cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13072943
title: <i>In vitro Candida albicans</i> biofilm formation on different titanium surface topographies

description: To investigate if differences in titanium implant surface topography influence <i>Candida albicans</i> biofilm formation. Titanium discs were prepared and characterized using a profilometer: Group A (<i>R</i><sub>a</sub> 0.15 µm, smooth), Group B (<i>R</i><sub>a</sub> 0.64 µm, minimally rough) and Group C (<i>R</i><sub>a</sub> 1.3 µm, moderately rough). Contact angle and surface free energy (SFE) were determined for each group. Non-preconditioned titanium discs were incubated with <i>C. albicans</i> for 24 h. In additional experiments, the titanium discs were initially coated with human saliva, bovine serum albumin or phosphate-buffered saline for 2 h before incubation with <i>C. albicans</i> for 24 h. The amount of fungal biofilm formation was quantified using a colorimetric assay. <i>C. albicans</i> biofilm formation was significantly lower (<i>p</i> p C. albicans biofilm formation than the other two groups. Salivary coating resulted in greater adherence of <i>C. albicans</i> with increased surface roughness. The minimally rough titanium discs displayed lowest SFE compared to smooth and moderately rough surfaces and showed the least <i>C. albicans</i> biofilm formation. This study demonstrated that <i>C. albicans</i> biofilm formation increased in a SFE-dependent manner. These findings suggest that SFE might be a more explanatory factor for <i>C. albicans</i> biofilm formation on titanium surfaces than roughness. The presence of a pellicle coating may negate the impact of SFE on <i>C. albicans</i> biofilm formation on titanium surfaces.
DOI: 10.6084/m9.figshare.12357419
title: Co-expressed functional module-related genes in ovarian cancer stem cells represent novel prognostic biomarkers in ovarian cancer

description: Ovarian cancer is the leading cause of death from gynecologic malignancies. Cancer stem cells (CSC) seem to play a crucial role in tumor metastasis, recurrence, and chemoresistance. Therefore, CSCs offer significant potential for developing therapeutic targets and to understand tumor recurrence and chemoresistance mechanisms. In the present study, our aim was the identification of the gene group in ovarian CSCs (O-CSCs) and the potential of the resultant gene group in ovarian cancer prognosis. Two different microarray data sets were analyzed by comparing gene expression levels between O-CSCs and cancer samples. The O-CSC co-expression network was reconstructed and its modules were identified. According to the analysis results, 74 mutual DEGs were identified. The O-CSC-specific co-expression network included 32 nodes and 95 edges (network density: 19%), while the co-expression network in cancer samples was reconstructed with 74 nodes and 1066 edges (network density: 39%). Understanding of the molecular mechanism and signatures of O-CSCs should provide valuable insight into chemotherapy resistance and recurrence of ovarian tumors. A highly connected 12 gene module in O-CSC samples of BAMB1, NFKB12, EZR, TNFAIP3, C1orf86, PMAIP1, GEM, KHDRBS3, FILIP1, FGFR2, TGFBR3 and PEG10, (network density: 67%) was identified. Prognostic performance of these genes was evaluated independently using six ovarian cancer datasets (n = 1933 patient samples) via survival analysis. These co-expressed genes were determined as prognostic targets in ovarian cancer. Through literature search validation, five genes (C1orf86, PMAIP1, FILIP1, NFKB12 and PEG10) suggested as novel molecular targets in ovarian cancer. The presented prognostic biomarkers here provide a resource for the understanding of tumor recurrence and chemoresistance and may facilitate critical research directions and development of new prognostic and therapeutic strategies for ovarian cancer. CSCs: cancer stem cells; O-CSCs: ovarian CSCs; FACS: fluorescence-activated cell sorting; SP: side population; MP: main population; TFs: transcription factors.
DOI: 10.6084/m9.figshare.12849782.v1
title: Transforming growth factor beta 1 (TGFβ1) polymorphisms and unexplained infertility: A genetic association study

