cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21929901
title: Supplementary Material for: Nucleotide Sequence and Chromosome mapping of 5S Ribosomal DNA from the Dojo Loach, Misgurnus anguillicaudatus

description: There are 2 genetically divergent groups in the dojo loach Misgurnus anguillicaudatus: A and B. Although most wild-type diploids reproduce sexually, clonal diploids (clonal loach) reproduce gynogenetically in certain areas. Clonal loaches produce unreduced isogenic eggs by premeiotic endomitosis, and such diploid eggs develop gynogenetically following activation by the sperm of sympatric wild-type diploids. These clonal loaches have presumably arisen from past hybridization events between 2 different ancestors. The genomic differences between these 2 groups have not been completely elucidated. Thus, new genetic and cytogenetic markers are required to distinguish between these 2 groups. Here, we compared the 5S rDNA region to develop markers for the identification of different dojo loach groups. The nontranscribed sequence (NTS) of the 5S rDNA was highly polymorphic and group-specific. NTS sequences were found in clades of 2 different groups in clonal loaches. In contrast, we did not find any group-specific sequences in the coding region of the 5S rRNA gene. Sequences were located near the centromere of the short arm of the largest submetacentric chromosomes in groups A and B and clonal loaches. Thus, the 5S rDNA of the dojo loach is conserved at the chromosomal location. Whereas, the sequences of the NTS regions evolved group-specifically in the dojo loach, with the sequences of both groups being conserved in clonal loaches.
DOI: 10.6084/m9.figshare.22021640
title: Supplementary Material for: The Effects of Different Sources and Modalities of Stuttering Disclosure on Listeners' Perceptions of a Child who Stutters

description: Introduction: Research reveals the clinical efficacy of both verbal and written stuttering disclosure statements provided by a child who stutters (CWS) and his advocates (i.e., mother or teacher) [1,2]. Although existing data reveals that both the source (i.e., self- vs. advocate-disclosure) and modality (i.e., verbal or written) of stuttering disclosure yields significant improvements in the perceptions of speech skills and personality characteristics of CWS, there is a paucity of research directly comparing the modality (verbal vs. written) and source (self, mother, teacher) of disclosure statements. Accordingly, this study analyzes listeners’ perceptions of a 12-year-old male CWS’ speech skills and personal characteristics, as a function of both the source and modality of factual stuttering disclosure statements [1,2]. Methods: A total of 641 college-aged adults participated in this analysis; study participants reported their perceptions of speech skills and personality characteristics of a 12 year-old CWS as a function of stuttering disclosure. Participants were randomly assigned to view one video containing one of two disclosure modalities (verbal or written), and one of three stuttering disclosure source conditions (self-disclosure, mother disclosure, teacher disclosure), or a no disclosure control condition. Participants in the control group viewed a brief video of a 12-year-old CWS reciting a short reading passage; participants in the experimental groups viewed their assigned disclosure statement followed by the same video used in the control condition. Immediately following the video, all participants completed a survey quantifying their perceptions of the child who stutters relative to his speech skills and personal characteristics. Results: Results reveal optimal results via verbal self-disclosure and verbal teacher disclosure. A limited number of nominally positive perceptual differences were noted within the written mother-disclosure group, while written CWS self-disclosure yielded significantly negative perceptions of the CWS. Overall, verbal disclosures yields far more significant and desirable perceptions of CWS’ speech skills and personal characteristics when compared to written stuttering disclosure. Discussion/Conclusion: Results of this analysis reveal that verbal stuttering disclosure is significantly more effective in improving listeners’ perceptions of a CWS, when compared to written stuttering disclosures. Despite the widespread adoption of written communication over digital media (e.g., email and text messages), these data support the notion that face-to-face or video verbal stuttering disclosure provide the most desirable perceptual benefits for CWS. Within verbal stuttering disclosure, verbal self-disclosure appears to be the single best overall disclosure methodology relative to clinical application.
DOI: 10.6084/m9.figshare.22147382
title: Supplementary Material for: Impact of macrocephaly, as an isolated trait, on EEG signal as measured by spectral power and multiscale entropy during the first year of life

