bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is it Reasonable to Study Decision‐Making Quantitatively?
Authors: Shiffrin Richard M. 
Published: May 2021

AbstractScientists studying decision‐making often provide a set of choices, each specified with values or distributions of values, and probabilities or distributions of probabilities. For example, “Would you prefer $100 with probability 1.0 or $1 with probability .9 and $1,000 with probability 0.1?” Other decision research examines choices made in the absence of most quantitative information; for example, “Would you prefer a Ford now or a Porsche a year from now?,” “Which food would you prefer,” but models the findings with precise quantitative assumptions. Yet other research does neither; for example, modeling verbally stated choices with verbally stated heuristics. This article asks about the relevance of the first two research approaches for much of the decision‐making made in life. The use of quantitative research and modeling is unsurprising, given that this approach underlies most of science. In life, values and probabilities are almost always partly or wholly vague and qualitative rather than quantitative. For example, when deciding which house to buy, there are relevant features such as size, color, neighborhood schools, construction materials, attractiveness, and many more, but the decision‐maker finds it difficult and of little use to assign these precise values or weights. Nonetheless, humans have evolved to make decisions in such vaguely specified settings. I provide an example showing how a very high degree of uncertainty can defeat the application of quantitative decision‐making, but such a demonstration is not critical if quantitative research and modeling produce a good understanding of and a good approximation to decision‐making in the natural environment. This perspective addresses these issues.
Unlocking the nutrient value of sewage sludge
Authors: Singh Vipin , Phuleria Harish C. , Chandel Munish K. 
Published: May 2021

AbstractThis study characterises the sewage sludge from 26 sewage treatment plants in India, which demonstrates the nutrient potential and highlights the associated challenges in using the sludge. The dry sludge had 2.35%–4.2% N, 2.46–3.2% phosphorus (P2O5) and 0.83%–1.24% potassium oxide (K2O), whereas sludge ash contains ~13.6% and 2.7%, P2O5 and K2O, respectively. Total nutrient potential from the sludge of the existing sewage treatment facility was 97.5 × 103 tonne/year, which is equivalent to 0.92% urea or 0.19% NPK used presently as conventional fertilisers in India. However, pre‐treatment may be required for this sludge before using it in agricultural fields as heavy metals, such as Zn, Cu, Ni, Cd, and Cr, were found higher than the compost standards. This study would be useful for the researchers and policymakers globally and would motivate them to make policies and deploy suitable technologies towards the nutrient utilisation from sewage sludge.
Prevention of Lyme and other tickborne diseases using a rodent‐targeted approach: A randomized controlled trial in Connecticut
Authors: Hinckley Alison F. , Niesobecki Sara A. , Connally Neeta P. , Hook Sarah A. , Biggerstaff Brad J. , Horiuchi Kalanthe A. , Hojgaard Andrias , Mead Paul S. , Meek James I. 
Published: May 2021

SummaryTickborne diseases are an increasing public health problem in the northeastern USA. Bait boxes that apply acaricide to rodents have been shown in small field studies to significantly reduce abundance of Ixodes scapularis ticks as well as their pathogen infection rates in treated areas. The effectiveness of this intervention for preventing human tickborne diseases (TBDs) has not been demonstrated. During 2012–2016, TickNET collaborators conducted a randomized, blinded, placebo‐controlled trial among 622 Connecticut households. Each household received active (containing fipronil wick) or placebo (empty) bait boxes in their yards over two consecutive years. Information on tick encounters and TBDs among household members was collected through biannual surveys. Nymphal ticks were collected from a subset of 100 properties during spring at baseline, during treatment, and in the year post‐intervention. Demographic and property characteristics did not differ between treatment groups. There were no significant differences post‐intervention between treatment groups with respect to tick density or pathogen infection rates, nor for tick encounters or TBDs among household members. We found no evidence that rodent‐targeted bait boxes disrupt pathogen transmission cycles or significantly reduce household risk of tick exposure or TBDs. The effectiveness of this intervention may depend on scale of use or local enzootic cycles.
The Use of Recovery Strategies in Professional Soccer: A Worldwide Survey
Authors: Field Adam , Harper Liam D. , Chrismas Bryna C.R. , Fowler Peter M. , McCall Alan , Paul Darren J. , Chamari Karim , Taylor Lee 
Published: May 2021

