cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125198
title: Supplementary Material for: Effects of Buffering Properties and Undissociated Acid Concentration on Dissolution of Dental Enamel in Relation to pH and Acid Type

description: To quantify the relationships between buffering properties and acid erosion and hence improve models of erosive potential of acidic drinks, a pH-stat was used to measure the rate of enamel dissolution in solutions of citric, malic and lactic acids, with pH 2.4-3.6 and with acid concentrations adjusted to give buffer capacities (β) of 2-40 (mmol·l<sup>-1</sup>)·pH<sup>-1</sup> for each pH. The corresponding undissociated acid concentrations, [HA], and titratable acidity to pH 5.5 (TA<sub>5.5</sub>) were calculated. In relation to β, the dissolution rate and the strength of response to β varied with acid type (lactic &gt; malic ≥ citric) and decreased as pH increased. The patterns of variation of the dissolution rate with TA<sub>5.5</sub> were qualitatively similar to those for β, except that increasing pH above 2.8 had less effect on dissolution in citric and malic acids and none on dissolution in lactic acid. Variations of the dissolution rate with [HA] showed no systematic dependence on acid type but some dependence on pH. The results suggest that [HA], rather than buffering per se, is a major rate-controlling factor, probably owing to the importance of undissociated acid as a readily diffusible source of H<sup>+</sup> ions in maintaining near-surface dissolution within the softened layer of enamel. TA<sub>5.5</sub> was more closely correlated with [HA] than was β, and seems to be the preferred practical measure of buffering. The relationship between [HA] and TA<sub>5.5</sub> differs between mono- and polybasic acids, so a separate analysis of products according to predominant acid type could improve multivariate models of erosive potential.
DOI: 10.6084/m9.figshare.5125201
title: Supplementary Material for: Attitudes and Behaviour regarding Deep Dentin Caries Removal: A Survey among German Dentists

description: Incomplete removal of deep caries has been shown to reduce the risks of pulp exposure and postoperative pulpal complications. It is therefore of interest whether dentists perform one- or two-step incomplete excavation, and which criteria and methods they use to assess and provide removal of deep caries. This study investigated the attitudes and behaviour of dentists in northern Germany using a new, validated questionnaire. The survey included 2,346 practitioners, 821 (35%) of whom responded. Demographic and sensitivity analysis did not indicate selection bias. 50% of dentists considered only complete excavation, even if pulp exposure was likely. If caries was to be removed incompletely, 77% considered two-step excavation. Hardness was the most important criterion to assess excavation. To treat an exposed pulp, 75% of dentists considered direct capping, 70% refused incomplete excavation fearing caries progression or pulp damage, and 59% reported to prefer more invasive treatment to facilitate restoration longevity. Over 50% recognised an influence of professional regulations on their treatment decisions. There was a moderate correlation between attitudes and behaviour of dentists, with dentists who suspected residual caries to be harmful rejecting incomplete excavation and vice versa. Cluster analysis identified two groups of dentists with opposite attitudes and behaviour, independently from dentist's age or gender. In conclusion, the majority of surveyed dentists was sceptical about leaving caries during excavation and does not practice incomplete caries removal. Therefore, benefits of partial excavation should be highlighted in under- and postgraduate education and regulatory incentives modified to promote minimally invasive techniques.
DOI: 10.6084/m9.figshare.5125195
title: Supplementary Material for: Molecular Epidemiology and Genetic History of Hepatitis C Virus Subtype 3a Infection in Thailand

description: <b><i>Objective:</i></b> Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. <b><i>Methods:</i></b> Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. <b><i>Results:</i></b> Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. <b><i>Conclusion:</i></b> The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.
DOI: 10.6084/m9.figshare.5125198.v1
title: Supplementary Material for: Effects of Buffering Properties and Undissociated Acid Concentration on Dissolution of Dental Enamel in Relation to pH and Acid Type