description: The prevalence of infertility is increasing and worrisome. About 10 to 30% of infertility is classified as idiopathic or unexplained infertility (UI).<i>TGF-β</i> is multifunctional and immunoregulatry cytokine which regulates both implantation and adhesion of trophoblasts to the extracellular matrix during pregnancy. The aim of the current study was to investigate the association between two polymorphisms rs1800470 (C29T) and rs1800471 (G74C) of the <i>TGF-β1</i> gene in Iranian patients with unexplained infertility. A total of 250 UI patients and 484 healthy individuals with no history of infertility were included in the study. The amplification and sequencing of target DNA fragments were done using PCR and automated sequencing methods, respectively. The effects of these polymorphisms on both <i>TGF-β1</i> structure and function of mRNA and protein were analyzed using new in-silico tools. The frequency distribution of the alleles, genotypes, and haplotypes of both rs1800470 and rs1800471 polymorphisms had a statistically significant difference between subjects and controls. CC genotype of TGF-β1 rs1800470 (29C→T) increase the risk of UI in male UI patients. Moreover, C alleles of TGF-β1 rs1800471 was associated with increased risk of UI in female UI patients. Couples, subgroup analysis revealed a significant association between TGF-β1 polymorphisms (rs1800470, rs1800471) and the risk of UI in male, female, and all UI patients. The frequency of TG and CG haplotypes were statistically different in both UI and healthy subjects group (P TGF-β1 mRNA and resulted in the removal of one mRNA arm and creation of two new arms. Taken together, the results of the current study suggest that <i>TGF-β1</i> functional polymorphisms may play an important role in the susceptibility to UI in Iranian population. According to in silico analysis, polymorphisms in TGF-β1 can reduce mRNA half-life and, therefore, reduced <i>TGF-β1</i> expression.
DOI: 10.6084/m9.figshare.13487548.v1
title: Effect of online instruction on volunteers who support people with complex communication needs in active recreation

description: This study was conducted to teach and evaluate the effectiveness of an online training called The CAPTURE & Share program. The program was taught using online instruction in an asynchronous manner with six volunteers who facilitate recreational participation for individuals with complex communication needs. The online training focused on teaching volunteers how to support opportunities for individuals to capture photos and videos from recreation and then share them across their social networks. The first aim of the study was to teach the volunteers about implementation and use of the 8-step CAPTURE & Share program while the second aim was to evaluate the programs’ overall effectiveness. Two multiple baselines designs across three participants each were used to evaluate the volunteers’ written responses to probes delivered during baseline, intervention, maintenance, and generalization phases. Additionally, social validation data were collected. Results indicated that volunteers were not only successful in learning the program, but were also highly satisfied with the online training methods. Implications for using online instruction are discussed for speech-language pathologists, caregivers, individuals with complex communication needs, and recreational professionals.
DOI: 10.15468/tuqpre
title: An integrative description of Diploechiniscus oihonnae (Richters, 1903) population from near the original type locality in Merok (Norway)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kaczmarek, Łukasz, Kayastha, Pushpalata, Gawlak, Magdalena, Mioduchowska, Monika, Roszkowska, Milena (2021): An integrative description of Diploechiniscus oihonnae (Richters, 1903) population from near the original type locality in Merok (Norway). Zootaxa 4964 (1): 83-102, DOI: https://doi.org/10.11646/zootaxa.4964.1.4
DOI: 10.26208/x7z4-5j56
title: Supplementary data, code, and other information for ‘Discussion of: A Statistical Analysis of Multiple Temperature Proxies: Are Reconstructions of Surface Temperatures over the Last 1000 Years Reliable’ 

description: McShane and Wyner (2011) (henceforth MW) analyze a dataset of “proxy” climate records previously used by Mann et al. (2008) (henceforth M08) to attempt to assess their utility in reconstructing past temperatures. MW introduce new methods in their analysis, which is welcome. However, the absence of both proper data quality control and appropriate “pseudoproxy” tests to assess the performance of their methods invalidate their main conclusions.
DOI: 10.26208/aa8k-bm96
title: Supplementary data and code for ‘On smoothing potentially non-stationary climate time series’ (Geophysical Research Letters, Mann 2004)