Purpose: To survey soccer practitioners’ recovery strategy: (1) use, (2) perceived effectiveness, and (3) factors influencing their implementation in professional soccer. Methods: A cross-sectional convenience sample of professional soccer club/confederation practitioners completed a web-based survey (April to July 2020). Pearson chi-square and Fisher exact tests with Cramer V (φ − c) assessed relationships and their strength, respectively, between the perceived effectiveness and frequency of strategy use. Results: A total of 80 soccer practitioners (13 countries) completed the survey. The 3 most important recovery objectives were “alleviating muscle damage/fatigue,” “minimizing injury risk,” and “performance optimization.” The most frequently used strategies were active recovery, structured recovery day, extra rest day, massage, cold-water therapy, and carbohydrate provision (predominantly on match day and match day + 1). Relationships were identified between perceived effectiveness and frequency of strategy use for sleep medication (P < .001, φ − c = 0.48), carbohydrate provision (P = .007, φ − c = 0.60), protein provision (P = .007, φ − c = 0.63), an extra rest day (P < .001, φ − c = 0.56), and a structured recovery day (P = .049, φ − c = 0.50). Conclusions: The study demonstrates that professional soccer practitioners have a range of objectives geared toward enhancing player recovery. A disconnect is apparent between the perceived effectiveness of many recovery strategies and their frequency of use in an applied setting. Novel data indicate that strategies are most frequently employed around match day. Challenges to strategy adoption are mainly competing disciplinary interests and resource limitations. Researchers and practitioners should liaise to ensure that the complexities involved with operating in an applied environment are elucidated and apposite study designs are adopted, in turn, facilitating the use of practically effective and compatible recovery modalities.
WdChs4p, a Homolog of Chitin Synthase 3 in
Saccharomyces cerevisiae
, Alone Cannot Support Growth of
Wangiella
(
Exophiala
)
dermatitidis
at the Temperature of Infection
Authors: Wang Zheng , Zheng Li , Hauser Melinda , Becker Jeffery M. , Szaniszlo Paul J. 
Published: May 2021

ABSTRACT

By using improved transformation methods for
Wangiella dermatitidis
, and a cloned fragment of its chitin synthase 4 structural gene (
WdCHS4
) as a marking sequence, the full-length gene was rescued from the genome of this human pathogenic fungus. The encoded chitin synthase product (WdChs4p) showed high homology with Chs3p of
Saccharomyces cerevisiae
and other class IV chitin synthases, and Northern blotting showed that
WdCHS4
was expressed at constitutive levels under all conditions tested. Reduced chitin content, abnormal yeast clumpiness and budding kinetics, and increased melanin secretion resulted from the disruption of
WdCHS4
suggesting that WdChs4p influences cell wall structure, cellular reproduction, and melanin deposition, respectively. However, no significant loss of virulence was detected when the
wdchs4Δ
strain was tested in an acute mouse model. Using a
wdchs1Δ wdchs2Δ wdchs3Δ
triple mutant of
W. dermatitidis
, which grew poorly but adequately at 25°C, we assayed WdChs4p activity in the absence of activities contributed by its three other WdChs proteins. Maximal activity required trypsin activation, suggesting a zymogenic nature. The activity also had a pH optimum of 7.5, was most stimulated by Mg
2+
, and was more inhibited by polyoxin D than by nikkomycin Z. Although the WdChs4p activity had a broad temperature optimum between 30 to 45°C in vitro, this activity alone did not support the growth of the
wdchs1Δ wdchs2Δ wdchs3Δ
triple mutant at 37°C, a temperature commensurate with infection.
Differentiating
Taenia solium
and
Taenia saginata
Infections by Simple Hematoxylin-Eosin Staining and PCR-Restriction Enzyme Analysis
Authors: Mayta H. , Talley A. , Gilman R. H. , Jimenez J. , Verastegui M. , Ruiz M. , Garcia H. H. , Gonzalez A. E. 
Published: May 2021