description: To quantify the relationships between buffering properties and acid erosion and hence improve models of erosive potential of acidic drinks, a pH-stat was used to measure the rate of enamel dissolution in solutions of citric, malic and lactic acids, with pH 2.4-3.6 and with acid concentrations adjusted to give buffer capacities (β) of 2-40 (mmol·l<sup>-1</sup>)·pH<sup>-1</sup> for each pH. The corresponding undissociated acid concentrations, [HA], and titratable acidity to pH 5.5 (TA<sub>5.5</sub>) were calculated. In relation to β, the dissolution rate and the strength of response to β varied with acid type (lactic &gt; malic ≥ citric) and decreased as pH increased. The patterns of variation of the dissolution rate with TA<sub>5.5</sub> were qualitatively similar to those for β, except that increasing pH above 2.8 had less effect on dissolution in citric and malic acids and none on dissolution in lactic acid. Variations of the dissolution rate with [HA] showed no systematic dependence on acid type but some dependence on pH. The results suggest that [HA], rather than buffering per se, is a major rate-controlling factor, probably owing to the importance of undissociated acid as a readily diffusible source of H<sup>+</sup> ions in maintaining near-surface dissolution within the softened layer of enamel. TA<sub>5.5</sub> was more closely correlated with [HA] than was β, and seems to be the preferred practical measure of buffering. The relationship between [HA] and TA<sub>5.5</sub> differs between mono- and polybasic acids, so a separate analysis of products according to predominant acid type could improve multivariate models of erosive potential.
DOI: 10.6084/m9.figshare.5125204.v1
title: Supplementary Material for: A Tissue-Dependent Hypothesis of Dental Caries

description: Current understanding of dental caries considers this disease a demineralization of the tooth tissues due to the acid produced by sugar-fermenting microorganisms. Thus, caries is considered a diet- and pH-dependent process. We present here the first metagenomic analysis of the bacterial communities present at different stages of caries development, with the aim of determining whether the bacterial composition and biochemical profile are specific to the tissue affected. The data show that microbial composition at the initial, enamel-affecting stage of caries is significantly different from that found at subsequent stages, as well as from dental plaque of sound tooth surfaces. Although the relative proportion of <i>Streptococcus mutans</i> increased from 0.12% in dental plaque to 0.72% in enamel caries, <i>Streptococcus mitis</i> and <i>Streptococcus sanguinis</i> were the dominant streptococci in these lesions. The functional profile of caries-associated bacterial communities indicates that genes involved in acid stress tolerance and dietary sugar fermentation are overrepresented only at the initial stage (enamel caries), whereas other genes coding for osmotic stress tolerance as well as collagenases and other proteases enabling dentin degradation are significantly overrepresented in dentin cavities. The results support a scenario in which pH and diet are determinants of the disease during the degradation of enamel, but in dentin caries lesions not only acidogenic but also proteolytic bacteria are involved. We propose that caries disease is a process of varying etiology, in which acid-producing bacteria are the vehicle to penetrate enamel and allow dentin degrading microorganisms to expand the cavity.
DOI: 10.6084/m9.figshare.5125186
title: Supplementary Material for: Clinicians' Attitudes toward General Screening of the Ashkenazi-Jewish Population for Prevalent Founder <b><i>BRCA1/2</i></b> and <b><i>LRRK2</i></b> Mutations

description: <b><i>Aims:</i></b> Advances in genomics may eventually lead to genetic susceptibility screening of the general population, regardless of a personal or familial history of the disease in question. Yet, little is known about clinicians' attitudes toward such programs. We explored attitudes of family practitioners, medical geneticists and genetic counselors toward genetic screening of the general Ashkenazi-Jewish population for the common founder mutations in <i>BRCA1/2</i> and <i>LRRK2</i> genes (which increase the risk of hereditary breast/ovarian cancers and Parkinson's disease, respectively). <b><i>Methods:</i></b> Participants (n = 204) completed a specially designed questionnaire, distributed by e-mail, regular mail or in-person. <b><i>Results:</i></b> Slightly more than half (52%) were in favor of <i>BRCA</i> screening, while the vast majority (86%) opposed to <i>LRRK2</i> screening. About two-thirds (68%) of the respondents supported pre-test genetic counseling. Attitudes were largely independent of professional background and sociodemographic characteristics, though a correlation was found with personal interest in genetic self-testing for the above genes. Adverse psychological impact and discrimination in insurance and employment were the major concerns cited by respondents with regard to screening programs. <b><i>Conclusion:</i></b> Our findings suggest that the availability of measures for prevention and/or treatment is a major factor in the attitudes of healthcare providers toward population screening for late-onset conditions.
DOI: 10.6084/m9.figshare.5125189
title: Supplementary Material for: Immunostaining of Pulpal Nerve Fibre Bundle/Arteriole Associations in Ground Serial Sections of Whole Human Teeth Embedded in Technovit® 9100