description: A simple approach to the smoothing of a potentially non-stationary time series is presented which provides an optimal choice among three alternative, readily motivated and easily implemented boundary constraints. This method is applied to the smoothing of the instrumental Northern Hemisphere (NH) annual mean and coldseason North Atlantic Oscillation (NAO) time series, yielding an objective estimate of the smoothed decadalscale variations in these series including long-term trends.
DOI: 10.6069/5b38-fg24
title: Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring

description: Parallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM’s strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time of flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel, and that high-resolution data are not necessary to obtain high quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on a Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision, and that the linear ion trap’s superior sensitivity gives it better lower limits of quantitation on over 62% of peptides in the assay.
DOI: 10.26208/s591-rk61
title: Supplementary data and code for ‘Robust estimation of background noise and signal detection in climatic time series’ (Mann and Lees 1996)

description: We present a new technique for isolating climate signals in time series with a characteristic ‘red’ noise background which arises from temporal persistence. This background is estimated by a ‘robust’ procedure that, unlike conventional techniques, is largely unbiased by the presence of signals immersed in the noise. Making use of multiple-taper spectral analysis methods, the technique further provides for a distinction between purely harmonic (periodic) signals, and broader-band (‘quasiperiodic’) signals. The effectiveness of our signal detection procedure is demonstrated with synthetic examples that simulate a variety of possible periodic and quasiperiodic signals immersed in red noise. We apply our methodology to historical climate and paleoclimate time series examples. Analysis of a ˜ 3 million year sediment core reveals significant periodic components at known astronomical forcing periodicities and a significant quasiperiodic 100 year peak. Analysis of a roughly 1500 year tree-ring reconstruction of Scandinavian summer temperatures suggests significant quasiperiodic signals on a near-century timescale, an interdecadal 16–18 year timescale, within the interannual El Niño/Southern Oscillation (ENSO) band, and on a quasibiennial timescale. Analysis of the 144 year record of Great Salt Lake monthly volume change reveals a significant broad band of significant interdecadal variability, ENSO-timescale peaks, an annual cycle and its harmonics. Focusing in detail on the historical estimated global-average surface temperature record, we find a highly significant secular trend relative to the estimated red noise background, and weakly significant quasiperiodic signals within the ENSO band. Decadal and quasibiennial signals are marginally significant in this series.
DOI: 10.5281/zenodo.4740627
title: Supplementary data to paper "Ocean glider flight in the presence of surface waves" by Lucas M Merckelbach and Jeffrey R Carpenter, DOI: 10.1175/JTECH-D-20-0206.1

description: Supplementary data of glider data used in Figure 6 of "Ocean glider flight in the presence of surface waves" by Lucas M Merckelbach and Jeffrey R Carpenter, DOI: 10.1175/JTECH-D-20-0206.1
DOI: 10.5281/zenodo.4740626
title: Supplementary data to paper "Ocean glider flight in the presence of surface waves" by Lucas M Merckelbach and Jeffrey R Carpenter, DOI: 10.1175/JTECH-D-20-0206.1

description: Supplementary data of glider data used in Figure 6 of "Ocean glider flight in the presence of surface waves" by Lucas M Merckelbach and Jeffrey R Carpenter, DOI: 10.1175/JTECH-D-20-0206.1
DOI: 10.5281/zenodo.4740829
title: Automated Java Challenges' Security Assessment1for Training in Industry – Preliminary Results

description: The file contains the preliminary results of a survey conducted in the industry setting.
DOI: 10.5281/zenodo.4740828
title: Automated Java Challenges' Security Assessment1for Training in Industry – Preliminary Results

description: The file contains the preliminary results of a survey conducted in the industry setting.
DOI: 10.6084/m9.figshare.12931190.v1
title: Forecasting Causal Effects of Interventions versus Predicting Future Outcomes