description: Macrocephaly has been associated with neurodevelopmental disorders; however, it has been mainly studied in the context of pathological or high-risk populations and little is known about its impact, as an isolated trait, on brain development in general population. Electroencephalographic (EEG) power spectral density (PSD) and signal complexity have shown to be sensitive to neurodevelopment and its alterations. We aimed to investigate the impact of macrocephaly as isolated trait on EEG signal as measured by power spectral density (PSD) and Multiscale Entropy (MSE) during the first year of life. We recorded high density EEG resting state activity of 74 healthy full-term infants, 50 control (26 girls) and 24 macrocephalic (12 girls) aged between 3 and 11 months. We used linear regression models to assess group and age effects on EEG power spectral density (PSD) and signal complexity. Sex and brain volume measures, obtained via a 3D transfontanellar ultrasound, were also included into the models to evaluate their contribution. Our results showed lower PSD of the low alpha (8-10Hz) frequency band and lower complexity in the macrocephalic group compared to the control group. In addition, we found an increase in low alpha (8.5-10Hz) PSD and in the complexity index with age. These findings suggest that macrocephaly as an isolated trait has a significant impact on brain activity during the first year of life.
DOI: 10.6084/m9.figshare.22182145
title: Supplementary Material for: Cytogenetic analysis of the fungus-farming ant Cyphomyrmex rimosus (Spinola, 1851) (Formicidae: Myrmicinae: Attini) highlights karyotypic variation

description: The fungus-farming ant genus Cyphomyrmex (subtribe Attina, clade Neoattina) comprises 23 described species that are widely distributed throughout the Neotropics. Species within Cyphomyrmex have taxonomic issues such as Cyphomyrmex rimosus (Spinola, 1851) which is likely a species complex. Cytogenetics is a useful tool for evolutionary studies and understanding species with dubious taxonomy. In this study, we characterized the karyotype of C. rimosus from Viçosa, Minas Gerais state, southeastern Brazil using classical and molecular cytogenetic techniques to enrich the chromosomal information about Cyphomyrmex. The karyotype of C. rimosus from the rainforest of southeastern Brazil (2n = 22, 18m + 4sm) notably contrasts with that previously described for this species in Panama (2n = 32). This intraspecific chromosomal variation suggests the existence of a species complex within this taxon according to the previous hypothesis derived from morphological analysis. We detected GC-rich heterochromatic regions in C. rimosus and using repetitive DNA probes showed that this heterochromatin shares repetitive sequences with other Neoattina species already studied, enhancing the importance of this specific genome region in the understanding of Attina evolution. Mapping of microsatellite (GA)15 on C. rimosus was restricted to the euchromatic regions of all chromosomes. The single intrachromosomal rDNA sites observed in C. rimosus follow the general genomic organization trend of ribosomal genes in Formicidae. Our study extends the data of chromosome mapping on Cyphomyrmex and reinforces the importance of cytogenetic studies in different localities to better understand taxonomic issues in widely distributed taxa such as C. rimosus.
DOI: 10.6084/m9.figshare.22193290
title: Supplementary Material for: Pure Interstitial Trisomy 11q Arising from a Nonrecurrent 11q13.1q22.3 Mosaic Intrachromosomal Duplication in a Patient with Craniofacial Dysmorphism and Genital Anomalies

