heterogeneity was observed with the RAPD profiles, not only for field strains belonging to different serotypes but also for those within a given serotype.
Development of a TT Virus DNA Quantification System Using Real-Time Detection PCR
Authors: Kato Takanobu , Mizokami Masashi , Mukaide Motokazu , Orito Etsuro , Ohno Tomoyoshi , Nakano Tatsunori , Tanaka Yasuhito , Kato Hideaki , Sugauchi Fuminaka , Ueda Ryuzo , Hirashima Noboru , Shimamatsu Kazuhide , Kage Masayoshi , Kojiro Masamichi
Published: May 2021

Although TT virus (TTV) was isolated from a cryptogenic posttransfusion hepatitis patient, its pathogenic role remains unclear. It has been reported that the majority of the healthy population is infected with TTV. To elucidate the differences between TTV infection in patients with liver diseases and TTV infection in the healthy population, a quantification system was developed. TTV DNA was quantified by a real-time detection PCR (RTD-PCR) assay on an ABI Prism 7700 sequence detector. With this system, TTV DNA was quantified in 78 hepatitis C virus (HCV)-infected patients (63 with elevated serum alanine aminotransferase [ALT] levels and 15 with normal ALT levels) and in 70 voluntary blood donors (BDs). The quantification range was 2.08 to 7.35 log copies/ml. The intra-assay and interassay coefficients of variation were 0.37 to 6.33% and 0.60 to 7.07%, respectively. The mean serum TTV DNA levels in the HCV-infected patients with both elevated and normal ALT levels and BDs were 3.69 ± 0.89, 3.45 ± 0.76, and 3.45 ± 0.67 log copies/ml, respectively. Comparison of the serum TTV DNA levels among the HCV-infected patients revealed that they were not related to the serum ALT and HCV core protein levels or to the histopathological score on liver biopsy. This study showed that (i) the RTD-PCR assay for the detection of TTV was accurate and had a high degree of sensitivity, (ii) the mean serum TTV DNA level was similar among HCV-infected patients, irrespective of their ALT level, and also among BDs, and (iii) a high serum TTV DNA level does not affect the serum ALT and HCV levels or liver damage in HCV-infected patients.
Performance of Indirect Immunoglobulin M (IgM) Serology Tests and IgM Capture Assays for Laboratory Diagnosis of Measles
Authors: Ratnam Samuel , Tipples Graham , Head Carol , Fauvel Micheline , Fearon Margaret , Ward Brian J.
Published: May 2021

As progress is made toward elimination of measles, the laboratory confirmation of measles becomes increasingly important. However, both false-positive and false-negative results can occur with the routinely used indirect measles immunoglobulin M (IgM) serology tests. The measles IgM capture assay is considered to be more specific, and therefore, its use is indicated for confirmatory testing, but its relative performance has not been fully assessed. Four commercial indirect measles IgM serology test kits (the Behring, Clark, Gull, and PanBio assays) and a commercial IgM capture assay (the Light Diagnostics assay) were evaluated for their abilities to detect measles virus-specific IgM antibody with a total of 308 serum samples from patients involved in a measles outbreak and with confirmed cases of measles and 454 samples from subjects without measles. The Centers for Disease Control and Prevention (CDC) IgM capture assay was also used in a part of the evaluation. Among the indirect assays, the overall sensitivities ranged from 82.8% (Clark assay) to 88.6% (Behring assay) and specificity ranged from 86.6% (PanBio assay) to 99.6% (Gull assay). These rates were 92.2 and 86.6%, respectively, for the Light Diagnostics capture assay and 87.0 and 94.8%, respectively, for the CDC capture assay. While the Light Diagnostics capture assay had the best detection rate (80%) with the acute-phase samples compared with those for the rest of the tests (CDC capture assay, 77%; Behring assay, 70%; Gull assay, 69%; PanBio assay, 58%; and Clark assay, 57%), all tests showed a significantly improved sensitivity in the range of 92% (Clark and PanBio assays) to 97% (Light Diagnostics and CDC capture assays) with the convalescent-phase samples, as expected. The best seropositivity rates (in the range of 92 to 100%) were observed with samples collected 6 to 14 days after the onset of symptoms. The Gull assay showed the highest positive predictive value (99.6%), followed by the Behring assay (97.8%) and the CDC capture assay (96.1%). Overall, the Gull and Behring assays were found to be as good as or better than the capture assays. In conclusion, laboratory diagnosis of measles based on IgM serology varies depending on the timing of specimen collection and the test used, and the case for the use of the IgM capture assay as the confirmatory test appears to be uncertain.
Integrating Statistics with a Microbiology Laboratory Activity
Authors: LOROWITZ WILLIAM , SAXTON ELIZABETH , SONDOSSI MOHAMMAD , NAKAOKA KAREN
Published: May 2021

