bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recovery and Analysis of Human Immunodeficiency Virus Type 1 (HIV) RNA Sequences from Plasma Samples with Low HIV RNA Levels
Authors: Niubò Jordi , Li Wuyi , Henry Keith , Erice Alejo 
Published: May 2021

ABSTRACT

Amplification of human immunodeficiency virus type 1 (HIV) reverse transcriptase (RT) and protease (PT) sequences from plasma is difficult when HIV RNA levels are low, and it usually cannot be accomplished in samples with <1,000 HIV RNA copies/ml. Because the RNA extraction step is critical for the success of subsequent amplifications and sequence analyses, two RNA extraction methods were compared to study plasma samples with low HIV RNA levels. Forty-four plasma samples containing <500 HIV RNA copies/ml in a branched-DNA (bDNA) assay (Quantiplex HIV RNA assay version 2.0 [Chiron Corp., Emeryville, Calif.]) were studied. RNA was extracted by using two commercial kits (QIAamp Viral RNA kit [Qiagen, Hilden, Germany] and NucliSens kit [Organon Teknika, Boxtel, The Netherlands]). Fragments (1,144 bp) encompassing HIV PT and RT sequences were amplified by nested PCRs. Amplified products were sequenced by using a commercial kit (Applied Biosystems). HIV RNA was recovered from a total of 21 plasma samples, including 20 samples after extraction by the NucliSens method, and 8 samples after extraction by the QIAamp method (
P
< 0.05). Mean HIV RNA levels in these samples, measured by an ultrasensitive bDNA assay (Quantiplex HIV RNA assay version 3.0; Chiron Corp., Emeryville, Calif.), were 848 copies/ml (median, 666; range, 154 to 2,606 copies/ml). Analysis of RT and PT sequences in five samples demonstrated an average of 3.8 and 2.4 resistance mutations in these regions, respectively. The NucliSens RNA extraction kit is a valuable method for obtaining HIV RNA for genotypic studies from plasma fractions of individuals with low HIV RNA levels.
Direct Amplification of rRNA Genes in Diagnosis of Bacterial Infections
Authors: Rantakokko-Jalava Kaisu , Nikkari Simo , Jalava Jari , Eerola Erkki , Skurnik Mikael , Meurman Olli , Ruuskanen Olli , Alanen Anna , Kotilainen Esa , Toivanen Paavo , Kotilainen Pirkko 
Published: May 2021

ABSTRACT
A broad-range bacterial PCR targeting rRNA genes (rDNAs) was used to directly analyze 536 clinical samples obtained from 459 hospitalized patients during a 4-year study period. The molecular diagnosis based on DNA sequencing of the PCR product was compared to that obtained by bacterial culture. The bacteriological diagnosis was concordant for 447 (83%) specimens. Broad-range rDNA PCR was the only method that yielded an etiologic diagnosis for 11 (2.4%) of 459 patients. Compared to culture and clinical assessment, the sensitivity of the PCR method combined with sequencing was 74.2%, and the specificity was between 98.7 and 99.6%. At present, the described molecular approach proved superior to bacterial culture in two clinical situations: infections caused by bacteria with unusual growth requirements and specimens taken during antimicrobial treatment of the patient.
Antifungal Susceptibility Testing of Dermatophytes: Establishing a Medium for Inducing Conidial Growth and Evaluation of Susceptibility of Clinical Isolates
Authors: Jessup C. J. , Warner J. , Isham N. , Hasan I. , Ghannoum M. A. 
Published: May 2021

ABSTRACT

A standardized reference method for dermatophyte in vitro susceptibility testing is lacking. In a previous study, Norris et al. (H. A. Norris, B. E. Elewski, and M. A. Ghannoum, J. Am. Acad. Dermatol. 40(6, part 2):S9–S13) established the optimal medium and other growth variables. However, the earlier study did not address two issues: (i) selection of an optimal medium for conidial formation by dermatophytes and (ii) validation of the method with a large number of dermatophytes. The present study addresses these two points. To select which agar medium best supported conidial growth, representative isolates of dermatophytes were grown on different agars. Preliminary experiments showed that only oatmeal cereal agar supported the production of conidia by
Trichophyton rubrum
. We tested the abilities of 251
T. rubrum
isolates to form conidia using three different cereal agars and potato dextrose agar. Overall, oatmeal cereal and rice agar media were comparable in their abilities to support
T. rubrum
conidial growth. Next, we used the oatmeal cereal agar for conidial formation along with the optimal conditions for dermatophyte susceptibility testing proposed by Norris et al. and determined the antifungal susceptibilities of 217 dermatophytes to fluconazole, griseofulvin, itraconazole, and terbinafine. Relative to the other agents tested, terbinafine possessed the highest antifungal activity against all of the dermatophytes. The mean ± standard error of the mean MICs of fluconazole, itraconazole, terbinafine, and griseofulvin were 2.07 ± 0.29, 0.13 ± 0.01, 0.002 ± 0.0003, and 0.71 ± 0.05 μg/ml, respectively. This study is the first step in the identification of optimal conditions that could be used for the standardization of the antifungal susceptibility testing method for dermatophytes. Inter- and intralaboratory agreement as well as clinical correlations need to be established.
Identification and Characterization of Immunoglobulin G in Blood as a Major Inhibitor of Diagnostic PCR
Authors: Al-Soud Waleed Abu , Jönsson Leif J. , Rådström Peter 
Published: May 2021