description: <b><i>Introduction:</i></b> The pure interstitial trisomy 11q11q23.2 is an uncommon genomic disorder associated with nonrecurrent intrachromosomal duplications. The phenotype is characterized by intellectual disability and craniofacial abnormalities. Given their uncommonness, a comprehensive genotype-phenotype correlation has not fully been defined. <b><i>Case Presentation:</i></b> We report the clinical and cytogenomic characterization of a 5-year-old boy with intellectual disability, psychomotor retardation, craniofacial dysmorphism, genital anomalies, and pure interstitial trisomy 11q arising from a nonrecurrent 11q13.1q22.3 intrachromosomal duplication in a high-mosaic state (&gt;80%). The duplicated chromosome was characterized by cytogenetics, multicolor banding FISH, and SNP array. We demonstrated the wide mosaic distribution of the 11q duplication by interphase FISH in tissues from different embryonic germ layers. The duplication involves a copy number gain of 45.3 Mb containing 22 dosage-sensitive genes. We confirmed the overexpression of dosage-sensitive genes along the duplicated region using RT-qPCR. <b><i>Discussion:</i></b> Only 8 patients have been described. Our patient shares clinical features with previous reports but differs from them by the presence of genital anomalies. We provide a detailed clinical review and an accurate genotype-phenotype correlation and propose <i>PC</i>, <i>NDUFV1</i>, <i>FGF3</i>, <i>FGF4</i>, and <i>DHCR7</i> as dosage-sensitive genes with a possible role in the clinical spectrum of our patient; however, expression changes of <i>FGF3/4</i> were not detected since they must be regulated in a spatiotemporal way. This patient contributes to the accurate description of the pure interstitial trisomy 11q. Future reports could continue to delineate the description, considering the relationship between the chromosome segment and the genes involved.
DOI: 10.6084/m9.figshare.22232029
title: Supplementary Material for: Renal Lipoma-Like Angiomyolipoma of Tumour Thrombus Extending to the Confluence of Inferior Vena Cava with Right Atrium: A Rare Case Report and Literature Review

description: Angiomyolipoma (AML) complicated with tumour thrombus extending to the confluence of inferior vena cava (IVC) with right atrium is rarely observed. We report a female AML patient admitted to our centre on January 21, 2020, with complication of tumour thrombus extending to the confluence of IVC with right atrium and had no sign of difficult breathing. She underwent whole-abdominal enhanced CT for abdominal pain and was diagnosed with a possible renal AML with tumour thrombus. Open radical nephrectomy and thrombectomy of vena cava were performed. Intraoperative transoesophageal echocardiography indicated that the tumour thrombus has reached the confluence of IVC with right atrium. The operation took 255 min with an intraoperative haemorrhage of 800mL. The patient was discharged 7 days after surgery. Pathology revealed lipoma-like AML. Immunohistochemistry showed vimentin (+), EMA (−), HMB45 (+), S-100 (−), SMA (+), TFE-3 (−), melan A (+). After 2 years of follow-up, we found that the patient showed full recovery and had no recurrence. Therefore, lipoma-like AML should also be followed closely for recurrence and metastasis. When AML involves IVC tumour thrombus, open thrombectomy and radical nephrectomy are safe and effective methods.
DOI: 10.6084/m9.figshare.22346569
title: Supplementary Material for: Genomic and Immune Features in an Intrahepatic Cholangiocarcinoma Patient with Microsatellite Instability-High Suffered Rapid Acquired Resistance to PD-1 Inhibitor

description: Introduction: Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive liver malignancy with poor prognosis. Recently, the development of immune checkpoint inhibitors (ICIs), such as programmed cell death 1 (PD-1) inhibitors, has emerged as a promising strategy in multiple tumor types, including ICC. Microsatellite instability-high (MSI-H) is an important biomarker for ICIs in solid tumors. The response rate in patients with MSI-H is significantly higher than in those with microsatellite stability/ microsatellite instability-low (MSS/MSI-L). And approximately 80% to 90% of the patients with MSI-H could maintain sustained clinical benefits once they had an initial response. However, some patients could have primary resistance at the beginning, and some might have acquired resistance after long-term treatment. Case Presentation: We present the case of an ICC patient with MSI-H who suffered rapid progression after a short-term remission with Camrelizumab, a kind of PD-1 inhibitor, as second-line treatment. The patient’s genomic and immune features were analyzed by next-generation sequencing and multiplex immunofluorescence staining (mIF) to explore the possible mechanisms of the rapidly acquired resistance of ICIs in this MSI-H case. Discussion/Conclusion: The genomic and immunohistochemical analysis showed that TGFBR2 mutation, loss of HLA B44 supertype, carrying B62 supertype, and increased PD-L1+ cells, macrophages and Tregs in the tumor microenvironment might be related to the non-sustain benefit of ICIs in this MSI-H patient.
DOI: 10.6084/m9.figshare.22360795
title: Supplementary Material for: A Missense Pathogenic Variant in a Conserved Region of <b><i>CNTNAP2</i></b> Is Associated with Obesity, Seizures, and Language Impairment in a Pakistani Family