ABSTRACT

Species-specific identification of human tapeworm infections is important for public health purposes, because prompt identification of
Taenia solium
carriers may prevent further human cysticercosis infections (a major cause of acquired epilepsy). Two practical methods for the differentiation of cestode proglottids, (i) routine embedding, sectioning, and hematoxylin-eosin (HE) staining and (ii) PCR with restriction enzyme analysis (PCR-REA), were tested on samples from 40 individuals infected with
T. solium
(
n
= 34) or
Taenia saginata
(
n
= 6). Microscopic examination of HE staining of sections from 24 cases, in which conserved proglottids were recovered, clearly revealed differences in the number of uterine branches. Distinct restriction patterns for
T. solium
and
T. saginata
were observed when the PCR products containing the ribosomal 5.8S gene plus internal transcribed spacer regions were digested with either
Alu
I,
Dde
I, or
Mbo
I. Both HE histology and PCR-REA are useful techniques for differentiating
T. solium
from
T. saginata
. Importantly, both techniques can be used in zones of endemicity. HE histology is inexpensive and is currently available in most regions of endemicity, and PCR-REA can be performed in most hospital centers already performing PCR without additional equipment or the use of radioactive material.
Differentiation among Members of the
Mycobacterium tuberculosis
Complex by Molecular and Biochemical Features: Evidence for Two Pyrazinamide-Susceptible Subtypes of
M. bovis
Authors: Niemann Stefan , Richter Elvira , Rüsch-Gerdes Sabine 
Published: May 2021

ABSTRACT

The variations in biochemical as well as molecular characteristics among several members of the
Mycobacterium tuberculosis
complex that are not
M. tuberculosis
have been assessed to facilitate an unambiguous species identification. Altogether, 96
M. tuberculosis
complex strains including 52
M. bovis
isolates and 44
M. africanum
isolates were analyzed by spoligotyping. The strains could be clustered into five spoligotype groups. All
M. bovis
isolates showed the typical absence of the spacers 39 to 43 and typical biochemical properties. However, within these strains we found a group of strains that had a spoligotype pattern which is clearly defined by the additional absence of spacers 3 to 16 and that were uncommonly susceptible to pyrazinamide (PZA). This spoligotype pattern has previously been described as being typical for a caprine genotype because of its predominant isolation from sheep and goats. Due to the clinical importance of PZA resistance, we propose two
M. bovis
subtypes:
M. bovis
subtype
bovis
, which is resistant to PZA, and
M. bovis
subtype
caprae
, which is susceptible to PZA. Two additional strains that clustered in group 3 showed biochemical and genetic properties typical for
M. bovis
and were also sensitive to PZA; thus, they may represent a third PZA-susceptible
M. bovis
subtype. The
M. africanum
isolates could be clustered into two spoligotype groups which can be differentiated from
M. bovis
by hybridization to spacers 39 to 43. These groups correspond to the previously described
M. africanum
subtypes I and II and can be clearly distinguished from each other by spoligotyping and resistance to thiophen-2-carboxylic acid hydrazide. Our results demonstrate that spoligotyping is a useful tool for differentiation of
M. bovis
and
M. africanum
. Moreover, we describe two PZA-susceptible
M. bovis
subtypes and describe a method that facilitates an unambiguous differentiation of the two
M. africanum
subtypes.
Identification of
Nocardia
Species by Restriction Endonuclease Analysis of an Amplified Portion of the 16S rRNA Gene
Authors: Conville Patricia S. , Fischer Steven H. , Cartwright Charles P. , Witebsky Frank G. 
Published: May 2021