description: A technique for embedding human undecalcified tooth specimens in Technovit® 9100 was developed, which permits immunohistological evaluation of pulp tissue in serial ground sections. Human molars were divided into 14-18 sections of about 23 µm thickness. Immunohistological double staining for S-100 and CD34 revealed unique associations of myelinated nerve fibre bundles with arterioles, which continued through the entire tooth pulp. These arterioles were not only accompanied by, but partially or totally enveloped in longitudinally orientated myelinated nerve fibre bundles. We speculate that this unique arrangement may mechanically support the arterioles and alleviate detection or regulation of their contraction state by sensory nerve cells.
DOI: 10.6084/m9.figshare.5125195.v1
title: Supplementary Material for: Molecular Epidemiology and Genetic History of Hepatitis C Virus Subtype 3a Infection in Thailand

description: <b><i>Objective:</i></b> Among all hepatitis C virus (HCV) infections, subtype 3a is the most common genotype in Thailand. This study investigates the molecular epidemiology and epidemic history of HCV subtype 3a in Thailand. <b><i>Methods:</i></b> Three hundred and fifty-six serum samples were collected from HCV-infected Thai patients. The virus was isolated, after which the core and NS5B regions were sequenced. Subsequently, the HCV genotype was classified by phylogenetic analysis based on the core and NS5B regions. Molecular evolution analysis of HCV subtype 3a was estimated using BEAST (Bayesian Evolutionary Analysis by Sampling Trees) v.1.5.4. <b><i>Results:</i></b> Based on our phylogenetic analyses, subtype 3a (38.5%) was the most prevalent, followed by 1a (21%), 1b (13.8%), genotype 6 (19.9%) [comprised of subtypes 6e (0.3%), 6f (11%), 6i (1.9%), 6j (1.9%) and 6n (4.8%)] and 3b (5.6%). Our phylogenetic tree indicates the existence of a specific group of HCV subtype 3a strains in the Thai population. Molecular evolutionary analysis dated the most recent common ancestor of the Thai HCV subtype 3a strains as existing approximately 200 ago, and a Bayesian skyline plot showed that this particular strain spread to Thailand during the mid-1970s and early 1980s. This period overlaps with the Vietnam War (1955-1975) and the widespread use of injection stimulants introduced by the US Army during this time. <b><i>Conclusion:</i></b> The estimated history of HCV subtype 3a infection in Thailand may help to predict the future burden of HCV-related diseases and facilitate better public health control and surveillance.
DOI: 10.6084/m9.figshare.5125201.v1
title: Supplementary Material for: Attitudes and Behaviour regarding Deep Dentin Caries Removal: A Survey among German Dentists