Statistics is an important tool for microbiologists but is virtually absent from undergraduate laboratory activities. The variables in a stringent protocol, the antibiotic disk diffusion assay described by the National Committee for Clinical Laboratory Standards, were examined by the authors as a means for introducing hypothesis testing and the application of elementary statistical tools. After several experiments, a lab activity was developed where students examine the effect of cell concentration on antibiotic activity and analyze data with thettest. They also collect data independently from the same samples and compare their measurements using analysis of variance (ANOVA). The outcome of the activity, including an assessment tool, indicated that students learned the appropriate use of thettest and ANOVA, gained an appreciation for standardized protocols, and enjoyed the experience.
Assessment of Student Skills for Critiquing Published Primary Scientific Literature Using a Primary Trait Analysis Scale
Authors: VARELA MANUEL F. , LUTNESKY MARVIN M. F. , OSGOOD MARCY P.
Published: May 2021

Instructor evaluation of progressive student skills in the analysis of primary literature is critical for the development of these skills in young scientists. Students in a senior or graduate-level one-semester course in Immunology at a Masters-level comprehensive university were assessed for abilities (primary traits) to recognize and evaluate the following elements of a scientific paper: Hypothesis and Rationale, Significance, Methods, Results, Critical Thinking and Analysis, and Conclusions. We tested the hypotheses that average recognition scores vary among elements and that scores change with time differently by trait. Recognition scores (scaled 1 to 5), and differences in scores were analyzed using analysis of variance (ANOVA), regression, and analysis of covariance (ANCOVA) (
n
= 10 papers over 103 days). By multiple comparisons testing, we found that recognition scores statistically fell into two groups: high scores (for Hypothesis and Rationale, Significance, Methods, and Conclusions) and low scores (for Results and Critical Thinking and Analysis). Recognition scores only significantly changed with time (increased) for Hypothesis and Rationale and Results. ANCOVA showed that changes in recognition scores for these elements were not significantly different in slope (F
1,16
= 0.254,
P
= 0.621) but the Results trait was significantly lower in elevation (F
1,17
= 12.456,
P
= 0.003). Thus, students improved with similar trajectories, but starting and ending with lower Results scores. We conclude that students have greatest difficulty evaluating Results and critically evaluating scientific validity. Our findings show extant student skills, and the significant increase in some traits shows learning. This study demonstrates that students start with variable recognition skills and that student skills may be learned at differential rates. Faculty can use these findings or the primary trait analysis scoring scale to focus on specific paper elements for which they desire to improve recognition.
Intermittent percutaneous drainage of ovarian tumour
Authors: Oya Kiyofumi , Kuboyama Yusuke , Kashiwagi Hideyuki
Published: May 2021

Introduction

Abdominal pain and distention are common in ovarian tumours. When the ovarian tumour grows too large, the tumour can cause these symptoms. Percutaneous drainage from ovarian tumours, which can alleviate symptoms, is traditionally discouraged for its potential risk of peritoneal tumour seeding.

Case

A 73-year-old woman with a multilocular ovarian tumour reporting abdominal fullness and pain was referred to the palliative care outpatient department. The multilocular tumour occupied most of the intra-abdominal space, which was determined to cause her symptoms. To alleviate her symptoms, we performed intermittent percutaneous drainage for 1.5 years. A clinical autopsy revealed the tumour was an ovarian mucinous carcinoma. Despite iterative tumour drainage, we observed no feature of peritoneal dissemination.