description: <b><i>Introduction:</i></b> In a consanguineous family, seven siblings born in three sibships showed a syndromic disorder characterized by obesity, seizures, and language impairment phenotypes, which appeared at early age or developed during early childhood. <b><i>Methods:</i></b> By whole-exome sequencing and subsequent Sanger sequencing, a novel homozygous missense variant (c.3371 T&gt;A [p.Ile1124Asn]) in exon 20 of the <i>CNTNAP2</i> gene was identified. <b><i>Results:</i></b> The pathogenic variant in this family is located within one of the laminin G-like 4 domains of CASPR2 and may cause loss of hydrophobic interactions of CASPR2 with its partner proteins. Single nucleotide and copy number variants in this gene have previously been related to Gilles de la Tourette syndrome, cortical dysplasia-focal epilepsy syndrome, schizophrenia, Pitt-Hopkins syndrome, and autism spectrum, attention deficit hyperactivity, and obsessive compulsive disorders. Yet, few studies described patients with <i>CNTNAP2</i> variants showing diet-induced obesity. <b><i>Conclusion:</i></b> This report expands the phenotypic spectrum of this rare syndrome and provides deeper insights by documenting the clinical features and genetic findings of the patients.
DOI: 10.6084/m9.figshare.22495153
title: Supplementary Material for: Single session Fractional CO2 laser following Urea occlusion in management of onychomycosis - A pilot study

description: Introduction Onychomycosis is a common nail disorders. Antifungal resistance, interactions and side-effects limit treatment options. Fractional CO2 laser(FCO2) along with topical antifungal is effective in multiple monthly sessions. A modification reducing repeated visits and hence, better compliance is preferable. Single-session FCO2 laser following urea occlusion is reported to be effective. Thus, we conducted a study to determine the efficacy of single-session of FCO2 laser with 1%terbinafine cream with and without ‘urea cream occlusion’ in managing onychomycosis. Methods Prospective, randomized, parallel-group study conducted at a tertiary centre. Onychomycosis was confirmed by positive fungal mount and culture. Patients were randomized into 2-groups and administered single-session of FCO2 Laser. Group-A treated after overnight urea cream occlusion and Group-B without occlusion. Both groups applied 1%terbinafine cream twice daily for 3 months. Response was assessed by improvement in Onychomycosis Severity Index(OSI) at 6 months. Results Group-A had 10 patients, 14 nails. Clinical improvement was seen in 12/14(85.7%) nails. Average reduction in OSI was 10.78. Group-B had 10 patients, 11 nails. Clinical improvement was seen in 5/11(45.5%) nails. Average reduction in OSI was 1.73. ‘Reduction in OSI’ was statistically significant(P&lt;0.05) only in group-A. Conclusion Single-session FCO2 laser following overnight Urea cream occlusion, followed by 1%terbinafine cream is effective for management of onychomycosis.
DOI: 10.6084/m9.figshare.22682509
title: Supplementary Material for: Diagnostic gene panel testing in (non)-syndromic patients with cleft lip, alveolus and/or palate in the Netherlands.

description: ABSTRACT Objectives Clefts of the lip, alveolus and/or palate (CLA/P) are the most common craniofacial congenital malformations in humans. These oral clefts can be divided into non-syndromic (isolated) and syndromic forms. Many cleft-related syndromes are clinically variable and genetically heterogeneous, making it challenging to distinguish syndromic from non-syndromic cases. Recognition of syndromic/genetic causes is important for personalized tailored care, identification of (unrecognized) co-morbidities and accurate genetic counseling. Therefore, Next Generation Sequencing (NGS) based targeted gene panel testing is increasingly implemented in diagnostics of CLA/P patients. In this retrospective study we assess the yield of NGS gene panel testing in a cohort of CLA/P cases. Methods Whole exome sequencing followed by variant detection and interpretation in an a-priori selected set of genes associated with CLA/P phenotypes was performed in 212 unrelated CLA/P patients after genetic counseling between 2015 and 2020. Medical records including family history and results of additional genetic tests were evaluated. Results In 24 CLA/P cases (11.3 %) a pathogenic genetic variant was identified. Twenty out of these 24 had a genetic syndrome requiring specific monitoring and follow-up. Six of these 24 cases (25%) were presumed to be isolated CLA/P cases prior to testing, corresponding to 2,8% of the total cohort. In eight CLA/P cases (3.8%) without a diagnosis after NGS based gene panel testing, a molecular diagnosis was established by additional genetic analyses (e.g., SNP array, single gene testing, trio WES). Conclusion This study illustrates NGS based gene panel testing as a powerful diagnostic tool in the diagnostic work-up of CLA/P patients. Also, in apparently isolated cases and non- familial cases a genetic diagnose could be identified. Early diagnosis facilitates personalized care for patients and accurate genetic counseling of their families.
DOI: 10.6084/m9.figshare.23214551
title: Supplementary Material for: Phacoemulsification with and without iStent: a systematic review and meta-analysis of comparative studies

