cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25237711
title: Supplementary Material for: Hashimoto’s thyroiditis negatively influences ICSI outcome in euthyroid women on T4 substitution therapy; a retrospective study

description: Abstract
Objective:
To analyze the impact of thyroid autoimmunity (TAI) on reproductive outcome parameters of ICSI cycles as compared to TAI negative ICSI cycles. 
Design: 
In this single IVF center retrospective study 86 infertile women with elevated TPOAb or TGAb levels, but euthyroid after thyroxine replacement (study group), were compared to 69 female patients with no thyroid abnormalities (controls). Following ICSI treatment fertilization rate (FR), clinical pregnancy rate (CPR), miscarriage rate (MR) and live birth rate (LBR) were analyzed.
Materials, Setting, Methods:
All subjects with various infertility factors were treated with ICSI in university based IVF center. Patients in the study group received thryroxine replacement and were euthyreoid at IVF treatment. Before the IVF cycles endocrinological parameters were uniformly assessed: thyroid function and antibodies, reproductive hormones (AMH, FSH, LH, E2, PRL, testosterone, DHEAS, 17-OHP, AD) and OGTT (0-60-120 min glucose and insulin). Following descriptive comparison of laboratory parameters, age adjusted analyses of FR, CPR, MR and LBR were performed.
Results: TAI positive women were older (mean age 35.31±4.95 vs. 32.15±4.87 years; p=0.002), had higher FSH (8.4±3.4 vs. 7.4±2.32 U/L; p=0.024), higher E2 (53.94±47.61 vs. 42.93±18.92 pg/ml; p=0.025) levels, while AMH (2.88±2.62 vs. 3.61±1.69 ng/ml; p=0.0002) was lower. There were no differences in TSH levels (1.64±0.96 vs. 1.66±0.65 uIU/ml; p=0.652) between the two groups. FT3 (2.63±0.58 vs. 2.98±0.55 pg/ml; p=0.002) was lower and FT4 (1.3±0.29 vs. 1.13±0.21 ng/dl; p=0.0002) was higher in the TAI positive group, reflecting clinically irrevelant differences.
Egg cell counts (6±3.8 vs. 7.5±3.95; p=0.015) were lower in TAI and remained so following age adjustment. Although the overall ICSI FR did not differ (62.9 % vs. 69.1 %, p=0.12), it was lower for patients under 35 with TAI showing decreasing differences in line with age. The CPR (36.04 % vs. 69.56 %; p&lt;0.001), LBR (23.25 % vs. 60.86 %; p&lt;0.001) were lower, the MR (35.48 % vs. 12.5 %; p=0.024) was higher in the TAI group and these differences remained after age adjustment. 
Limitations: Since the higher age of the study group may interfere with the effect of TAI, age adjustment calculations were necessary to perform to eliminate this confounding factor.
Conclusion: Despite optimal thyroid supplementation in clinical or subclinical hypothyreoidism, the presence of TAI negatively influences clinical pregnancy rate and is connected to a higher miscarriage rate, thus resulting in a lower live birth rate after ICSI. Decreased fertilization rate with ICSI in TAI patients may also contribute to poorer outcomes, especially in younger women.
DOI: 10.6084/m9.figshare.25441195
title: Supplementary Material for: COMPUTED TOMOGRAPHY PERFUSION IN ACUTE STROKE ASSESSMENT

description: Background: Traditionally, non-contrast computed tomography (CT) alone was used in the initial assessment of acute ischaemic stroke patients mainly to exclude haemorrhage or alternative pathology. 
Summary: Late-window (beyond 6 hours) and recent large-volume endovascular mechanical thrombectomy (MT) trials integrated CT Perfusion (CTP) imaging to guide MT and/or intravenous thrombolysis (IVT) decision-making in stroke patients. 
Key Messages: In current clinical practice, many patients are being excluded from reperfusion therapy due to a lack of data from urgent investigations to assess cerebral vasculature and perfusion. Here, we explore the potential benefits of CTP incorporated into the initial CT protocol assessment of stroke patients.
DOI: 10.18462/iir.icr.2015.0523
title: CFD study of oscillatory flow through 90° bends of thermoacoustic devices.