description: The present article provides a didactic presentation and extension of selected features of Pearl’s DAG-based approach to causal inference for researchers familiar with structural equation modeling. We illustrate key concepts using a cross-lagged panel design. We distinguish between (a) forecasts of the value of an outcome variable after an intervention and (b) predictions of future values of an outcome variable. We consider the mean level and variance of the outcome variable as well as the probability that the outcome will fall within an acceptable range. We extend this basic approach to include additive random effects, allowing us to distinguish between average effects of interventions and person-specific effects of interventions. We derive optimal person-specific treatment levels and show that optimal treatment levels may differ across individuals. We present worked examples using simulated data based on the results of a prior empirical study of the relationship between blood insulin and glucose levels.
DOI: 10.5281/zenodo.4740790
title: zhgarfield/reputationdiversitydata: Initial release of the reputationdiversitydata package

description: This release publishes the reputationdiversitydata package produced by, and which includes data for, the publication "The content and structure of reputation domains across human societies: a view from the evolutionary social sciences" by Zachary H. Garfield, Ryan Schacht, Emily R. Post, Dominique Ingram, Andrea Uehling, and Shane J. Macfarlan.
DOI: 10.6084/m9.figshare.13109536.v1
title: Genomic diversity of the Muslim population from Telangana (India) inferred from 23 autosomal STRs

description: This study aimed to investigate the genomic diversity and population structure in the Muslim community of Telangana, India, using 23 autosomal microsatellite genetic markers. We also examined genetic relatedness between Muslim and non-Muslim populations of India. A sample of 184 randomly selected unrelated healthy Muslim individuals from the Telangana state were included in this study. The genotyping of 23 autosomal STR markers included in PowerPlex<sup>®</sup> Fusion 6 C multiplex system (Promega)was done. A total of 273 alleles were observed in the studied population, and locus SE33 showed 37 observed alleles, which is the highest number of observed alleles among all the studied loci. Among all the studied loci the most polymorphic and discriminatory locus was SE33, with the values of polymorphic information content (PIC) = 9.411E–01 and power of discrimination (PD) = 9.865E–01. Observed heterozygosity ranged from 6.630E–01 (D22S1045) to 9.239E–01 (SE33). Discrimination power, exclusion power, matching probability and paternity index for all the studied loci were 1.00E + 00, 1.00E + 00, 2.01E–28, and 5.68E + 09, respectively. The studied Muslim population showed genetic relatedness with non-Muslim populations i.e. populations of central India, Jharkhand, and Uttar Pradesh, suggesting the conversion of Hindus during the Muslim invasion. Neighbor-joining (NJ) tree and principal component analysis (PCA) revealed that the studied population showed genetic affinity with communities of Jharkhand, Madhya Pradesh and Uttar Pradesh states. The genetic data of this study may be useful for forensic, medical, and anthropological studies.
DOI: 10.6084/m9.figshare.13109536
title: Genomic diversity of the Muslim population from Telangana (India) inferred from 23 autosomal STRs

description: This study aimed to investigate the genomic diversity and population structure in the Muslim community of Telangana, India, using 23 autosomal microsatellite genetic markers. We also examined genetic relatedness between Muslim and non-Muslim populations of India. A sample of 184 randomly selected unrelated healthy Muslim individuals from the Telangana state were included in this study. The genotyping of 23 autosomal STR markers included in PowerPlex<sup>®</sup> Fusion 6 C multiplex system (Promega)was done. A total of 273 alleles were observed in the studied population, and locus SE33 showed 37 observed alleles, which is the highest number of observed alleles among all the studied loci. Among all the studied loci the most polymorphic and discriminatory locus was SE33, with the values of polymorphic information content (PIC) = 9.411E–01 and power of discrimination (PD) = 9.865E–01. Observed heterozygosity ranged from 6.630E–01 (D22S1045) to 9.239E–01 (SE33). Discrimination power, exclusion power, matching probability and paternity index for all the studied loci were 1.00E + 00, 1.00E + 00, 2.01E–28, and 5.68E + 09, respectively. The studied Muslim population showed genetic relatedness with non-Muslim populations i.e. populations of central India, Jharkhand, and Uttar Pradesh, suggesting the conversion of Hindus during the Muslim invasion. Neighbor-joining (NJ) tree and principal component analysis (PCA) revealed that the studied population showed genetic affinity with communities of Jharkhand, Madhya Pradesh and Uttar Pradesh states. The genetic data of this study may be useful for forensic, medical, and anthropological studies.
DOI: 10.6084/m9.figshare.12841696.v1
title: Concurrent sodium channelopathies and amyotrophic lateral sclerosis supports shared pathogenesis