Conclusion

Intermittent percutaneous drainage of ovarian tumours could reduce tumour-related abdominal symptoms without pathological evidence of peritoneal dissemination. This procedure can be a new palliative treatment option for ovarian tumour-related abdominal symptoms.
Thin accretion disks around rotating black holes in 4D Einstein–Gauss–Bonnet gravity
Authors: Heydari-Fard Mohaddese , Heydari-Fard Malihe , Sepangi Hamid Reza
Published: May 2021

Recently, Kumar and Ghosh have derived Kerr-like rotating black hole solutions in the framework of four-dimensional Einstein–Gauss–Bonnet theory of gravity and investigated the black hole shadow. Using the steady-state Novikov–Thorne model, we study thin accretion disk processes for such rotating black holes including the energy flux, temperature distribution, emission spectrum, energy conversion efficiency as well as the radius of the innermost stable circular orbit. We also study the effects of the Gauss–Bonnet coupling parameter $$\alpha $$
α
on these quantities. The results are compared to slowly rotating relativistic Kerr black holes which show that for a positive Gauss–Bonnet coupling, thin accretion disks around rotating black holes in four-dimensional Einstein–Gauss–Bonnet gravity are hotter and more efficient than that for Kerr black holes with the same rotation parameter a, while for a negative coupling they are cooler and less efficient. Thus the accretion disk processes may be considered as tools for testing Einstein–Gauss–Bonnet gravity using astrophysical observations.
Neuroplasticity: A Key Player in the Antidepressant Action of Chinese Herbal Medicine
Authors: Xia Baomei , Chen Chang , Tao Weiwei
Published: May 2021

Traditional Chinese medicine (TCM) is a systematic medicine. It provides alternative strategies for the treatment of depression with its clinical experience, comprehensive diagnosis, and treatment theory. Chinese herbal medicine (CHM) is the major form of TCM prescription, and numerous CHMs have been demonstrated to possess remarkable antidepressant-like properties. A diversity of mechanisms have been implicated in CHM-associated antidepressant property. This paper reviewed the neuroplastic mechanisms underlying the antidepressant actions of CHM, finding that CHM repairs neuroplasticity by improving neurogenesis, neurotrophic factors, synaptic spine morphology, cell signaling, glutamatergic system, monoamine neurotransmitters, and neural apoptosis. CHM thereby exerts an antidepressant effect, attempting to offer a better understanding of the mechanisms implicated in TCM-related antidepressant-like efficacy and laying a foundation for the scientific evaluation and development of TCM in treating depression.
Efficacy of Acupuncture for Insomnia: A Systematic Review and Meta-Analysis
Authors: Kim Sung-A , Lee Sook-Hyun , Kim Jang-Hoon , van den Noort Maurits , Bosch Peggy , Won Tiana , Yeo Sujung , Lim Sabina
Published: May 2021

Patients with insomnia frequently use acupuncture as an alternative treatment to pharmacotherapy globally. The aim of this paper is to assess the effect of acupuncture on insomnia. Seven medical databases, including MEDLINE, EMBASE, CENTRAL, CNKI, RISS, NDSL, and OASIS, were used to identify studies published through July 09, 2020. Twenty-four randomized controlled trials (RCTs) were included in this qualitative review comparing acupuncture to either pharmacotherapy or sham-acupuncture therapy. Methodological quality was assessed, using the Cochrane risk of bias (ROB). In the subsequent quantitative meta-analysis of studies comparing acupuncture versus pharmacotherapy, fifteen RCTs demonstrated that acupuncture had a significant effect on patients with insomnia as assessed by the Pittsburgh sleep quality index (PSQI) (RR: –0.74; 95% CI: –1.07 to –0.40; [Formula: see text] ¡0.0001; [Formula: see text] = 89%; [Formula: see text] = 1475). A subgroup analysis showed that there was no significant effect after weeks 1 and 2, but six studies found that acupuncture had a significant effect insomnia at week 3 (RR: –0.97; 95% CI: –1.65 to –0.28; [Formula: see text] = 0.006; [Formula: see text] = 91%; [Formula: see text] = 463) and nine studies demonstrated a significant effect at week 4 (RR: –0.70; 95% CI: –1.15 to –0.25; [Formula: see text] = 0.002; [Formula: see text] = 85%; [Formula: see text] = 594). These results suggest that insomnia patients may experience significant improvement in symptoms after more than three weeks of acupuncture treatment compared to pharmacological treatments.
Conjugated-linker dependence of the photophysical properties and electronic structure of chlorin dyads
Authors: Kang Hyun Suk , Satraitis Andrius , Meares Adam , Bhagavathy Ganga Viswanathan , Diers James R. , Niedzwiedzki Dariusz M. , Kirmaier Christine , Ptaszek Marcin , Bocian David F. , Holten Dewey
Published: May 2021