description: Numerical simulation is performed to investigate oscillatory flow through 90° bends of a thermoacoustic system. Bends are often used in thermoacoustic systems as parts of acoustic networks. In the feedback loop, geometrical changes can cause system losses and it is often important to find optimal bend curvature radius that keeps the losses to the minimum. This paper investigates the effects of radius of curvature on the properties of the acoustic wave propagating through 90° bends, using 3D Computational Fluid Dynamics (CFD) simulation approach. Oscillatory flow phenomena are investigated using RANS method with SST k-ω turbulent model. Two curvature radii are considered with the drive ratio of acoustic excitation up to 0.65%. The simulation results are analysed with respect to the acoustic Dean Number and the associated flow phenomena causing losses in the bend are described. The results suggest an interesting lead that is worthy of further investigation.
DOI: 10.35097/1666
title: On iterative pre-compensation of 3D laser-printed micro-optical components using confocal-optical microscopy - Data
DOI: 10.5281/zenodo.7381807
title: The central nervous system's proteogenomic and spatial imprint upon systemic viral infection, like SARS-CoV-2

description: Data set including image files of histological stainings, immunohistochemistry, MELC, and spatial transcriptomics associated with the study mentioned above.
description: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC-2049-390688087, as well as SFB TRR 167 and HE 3130/6-1 to F.L.H., CRC130 P17 to H.R. and A.E.H., HA 5354/10-1 to A.E.H. and RA 2491/1-1 to H.R.; by the German Center for Neurodegenerative Diseases (DZNE) Berlin, by the European Union (PHAGO, 115976; Innovative Medicines Initiative-2; FP7-PEOPLE-2012-ITN: NeuroKine) and by the Ministry for Science and Education of Lower Saxony through the program 'Niedersächsisches Vorab' to J.F.
DOI: 10.6084/m9.figshare.24089738
title: Forensic characterisation and polymorphism analysis of 16 X-chromosomal STRs in the Jining Han population in Eastern China

description: X-chromosomal short tandem repeats (X-STRs) are a useful supplementary approach to analysing autosomal markers in forensics and kinship studies; such markers are not well-characterised in many populations. To investigate population genetic polymorphism and forensic characterisation of 16 X-STRs in the Jining Han population, and analyse genetic relationships with other Chinese populations. Allele frequencies for 16 X-STR loci were obtained from a sample set of 527 unrelated individuals from the Jining Han population. Population genetic analyses of Jining Han and another 10 reference populations were conducted using phylogenetic tree, principal component analysis and multidimensional scaling. We detected 149 alleles, with frequencies ranging from 0.0013 to 0.8242. The combined powers of discrimination in males and females were 0.999999997194774 and 0.999999999999995, respectively. The combined mean exclusion change (MEC)<sub>Krüger</sub>, MEC<sub>Kishida</sub>, MEC<sub>Desmarais</sub>, and MEC<sub>Desmarais Duos</sub> values were 0.999974632649096, 0.999999976997582, 0.999999977013201, and 0.999993755768423, respectively. We detected relatively high genetic homogeneity in populations with similar ethnic or geographic origins, and a close relationship between the Jining Han and Beijing Han populations. The present findings indicate that the 16 X-STR loci examined are highly polymorphic in the Han population of Jining, providing useful information for forensic science and population genetics studies.
DOI: 10.6084/m9.figshare.24089738.v1
title: Forensic characterisation and polymorphism analysis of 16 X-chromosomal STRs in the Jining Han population in Eastern China

description: X-chromosomal short tandem repeats (X-STRs) are a useful supplementary approach to analysing autosomal markers in forensics and kinship studies; such markers are not well-characterised in many populations. To investigate population genetic polymorphism and forensic characterisation of 16 X-STRs in the Jining Han population, and analyse genetic relationships with other Chinese populations. Allele frequencies for 16 X-STR loci were obtained from a sample set of 527 unrelated individuals from the Jining Han population. Population genetic analyses of Jining Han and another 10 reference populations were conducted using phylogenetic tree, principal component analysis and multidimensional scaling. We detected 149 alleles, with frequencies ranging from 0.0013 to 0.8242. The combined powers of discrimination in males and females were 0.999999997194774 and 0.999999999999995, respectively. The combined mean exclusion change (MEC)<sub>Krüger</sub>, MEC<sub>Kishida</sub>, MEC<sub>Desmarais</sub>, and MEC<sub>Desmarais Duos</sub> values were 0.999974632649096, 0.999999976997582, 0.999999977013201, and 0.999993755768423, respectively. We detected relatively high genetic homogeneity in populations with similar ethnic or geographic origins, and a close relationship between the Jining Han and Beijing Han populations. The present findings indicate that the 16 X-STR loci examined are highly polymorphic in the Han population of Jining, providing useful information for forensic science and population genetics studies.
DOI: 10.6084/m9.figshare.24272164
title: Bioarchaeological study of ancient Teotihuacans based on complete mitochondrial genome sequences and diet isotopes