description: Amyotrophic lateral sclerosis (ALS) is an invariably fatal adult-onset neurodegenerative disorder; approximately 10% of ALS is monogenic but all ALS exhibits significant heritability. The skeletal muscle sodium channelopathies are a group of inherited, non-dystrophic ion channel disorders caused by heterozygous point mutations in the <i>SCN4A</i> gene, leading to clinical manifestations of congenital myotonia, paramyotonia, and periodic paralysis syndromes. We provide clinical and genetic evidence of concurrence of these two rare disorders which implies a possible shared underlying pathophysiology in two patients. We then identify an enrichment of ALS-associated mutations in another sodium channel, <i>SCN7A</i>, from whole genome sequencing data of 4495 ALS patients and 1925 controls passing multiple testing correction (67 variants, <i>p</i> = 0.0002, Firth logistic regression). These findings suggest dysfunctional sodium channels may play a role upstream in the pathogenesis of ALS in a subset of patients, potentially opening the door to novel personalized medicine approaches.
DOI: 10.6084/m9.figshare.12841696
title: Concurrent sodium channelopathies and amyotrophic lateral sclerosis supports shared pathogenesis

description: Amyotrophic lateral sclerosis (ALS) is an invariably fatal adult-onset neurodegenerative disorder; approximately 10% of ALS is monogenic but all ALS exhibits significant heritability. The skeletal muscle sodium channelopathies are a group of inherited, non-dystrophic ion channel disorders caused by heterozygous point mutations in the <i>SCN4A</i> gene, leading to clinical manifestations of congenital myotonia, paramyotonia, and periodic paralysis syndromes. We provide clinical and genetic evidence of concurrence of these two rare disorders which implies a possible shared underlying pathophysiology in two patients. We then identify an enrichment of ALS-associated mutations in another sodium channel, <i>SCN7A</i>, from whole genome sequencing data of 4495 ALS patients and 1925 controls passing multiple testing correction (67 variants, <i>p</i> = 0.0002, Firth logistic regression). These findings suggest dysfunctional sodium channels may play a role upstream in the pathogenesis of ALS in a subset of patients, potentially opening the door to novel personalized medicine approaches.
DOI: 10.6084/m9.figshare.12514880
title: Levels of clusterin, CD5L, ficolin-3, and gelsolin in ALS patients and controls

description: In amyotrophic lateral sclerosis, there is a need for biomarkers to distinguish patients from controls, to follow disease progression and to provide information about the pathogenesis of disease. In a previous mass spectrometry study that searched for potential proteins of interest, we identified clusterin, CD5L, ficolin-3, and gelsolin as molecules that differed in abundance between ALS patients and controls, with a greater difference in patients with cognitive impairment. Here, we have measured levels of these molecules in plasma from a separate cohort of ALS patients and controls. The plasma was depleted of abundant plasma proteins. We confirmed our previous findings that levels of clusterin are decreased and ficolin-3 are increased in ALS patients compared to controls. In this study, we found that levels of CD5L were increased in patients with ALS and levels correlated with survival. We found that levels of gelsolin were modestly increased in ALS compared to controls whereas in our previous study these were decreased, especially in patients with cognitive impairment who were not included in this study. We suggest that clusterin and ficolin-3 deserve further study as potential ALS biomarkers.