description: Incomplete removal of deep caries has been shown to reduce the risks of pulp exposure and postoperative pulpal complications. It is therefore of interest whether dentists perform one- or two-step incomplete excavation, and which criteria and methods they use to assess and provide removal of deep caries. This study investigated the attitudes and behaviour of dentists in northern Germany using a new, validated questionnaire. The survey included 2,346 practitioners, 821 (35%) of whom responded. Demographic and sensitivity analysis did not indicate selection bias. 50% of dentists considered only complete excavation, even if pulp exposure was likely. If caries was to be removed incompletely, 77% considered two-step excavation. Hardness was the most important criterion to assess excavation. To treat an exposed pulp, 75% of dentists considered direct capping, 70% refused incomplete excavation fearing caries progression or pulp damage, and 59% reported to prefer more invasive treatment to facilitate restoration longevity. Over 50% recognised an influence of professional regulations on their treatment decisions. There was a moderate correlation between attitudes and behaviour of dentists, with dentists who suspected residual caries to be harmful rejecting incomplete excavation and vice versa. Cluster analysis identified two groups of dentists with opposite attitudes and behaviour, independently from dentist's age or gender. In conclusion, the majority of surveyed dentists was sceptical about leaving caries during excavation and does not practice incomplete caries removal. Therefore, benefits of partial excavation should be highlighted in under- and postgraduate education and regulatory incentives modified to promote minimally invasive techniques.
DOI: 10.6084/m9.figshare.5125180
title: Supplementary Material for: Chicken MDA5 Senses Short Double-Stranded RNA with Implications for Antiviral Response against Avian Influenza Viruses in Chicken

description: Mammalian melanoma differentiation-associated gene-5 (MDA5) and retinoic acid-inducible gene-I (RIG-I) selectively sense double-stranded RNA (dsRNA) according to length, as well as various RNA viruses to induce an antiviral response. RIG-I, which plays a predominant role in the induction of antiviral responses against influenza virus infection, has been considered to be lacking in chicken, putting the function of chicken MDA5 (chMDA5) under the spotlight. Here, we show that chMDA5, unlike mammalian MDA5, preferentially senses shorter dsRNA synthetic analogues, poly(I:C), in chicken DF-1 fibroblasts. A requirement for caspase activation and recruitment domains for chMDA5-mediated chicken interferon beta (chIFNβ) induction and its interaction with mitochondrial antiviral signaling proteins were demonstrated. We also found that chMDA5 is involved in chIFNβ induction against avian influenza virus infection. Our findings imply that chMDA5 compensates in part the function of RIG-I in chicken, and highlights the importance of chMDA5 in the innate immune response in chicken.
DOI: 10.6084/m9.figshare.5125183
title: Supplementary Material for: Thymosin α<sub>1</sub> Activates Complement Receptor-Mediated Phagocytosis in Human Monocyte-Derived Macrophages

description: Thymosin α<sub>1</sub> (Tα1) is a naturally occurring thymic peptide used worldwide in clinical trials for the treatment of infectious diseases and cancer. The immunomodulatory activity of Tα1 on innate immunity effector cells has been extensively described, but its mechanism of action is not completely understood. We report that Tα1-exposed human monocyte-derived macrophages (MDMs) assume the typical activated morphology also exhibited by lipopolysaccharide-activated MDMs, but show a comparatively higher ability of internalizing fluorescent beads and zymosan particles. Tα1 exposure also promptly and dramatically stimulates MDM phagocytosis and killing of <i>Aspergillus niger</i> conidia starting as soon as 30 min after challenge. The effect is dose dependent and early coupled to low transcription of the proinflammatory cytokines tumor necrosis factor α and interleukin-6 and unmodified Toll-like receptor expression. The Tα1-stimulated phagocytosis is strictly dependent on the integrity of the microtubule network and protein kinase C activity and occurs by a variation in the classic zipper model, with recruitment of vinculin and actin at the phagosome exhibiting a punctate distribution. These findings indicate that, in human mature MDMs, Tα1 implements pathogen internalization and killing via the stimulation of the complement receptor-mediated phagocytosis. Our observations document that Tα1 is an early and potent activator of innate immunity and reinforce the concept of its pleiotropy.
DOI: 10.6084/m9.figshare.5125189.v1
title: Supplementary Material for: Immunostaining of Pulpal Nerve Fibre Bundle/Arteriole Associations in Ground Serial Sections of Whole Human Teeth Embedded in Technovit® 9100