ABSTRACT

A major inhibitor of diagnostic PCR in human plasma was identified and the mechanism of inhibition was characterized. Human blood was divided by centrifugation into buffy coat, plasma, platelets, and erythrocytes. All these blood fractions were found to be highly inhibitory to a standardized PCR mixture containing the thermostable DNA polymerase Ampli
Taq
Gold. PCR inhibitors in human plasma were purified by chromatographic procedures and were characterized by a process of elimination, so that the PCR-inhibitory effects of plasma fractions were tested after each purification step. The major inhibitor in human plasma, as determined by size-exclusion chromatography, anion-exchange chromatography, and chromatofocusing, was found to be immunoglobulin G (IgG) on the basis of N-terminal amino acid sequencing and electrophoretic analysis of the purified polypeptide. When different concentrations of purified plasma IgG (PIgG) were added to PCR mixtures containing 11 different thermostable DNA polymerases and 1 ng of
Listeria monocytogenes
DNA as template DNA, the only polymerase that resisted inhibition was
rTth
. The inhibitory effect was reduced when PIgG was heated at 95°C before it was added to PCR or after the addition of excess nontarget DNA to the PCR mixture. However, heating of PIgG together with target DNA at 95°C was found to block the amplification. Inhibition by PIgG may be due to an interaction with single-stranded DNA, which makes the target DNA unavailable for 10 of the DNA polymerases tested. The results show the danger of using boiling as a method of sample pretreatment or using a hot start prior to PCR. The effect of plasma PCR inhibition could be removed by mixing plasma with DNA-agarose beads prior to amplification, while plasma PCR inhibitors were found to bind to the DNA-agarose beads.
Pulmonary Infection Caused by
Gymnascella hyalinospora
in a Patient with Acute Myelogenous Leukemia
Authors: Iwen Peter C. , Sigler Lynne , Tarantolo Stefano , Sutton Deanna A. , Rinaldi Michael G. , Lackner Rudy P. , McCarthy Dora I. , Hinrichs Steven H. 
Published: May 2021

ABSTRACT

We report the first case of invasive pulmonary infection caused by the thermotolerant ascomycetous fungus
Gymnascella hyalinospora
in a 43-year-old female from the rural midwestern United States. The patient was diagnosed with acute myelogenous leukemia and treated with induction chemotherapy. She was discharged in stable condition with an absolute neutrophil count of 100 cells per μl. Four days after discharge, she presented to the Cancer Clinic with fever and pancytopenia. A solitary pulmonary nodule was found in the right middle lobe which was resected by video-assisted thoracoscopy (VATHS). Histopathological examination revealed septate branching hyphae, suggesting a diagnosis of invasive aspergillosis; however, occasional yeast-like cells were also present. The culture grew a mold that appeared dull white with a slight brownish tint that failed to sporulate on standard media. The mold was found to be positive by the AccuProbe
Blastomyces dermatitidis
Culture ID Test (Gen-Probe Inc., San Diego, Calif.), but this result appeared to be incompatible with the morphology of the structures in tissue. The patient was removed from consideration for stem cell transplant and was treated for 6 weeks with amphotericin B (AmB), followed by itraconazole (Itr). A VATHS with biopsy performed 6 months later showed no evidence of mold infection. In vitro, the isolate appeared to be susceptible to AmB and resistant to fluconazole and 5-fluorocytosine. Results for Itr could not be obtained for the case isolate due to its failure to grow in polyethylene glycol used to solubilize the drug; however, MICs for a second isolate appeared to be elevated. The case isolate was subsequently identified as
G. hyalinospora
based on its formation of oblate, smooth-walled ascospores within yellow or yellow-green tufts of aerial hyphae on sporulation media. Repeat testing with the
Blastomyces
probe demonstrated false-positive results with the case isolate and a reference isolate of
G. hyalinospora
. This case demonstrates that both histopathologic and cultural features should be considered for the proper interpretation of this molecular test and extends the list of fungi recognized as a cause of human mycosis in immunocompromised patients.
Polyomaviruria in Renal Transplant Patients Is Not Correlated to the Cold Ischemia Period or to Rejection Episodes
Authors: Priftakis P. , Bogdanovic G. , Tyden G. , Dalianis T. 
Published: May 2021