The synthesis, photophysical properties and electronic structure of seven new chlorin dyads and associated benchmark monomers are described. Each dyad contains two identical chlorins linked at the macrocycle [Formula: see text]-pyrrole 13-position. The extent of electronic communication between chlorin constituents depends on the nature of the conjugated linker. The communication is assessed by modification of prominent ground-state absorption and redox properties, rate constants and yields of excited-state decay processes, and molecular-orbital characteristics. Relative to the benchmark monomers, the chlorin dyads in toluene exhibit a substantial bathochromic shift of the long-wavelength absorption band (30 nm average), two-fold increased radiative rate constant [average (10 ns)[Formula: see text] vs. (22 ns)[Formula: see text]], reduced singlet excited-state lifetimes (average 5.0 ns vs. 8.2 ns), and increased fluorescence quantum yields (average 0.56 vs. 0.42). The excited-state lifetime and fluorescence yield for the chlorin dyad with a benzothiadiazole linker are reduced substantially in benzonitrile vs. toluene due largely to [Formula: see text]25-fold accelerated internal conversion. The results aid design strategies for molecular architectures that may find utility in solar-energy conversion and photomedicine.
Meso-tetra(dioxanyl)porphyrins: Neutral, low molecular weight, and chiral porphyrins with solubility in aqueous solutions
Authors: Jiang Xu-Liang , Damunupola Dinusha , Bruckner Christian
Published: May 2021

The synthesis of the low-molecular weight, meso-tetra(dioxan-2-yl)porphyrin with considerable solubility in aqueous solution is described. The key intermediate dioxan-2-carbaldehyde is accessible in either racemic or in stereo-pure forms from commercially available starting materials in three steps. Using 4 × 1 or 2 + 2-type syntheses provide the porphyrin in modest yields. While the racemic aldehyde created an intractable mixture of diastereomers, the enantiopure aldehyde created a single enantiomer of the target porphyrin. The porphyrin was spectroscopically characterized. As its free base or zinc complex, it showed excellent solubility properties in organic and aqueous solvents, though free water-solubility was not achieved. The work expands on the availability of chiral porphyrins and neutral porphyrins with considerable solubility in aqueous solution.
Climate Risk Management
Authors: Keller Klaus , Helgeson Casey , Srikrishnan Vivek
Published: May 2021

Accelerating global climate change drives new climate risks. People around the world are researching, designing, and implementing strategies to manage these risks. Identifying and implementing sound climate risk management strategies poses nontrivial challenges including ( a) linking the required disciplines, ( b) identifying relevant values and objectives, ( c) identifying and quantifying important uncertainties, ( d) resolving interactions between decision levers and the system dynamics, ( e) quantifying the trade-offs between diverse values under deep and dynamic uncertainties, ( f) communicating to inform decisions, and ( g) learning from the decision-making needs to inform research design. Here we review these challenges and avenues to overcome them. ▪  People and institutions are confronted with emerging and dynamic climate risks. ▪  Stakeholder values are central to defining the decision problem. ▪  Mission-oriented basic research helps to improve the design of climate risk management strategies.
Investigating the Role of Energy Density in Thermal Runaway of Lithium-Ion Batteries with Accelerating Rate Calorimetry
Authors: Lamb Joshua , Torres-Castro Loraine , Hewson John C. , Shurtz Randy C. , Preger Yuliya
Published: May 2021