ABSTRACT

Identification of clinical isolates of
Nocardia
to the species level is important for defining the spectrum of disease produced by each species and for predicting antimicrobial susceptibility. We evaluated the usefulness of PCR amplification of a portion of the
Nocardia
16S rRNA gene and subsequent restriction endonuclease analysis (REA) for species identification. Unique restriction fragment length polymorphism (RFLP) patterns were found for
Nocardia
sp. type strains (except for the
N. asteroides
type strain) and representative isolates of the drug pattern types of
Nocardia asteroides
(except for
N. asteroides
drug pattern type IV, which gave inconsistent amplification). A variant RFLP pattern for
Nocardia nova
was also observed. Twenty-eight clinical isolates were evaluated both by traditional biochemical identification and by amplification and REA of portions of the 16S rRNA gene and the 65-kDa heat shock protein (HSP) gene. There was complete agreement among the three methods on identification of 24 of these isolates. One isolate gave a 16S rRNA RFLP pattern consistent with the biochemical identification but was not identifiable by its HSP gene RFLP patterns. Three isolates gave 16S rRNA RFLP patterns which were inconsistent with the identification obtained by both biochemical tests and HSP gene RFLP; sequence analysis suggested that two of these isolates may belong to undefined species. The PCR and REA technique described appears useful both for the identification of clinical isolates of
Nocardia
and for the detection of new or unusual species.
Recovery of
Candida dubliniensis
from Non-Human Immunodeficiency Virus-Infected Patients in Israel
Authors: Polacheck Itzhack , Strahilevitz Jacob , Sullivan Derek , Donnelly Samantha , Salkin Ira F. , Coleman David C. 
Published: May 2021

ABSTRACT

Candida dubliniensis
is a recently discovered yeast species principally associated with carriage and disease in the oral cavities of human immunodeficiency virus (HIV)-infected individuals. To date the majority of isolates of this species have been identified in Europe and North America. In this study, five
Candida
isolates recovered from separate HIV-negative hospitalized patients in Jerusalem, Israel, were presumptively identified as
C. dubliniensis
on the basis of their dark green coloration when grown on CHROMagar Candida medium. Their identification was confirmed by a variety of techniques, including carbohydrate assimilation profiles, absence of growth at 45°C, positive reaction with
C. dubliniensis
-specific antibodies as determined by indirect immunofluorescence analysis, and positive amplification with
C. dubliniensis
-specific PCR primers. All five strains were shown to be susceptible to a range of antifungal agents, including fluconazole. One of the five isolates was recovered from urine specimens, while the remaining four were recovered from upper respiratory tract and oral samples. While none of the patients was HIV positive, all were receiving broad-spectrum antibacterials at the time isolates of
C. dubliniensis
were obtained from clinical specimens. This study describes the first isolates of
C. dubliniensis
from the Middle East and confirms that this yeast can be associated with carriage and infection in the absence of HIV infection.
Escherichia coli
Serotype O15:K52:H1 as a Uropathogenic Clone
Authors: Prats Guillem , Navarro Ferran , Mirelis Beatriz , Dalmau David , Margall Nuria , Coll Pere , Stell Adam , Johnson James R. 
Published: May 2021

ABSTRACT

To clarify the clinical and bacteriological correlates of urinary-tract infection (UTI) due to
Escherichia coli
O15:K52:H1, during a 1-year surveillance period we prospectively screened all 1,871 significant
E. coli
urine isolates at the Hospital de la Santa Creu i Sant Pau, Barcelona, Spain, for this serotype and assessed the epidemiological features of community-acquired UTI due to
E. coli
O15:K52:H1 versus other
E. coli
serotypes. We also compared the 25 O15:K52:H1 UTI isolates from the present study with 22 O15:K52:H1 isolates from other, diverse geographic locales and with 23 standard control strains (8 strains from the ECOR reference collection and 15 strains of nonpathogenic O:K:H serotypes) with respect to multiple phenotypic and genotypic traits. Although
E. coli
O15:K52:H1 caused only 1.4% of community-acquired
E. coli
UTIs during the surveillance period, these UTIs were more likely to present as pyelonephritis and to occur in younger hosts, with similar risk factors, than were UTIs due to other
E. coli
serotypes. Irrespective of geographic origin,
E. coli
O15:K52:H1 strains exhibited a comparatively restricted repertoire of distinctive virulence factor profiles (typically, they were positive for
papG
allele II,
papA
allele F16, and
aer
and negative for
sfa
,
afa
,
hly
, and
cnf1
), biotypes, ribotypes, and amplotypes, consistent with a common clonal origin. In contrast, their antimicrobial resistance profiles were more extensive and more diverse than those of control strains. These findings indicate that
E. coli
O15:K52:H1 constitutes a broadly distributed and clinically significant uropathogenic clone with fluid antimicrobial resistance capabilities.
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

ABSTRACTThe 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

ABSTRACT
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

ABSTRACT

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
.