ABSTRACT
Polyomaviruria was observed in one-third of all renal transplant patients, irrespective of whether their renal grafts came from a living or cadaver donor, and was not correlated to graft rejection episodes. This suggests that the renal graft ischemia period is not the major cause of polyomavirus reactivation and that reactivation of polyomavirus is not a dominant cause of graft rejection.
Fungemia Due to
Fusarium sacchari
in an Immunosuppressed Patient
Authors: Guarro Josep , Nucci Marcio , Akiti Tiyomi , Gené Josepa , Barreiro M. Da Gloria C. , Gonçalves Renato T. 
Published: May 2021

ABSTRACT

The fungus
Fusarium sacchari
was isolated repeatedly from the blood of an immunosuppressed host. The infection was treated successfully with a small dose of amphotericin B. The strain was resistant to this antifungal in vitro. MICs and minimum fungicidal concentrations of six antifungals for the clinical isolate are provided. To our knowledge, this is the first report involving this fungus in a case of fungemia.
2-Hour Cytomegalovirus pp65 Antigenemia Assay for Rapid Quantitation of Cytomegalovirus in Blood Samples
Authors: Landry Marie L. , Ferguson David 
Published: May 2021

ABSTRACT
Of 109 blood samples tested for cytomegalovirus (CMV) antigenemia, 18 (16.5%) were positive. CMV Brite detected 13 and CMV Brite Turbo detected 16 of the 18 positives. There was no significant difference in the number of positive cells detected per sample. The seven discrepant samples contained a median of only one positive cell.
CagA Antibodies in Japanese Children with Nodular Gastritis or Peptic Ulcer Disease
Authors: Kato Seiichi , Sugiyama Toshiro , Kudo Mineo , Ohnuma Kenji , Ozawa Kyoko , Iinuma Kazuie , Asaka Masahiro , Blaser Martin J. 
Published: May 2021

ABSTRACT

cagA
+
Helicobacter pylori
strains have been linked to more severe gastric inflammation, peptic ulcer disease, and gastric cancer in adults, but there have been few studies of
cagA
in children. We examined the relationship between
H. pylori cagA
status and clinical status in Japanese children. Forty
H. pylori
-positive children were studied: 15 with nodular gastritis, 5 with gastric ulcers, and 20 with duodenal ulcers.
H. pylori
status was confirmed by biopsy-based tests and serum anti-
H. pylori
immunoglobulin G (IgG) antibody. As controls, 77 asymptomatic children with sera positive for anti-
H. pylori
IgG were enrolled. Levels of IgG antibodies to CagA in serum were measured by an antigen-specific enzyme-linked immunosorbent assay. In 16 patients with successful
H. pylori
eradication, posttreatment levels of CagA and
H. pylori
IgG antibodies also were studied. The CagA antibody seropositivities of asymptomatic controls (81.8%) and patients with nodular gastritis, gastric ulcers, and duodenal ulcers (80.0 to 95.0%) were not significantly different. Compared with pretreatment levels of CagA antibodies, posttreatment levels decreased progressively and significantly. We conclude that, as in Japanese adults, a high prevalence of
cagA
+
H. pylori
strains was found in Japanese children, and that there was no association with nodular gastritis or peptic ulcer disease. In the assessment of eradicative therapies, monitoring of serum anti-CagA antibodies does not appear to offer any direct benefit over monitoring of anti-
H. pylori
antibodies.
Characterization of
Escherichia coli
Strains from Cases of Childhood Diarrhea in Provincial Southwestern Nigeria
Authors: Okeke Iruka N. , Lamikanra Adebayo , Steinrück Hartmut , Kaper James B. 
Published: May 2021