description: A technique for embedding human undecalcified tooth specimens in Technovit® 9100 was developed, which permits immunohistological evaluation of pulp tissue in serial ground sections. Human molars were divided into 14-18 sections of about 23 µm thickness. Immunohistological double staining for S-100 and CD34 revealed unique associations of myelinated nerve fibre bundles with arterioles, which continued through the entire tooth pulp. These arterioles were not only accompanied by, but partially or totally enveloped in longitudinally orientated myelinated nerve fibre bundles. We speculate that this unique arrangement may mechanically support the arterioles and alleviate detection or regulation of their contraction state by sensory nerve cells.
DOI: 10.6084/m9.figshare.5125192
title: Supplementary Material for: Involvement of Heat Shock Proteins in <b><i>Candida albicans</i></b> Biofilm Formation

description: Biofilm growth represents one of the most challenging problems associated with <i>Candida</i> infections, largely due to the natural resistance of biofilm to the common antifungal drugs. As elevated expression of heat shock proteins (HSP) promotes <i>Candida</i> yeast-hyphae switch, which is an essential step in biofilm formation, we investigated the expression of <i>hsp</i> genes during <i>Candida albicans</i> biofilm development. By measuring mRNA levels using qRT-PCR, we found that all three <i>hsp</i> genes that we monitored are overexpressed in the initial stage of <i>C. albicans</i> biofilm formation. To corroborate this finding, we examined the effect of 17-DMAG, a specific Hsp90 inhibitor, on the formation of <i>C. albicans</i> biofilm. Our results indicate the requirement of HSP during the early phase of <i>Candida</i> biofilm development.
DOI: 10.6084/m9.figshare.5125180.v1
title: Supplementary Material for: Chicken MDA5 Senses Short Double-Stranded RNA with Implications for Antiviral Response against Avian Influenza Viruses in Chicken

description: Mammalian melanoma differentiation-associated gene-5 (MDA5) and retinoic acid-inducible gene-I (RIG-I) selectively sense double-stranded RNA (dsRNA) according to length, as well as various RNA viruses to induce an antiviral response. RIG-I, which plays a predominant role in the induction of antiviral responses against influenza virus infection, has been considered to be lacking in chicken, putting the function of chicken MDA5 (chMDA5) under the spotlight. Here, we show that chMDA5, unlike mammalian MDA5, preferentially senses shorter dsRNA synthetic analogues, poly(I:C), in chicken DF-1 fibroblasts. A requirement for caspase activation and recruitment domains for chMDA5-mediated chicken interferon beta (chIFNβ) induction and its interaction with mitochondrial antiviral signaling proteins were demonstrated. We also found that chMDA5 is involved in chIFNβ induction against avian influenza virus infection. Our findings imply that chMDA5 compensates in part the function of RIG-I in chicken, and highlights the importance of chMDA5 in the innate immune response in chicken.
DOI: 10.6084/m9.figshare.5125177
title: Supplementary Material for: Impact of Age on the Management of Primary Melanoma Patients

description: <b><i>Objectives:</i></b> Age is an understudied factor when considering treatment options for melanoma. Here, we examine the impact of age on primary melanoma treatment in a prospective cohort of patients. <b><i>Methods:</i></b> We used logistic regression models to examine the associations between age and initial treatment, using recurrence and melanoma-specific survival as endpoints. <b><i>Results:</i></b> 444 primary melanoma patients were categorized into three groups by age at diagnosis: 19-45 years (24.3%), 46-70 (50.2%), and 71-95 (25.5%). In multivariate models, older patients experienced a higher risk of recurrence (hazard ratio 3.34, 95% confidence interval, CI, 1.53-7.25; p &lt; 0.01). No significant differences were observed in positive biopsy margin rates or extent of surgical margins across age groups. Patients in the middle age group were more likely to receive adjuvant therapy than those in the older group (odds ratio 2.78, 95% CI 1.19-6.45; p = 0.02) and showed a trend to longer disease-free survival when receiving adjuvant therapy (p = 0.09). <b><i>Conclusion:</i></b> Our data support age as an independent negative prognostic factor in melanoma. Our data suggest that age does not affect primary surgical treatment but may affect decisions of whether or not patients receive postoperative treatment(s). Further work is needed to better understand the biological variables affecting treatment decisions and efficacy in older patients.