This work uses accelerating rate calorimetry to evaluate the impact of cell chemistry, state of charge, cell capacity, and ultimately cell energy density on the total energy release and peak heating rates observed during thermal runaway of Li-ion batteries. While the traditional focus has been using calorimetry to compare different chemistries in cells of similar sizes, this work seeks to better understand how applicable small cell data is to understand the thermal runaway behavior of large cells as well as determine if thermal runaway behaviors can be more generally tied to aspects of lithium-ion cells such as total stored energy and specific energy. We have found a strong linear correlation between the total enthalpy of the thermal runaway process and the stored energy of the cell, apparently independent of cell size and state of charge. We have also shown that peak heating rates and peak temperatures reached during thermal runaway events are more closely tied to specific energy, increasing exponentially in the case of peak heating rates.
LR12 Promotes Liver Repair by Improving the Resolution of Inflammation and Liver Regeneration in Mice with Thioacetamide- (TAA-) Induced Acute Liver Failure
Authors: Wang Yongjuan , Xie Xiaoli , Liu Hongqun , Liu Huimin , Jiang Huiqing
Published: May 2021

Background. Triggering receptor expressed on myeloid cells-1 (TREM-1) controls the mobilization of inflammatory cells in response to injury and consequently enhances liver damage. LR12 is a TREM-1 inhibitory peptide. However, the role of LR12 in acute liver failure (ALF) has remained elusive. This study was aimed at indicating whether LR12 could promote liver repair in mice with thioacetamide- (TAA-) induced ALF. Methods. BALB/c mice were intraperitoneally injected with TAA, followed by intravenous injection of LR12. Damage and regeneration of the liver were assessed. LO2 cells and macrophages were used to assess the therapeutic effects of LR12. Results. Mice treated with TAA for 24 h developed ALF, while liver inflammation was alleviated after LR12 treatment. Moreover, LR12 promoted hepatocyte regeneration in mice with TAA-induced ALF. In vitro, the supernatant from TAA+LR12-treated macrophages promoted the proliferation of LO2 cells. Cytokine protein microarray analysis suggested that LR12 promoted the secretion of C-C chemokine ligand 20 (CCL20) from macrophages. Besides, neutralization of CCL20 blocked the effects of LR12, thus inhibited the proliferation of LO2 cells in vitro, aggregated the liver inflammation, and restrained hepatocyte regeneration in ALF mice in vivo. Furthermore, we also found that LR12 activated the p38 mitogen-activated protein kinase (MAPK) pathway in hepatocytes through promoting the secretion of CCL20 from macrophages. Conclusions. LR12 could improve the resolution of inflammation and liver regeneration in mice with TAA-induced ALF by promoting the secretion of CCL20 from macrophages and activating the p38 MAPK pathway. Therefore, LR12 could be an attractive therapeutic target for the treatment of ALF.
ITDPM: An Internet Topology Dynamic Propagation Model Based on Generative Adversarial Learning
Authors: Hu Hangyu , Zhai Xuemeng , Fei Gaolei , Hu Guangmin
Published: May 2021

Network information propagation analysis is gaining a more important role in network vulnerability analysis domain for preventing potential risks and threats. Identifying the influential source nodes is one of the most important problems to analyze information propagation. Traditional methods mainly focus on extracting nodes that have high degrees or local clustering coefficients. However, these nodes are not necessarily the high influential nodes in many real-world complex networks. Therefore, we propose a novel method for detecting high influential nodes based on Internet Topology Dynamic Propagation Model (ITDPM). The model consists of two processing stages: the generator and the discriminator like the generative adversarial networks (GANs). The generator stage generates the optimal source-driven nodes based on the improved network control theory and node importance characteristics, while the discriminator stage trains the information propagation process and feeds back the outputs to the generator for performing iterative optimization. Based on the generative adversarial learning, the optimal source-driven nodes are then updated in each step via network information dynamic propagation. We apply our method to random-generated complex network data and real network data; the experimental results show that our model has notable performance on identifying the most influential nodes during network operation.