ABSTRACT

In a study carried out in small-town and rural primary health care centers in southwestern Nigeria, 330
Escherichia coli
strains isolated from 187 children with diarrhea and 144 apparently healthy controls were examined for virulence traits. Based on the results of colony blot hybridization, strains were categorized as enteropathogenic
E. coli
(1.8%), enterotoxigenic
E. coli
(2.4%), enteroinvasive
E. coli
(1.2%), enterohemorrhagic
E. coli
(0.6%), enteroaggregative
E. coli
(10.3%), diffusely adherent
E. coli
(7.9%), cell-detaching
E. coli
(6.9%), and cytolethal distending toxin-producing
E. coli
(0.9%).
E. coli
strains that hybridized with a Shiga toxin gene probe but lacked other characteristics usually present in enterohemorrhagic
E. coli
constituted 8.4% of the isolates. Ninety-seven
E. coli
isolates adhered to HEp-2 cells in an aggregative fashion but did not hybridize with any of the probes employed in the study. Overall the pathotypes, apart from cytolethal distending toxin-producing
E. coli
, were recovered both from children with diarrhea and from children without diarrhea, though to a lower extent from the healthy children. All diarrheagenic
E. coli
strains were associated with diarrhea (
P
< 0.02). Heat-stable-enterotoxin-producing enterotoxigenic
E. coli
showed significant association with diarrhea (
P
< 0.02), as did strains that demonstrated aggregative adherence to HEp-2 cells (
P
< 0.04), but not those that hybridized with the CVD432 enteroaggregative probe.
Heterogeneity of
Actinobacillus actinomycetemcomitans
Strains in Various Human Infections and Relationships between Serotype, Genotype, and Antimicrobial Susceptibility
Authors: Paju Susanna , Carlson Petteri , Jousimies-Somer Hannele , Asikainen Sirkka 
Published: May 2021

ABSTRACT

Actinobacillus actinomycetemcomitans
, an oral pathogen, only occasionally causes nonoral infections. In this study 52
A. actinomycetemcomitans
strains from 51 subjects with nonoral infections were serotyped and genotyped by arbitrarily primed PCR (AP-PCR) to determine whether a certain clone(s) is specifically associated with nonoral infections or particular in vitro antimicrobial susceptibility patterns. The promoter structure of leukotoxin genes was additionally investigated to find the deletion characteristic of highly leukotoxic
A. actinomycetemcomitans
strains. The nonoral
A. actinomycetemcomitans
strains included all five known serotypes and nonserotypeable strains, the most common serotypes being b (40%) and c (31%). AP-PCR distinguished 10 different genotypes.
A. actinomycetemcomitans
serotype b strains were more frequently found in blood samples of patients with bacteremia or endocarditis than in patients with focal infections. One AP-PCR genotype was significantly more frequently found among strains originating in focal infections than in blood samples. Resistance to benzylpenicillin was significantly more frequent among
A. actinomycetemcomitans
serotype b strains than among strains of other serotypes. No differences in the leukotoxin gene promoter region or benzylpenicillin resistance between nonoral and oral
A. actinomycetemcomitans
strains were observed. Nonoral
A. actinomycetemcomitans
strains showed great similarity to the oral strains, confirming that the oral cavity is the likely source of nonoral
A. actinomycetemcomitans
infections. The predominance of serotype b strains in endocarditis and bacteremia supports the hypothesis of a relationship between certain
A. actinomycetemcomitans
clones and some nonoral infections. The mechanisms behind the exceptionally high rate of occurrence of benzylpenicillin resistance among
A. actinomycetemcomitans
serotype b strains are to be elucidated in further studies.
Relationship of Incremental Specimen Volumes and Enhanced Detection of Human Immunodeficiency Virus Type 1 RNA with Nucleic Acid Amplification Technology
Authors: Witt Donald J. , Kemper M. , Stead Andrew , Ginocchio Christine C. , Caliendo Angela M. 
Published: May 2021

ABSTRACT
The relationship between specimen input volume and the frequency of reported human immunodeficiency virus type 1 (HIV-1) RNA copy numbers by nucleic acid amplification technology (the NASBA HIV-1 RNA QT system) was investigated. Results obtained with both clinical specimens and dilution panels indicated that both the absolute number of reported results and the reported HIV-1 RNA copy number were directly proportional to the specimen input volumes evaluated (0.1, 0.5, and 1.0 ml). Conversion of the reported HIV-1 RNA copy numbers to a constant 1.0-ml volume indicated that the numerical relationship among the specimen input volumes and the HIV-1 RNA copy numbers was multiplicative. The HIV-1 RNA copy numbers reported for the 0.5-ml input volume were approximately 5-fold increased over those reported for the 0.1-ml input volume, and those reported for the 1.0-ml input volume were 10-fold increased over those reported for the 0.1-ml input volume. For the specimen input volumes investigated, a common linear range of 264 to 5,400,000 HIV-1 RNA copies was observed. The use of increased specimen input volumes did not result in a loss of assay specificity, as the results reported for specimens from 50 seronegative blood donors were negative at all three specimen input volumes. In conclusion, an increase in the input volume of specimens analyzed by nucleic acid amplification technology can be useful for the enhanced detection of HIV-1 RNA.
Identification of
Mycoplasma fermentans
in Synovial Fluid Samples from Arthritis Patients with Inflammatory Disease
Authors: Johnson Sheena , Sidebottom David , Bruckner Felix , Collins David 
Published: May 2021