description: Background: The iStent (Glaukos Corporation, Laguna Hills, CA, USA) is one of the minimally invasive glaucoma devices. It can be inserted at the time of phacoemulsification or as a stand-alone procedure to lower the intraocular pressure. Objective: Our aim is to conduct a systematic review and meta-analysis comparing the effect of iStent insertion at the time of phacoemulsification with phacoemulsification alone in patients with ocular hypertension or open-angle glaucoma. Methods We searched EMBASE, MEDLINE (OVID and Pubmed), CINAHL and Cochrane Library for articles published between 2008 and June 2022(PRISMA 2020 for checklist). Studies comparing the IOP lowering effect of iStent with phacoemulsification versus phacoemulsification alone were included. The endpoints were the reduction in IOP (IOPR) and the mean reduction in number of glaucoma drops. A quality-effects model was used to compare both surgical groups. Results 10 studies were included, reporting on 1,453 eyes. 853 eyes had the combined iStent and phacoemulsification, and 600 eyes underwent phacoemulsification alone. IOPR was higher in the combined surgery at of 4.7 ± 2. mmHg compared to 2.8 ± 1.9 mmHg in phacoemulsification alone. A greater decrease in post-operative eye drops was noted in the combined group having a decrease of 1.2 ± 0.3 eye drops vs of 0.6 ± 0.6 drops in isolated phacoemulsification. Quality effect model showed an IOPR weighted mean difference (WMD) of 1.22 mmHg (CI: [-0.43, 2.87]; Q=315.64; P&lt;0.01; I2=97%) and decreased eye drops WMD 0.42 drops (CI: [0.22, 0.62]; Q=42.6; P&lt;0.01; I2=84%) between both surgical groups. Subgroup analysis shows that the new generation iStent may be more effective in reducing IOP. Conclusion iStent has a synergetic effect with phacoemulsification. The reduction of IOP and glaucoma eye drops was higher when iStent is combined with phacoemulsification compared with isolated phacoemulsification.
DOI: 10.6084/m9.figshare.23515569
title: Supplementary Material for: Cruciferous Vegetable Intake and Risk of Prostate Cancer: A Systematic Review and Meta-Analysis

description: <b><i>Introduction:</i></b> The relationship between cruciferous vegetables and prostate cancer (PCa) risk remains contentious. This study aimed to assess the association between consuming cruciferous vegetables and PCa risk. <b><i>Methods:</i></b> We carried out a systematic search through PubMed, Embase, Web of Science, and the Cochrane Library until September 20, 2022. The results of the article will be analyzed using the Stata 14 software. This meta-analysis was reported as directed by the PRISMA guidance, and the study protocol was recorded in PROSPERO (CRD42022361556). <b><i>Results:</i></b> 7 case-control studies and 9 cohort studies were eventually included, including 70,201 PCa cases and 1,264,437 members. The higher the intake of cruciferous vegetables, the lower the risk of PCa. In comparison to the lowest dose of cruciferous vegetables, the overall relative risk (RR) of cruciferous vegetables having the highest dose was 0.87 (95% confidence interval [CI]: 0.80–0.95; <i>I</i><sup>2</sup> = 59.2%). A significant linear trend (<i>p</i> = 0.002) was observed for the association, with a combined RR of 0.955 (95% CI: 0.928–0.982) for every 15 g of cruciferous vegetables per day. <b><i>Conclusions:</i></b> The study revealed that consumption of cruciferous vegetables may be linked to reduced PCa risk.