ABSTRACT

Since 1970
Mycoplasma fermentans
has been suspected of being associated with rheumatoid arthritis. However, this association has been difficult to prove, and this has been our goal. The distribution of
M. fermentans
was studied in the synovial fluid of patients suffering from different arthritides. Samples of synovial fluid were taken from patients with well-defined disease and a clear diagnosis. After removal of the inflammatory cells and hyaluran, they were treated with proteinase K and tested by a single or fully nested PCR with primers directed against part of the two 16S rRNA genes of
M. fermentans
. The product was sequenced automatically, by using an ALF Express automatic sequencer, to confirm the mycoplasma species and to identify the strain since the two genes were usually found to be polymorphic. This was also true of the type strain, strain PG18.
M. fermentans
was detected in 23 of 26 (88%) rheumatoid arthritis patients, and four different strains were found. It was also found in 7 of 8 (88%) of the nonrheumatoid inflammatory arthritis patient group, which consisted of one patient with reactive arthritis, one patient with pauciarticular juvenile chronic arthritis, two patients with gout, two patients with ankylosing spondylitis, and two patients with psoriatic arthritis, only one of whom was infected with
M. fermentans
. It was not detected in any of the 10 osteoarthritis patients.
M. fermentans
was therefore found to be a variable and very common organism in arthritic patients with inflammatory joint exudates and may well prove to be important in the etiology of the diseases.
Monitoring progress with national and subnational health goals by integrating verbal autopsy and medically certified cause of death data
Authors: Adair Tim , Firth Sonja , Phyo Tint Pa Pa , Bo Khin Sandar , Lopez Alan D 
Published: May 2021

IntroductionThe measurement of progress towards many Sustainable Development Goals (SDG) and other health goals requires accurate and timely all-cause and cause of death (COD) data. However, existing guidance to countries to calculate these indicators is inadequate for populations with incomplete death registration and poor-quality COD data. We introduce a replicable method to estimate national and subnational cause-specific mortality rates (and hence many such indicators) where death registration is incomplete by integrating data from Medical Certificates of Cause of Death (MCCOD) for hospital deaths with routine verbal autopsy (VA) for community deaths.MethodsThe integration method calculates population-level cause-specific mortality fractions (CSMFs) from the CSMFs of MCCODs and VAs weighted by estimated deaths in hospitals and the community. Estimated deaths are calculated by applying the empirical completeness method to incomplete death registration/reporting. The resultant cause-specific mortality rates are used to estimate SDG Indicator 23: mortality between ages 30 and 70 years from cardiovascular diseases, cancers, chronic respiratory diseases and diabetes. We demonstrate the method using nationally representative data in Myanmar, comprising over 42 000 VAs and 7600 MCCODs.ResultsIn Myanmar in 2019, 89% of deaths were estimated to occur in the community. VAs comprised an estimated 70% of community deaths. Both the proportion of deaths in the community and CSMFs for the four causes increased with older age. We estimated that the probability of dying from any of the four causes between 30 and 70 years was 0.265 for men and 0.216 for women. This indicator is 50% higher if based on CSMFs from the integration of data sources than on MCCOD data from hospitals.ConclusionThis integration method facilitates country authorities to use their data to monitor progress with national and subnational health goals, rather than rely on estimates made by external organisations. The method is particularly relevant given the increasing application of routine VA in country Civil Registration and Vital Statistics systems.
Universal behavior of mass gaps existing in the single heavy baryon family
Authors: Chen Bing , Luo Si-Qiang , Liu Xiang 
Published: May 2021

AbstractThe mass gaps existing in the discovered single heavy flavor baryons are analyzed, which show some universal behaviors. Under the framework of a constituent quark model, we quantitatively explain why such interesting phenomenon happens, when these established excited heavy baryons are regarded as the $$\lambda $$
λ
-mode excitations. Based on the universal behaviors of the discussed mass gaps, we may have three implications including the prediction of the masses of excited $$\Xi _b^0$$

Ξ
b
0

baryons which are still missing in the experiment. For completeness, we also discuss the mass gaps of these $$\rho $$
ρ
-mode excited single heavy flavor baryons.