description: The Teotihuacan civilisation was the largest one in ancient Mesoamerica. The Teotihuacan city was born in the north-eastern Basin of Mexico around the second century BC, reached its peak in the fourth century AD, and had cultural influence throughout Mesoamerica. At its peak, the size of the city reached more than 20 km<sup>2</sup>, and the total population is estimated to have increased from 100,000 to 200,000. However, knowledge of the genetic background of the Teotihuacan people is still limited. We aimed to determine the mitogenome sequences of the Teotihuacan human remains and compare the ancient and present Mesoamericans. In addition, we aimed to identify the food habits of ancient Teotihuacans. We determined the mitogenome sequences of human remains dated to 250–636 cal AD using target enrichment-coupled next generation sequencing. We also performed stable isotope analysis. We successfully obtained nearly full-length sequences newly unearthed from a civilian dwelling in the Teotihuacan site. Teotihuacan mitochondrial DNA was classified into the haplogroups in present and ancient Mesoamericans. In addition, Teotihuacan individuals had a diet dependent on C4 plants such as maize. Genetic diversity varied among the Teotihuacans.
DOI: 10.6084/m9.figshare.24272164.v1
title: Bioarchaeological study of ancient Teotihuacans based on complete mitochondrial genome sequences and diet isotopes

description: The Teotihuacan civilisation was the largest one in ancient Mesoamerica. The Teotihuacan city was born in the north-eastern Basin of Mexico around the second century BC, reached its peak in the fourth century AD, and had cultural influence throughout Mesoamerica. At its peak, the size of the city reached more than 20 km<sup>2</sup>, and the total population is estimated to have increased from 100,000 to 200,000. However, knowledge of the genetic background of the Teotihuacan people is still limited. We aimed to determine the mitogenome sequences of the Teotihuacan human remains and compare the ancient and present Mesoamericans. In addition, we aimed to identify the food habits of ancient Teotihuacans. We determined the mitogenome sequences of human remains dated to 250–636 cal AD using target enrichment-coupled next generation sequencing. We also performed stable isotope analysis. We successfully obtained nearly full-length sequences newly unearthed from a civilian dwelling in the Teotihuacan site. Teotihuacan mitochondrial DNA was classified into the haplogroups in present and ancient Mesoamericans. In addition, Teotihuacan individuals had a diet dependent on C4 plants such as maize. Genetic diversity varied among the Teotihuacans.
DOI: 10.6084/m9.figshare.23660553
title: Genetic diversity of 23 STR loci of the Guizhou Tujia ethnic minority and the phylogenetic relationships with 22 other populations

description: Short tandem repeats (STR) are highly polymorphic DNA markers utilised in forensic personal identification and human population genetic research. Guizhou Tujia is one of the ancient minority groups in southwest China, however, the population has not been studied using the highly discriminating 23 STR Huaxia Platinum Kit. To obtain genetic data from 23 autosomal STRs in Guizhou Tujia and examine the population’s relationship with others. A total of 480 individuals from the Guizhou Tujia population were analysed using 23 STR loci of Huaxia Platinum Kit. Allele frequencies and forensic parameters were estimated. Population genetic relationships were calculated by Nei’s genetic distances and visualised using a variety of biostatistical methods. A total of 264 alleles were found, with allelic frequencies ranging from 0.0010 to 0.5104. The combined discrimination power (CDP) and the combined probability of paternity (CPE) of 23 STR loci were 0.9999999999999999999999999996 and 0.999999999710422, respectively. Guizhou Tujia showed closer genetic relationships with Hubei Tujia, Guizhou Gelao, and Guizhou Miao than with other populations. We first obtained the population genetic data of Guizhou Tujia using the 23 STR system and demonstrated its value in forensic applications. Comprehensive population comparisons showed an evident genetic affinity pattern between populations that are geographically, ethnically and linguistically related.
DOI: 10.6084/m9.figshare.23660553.v1
title: Genetic diversity of 23 STR loci of the Guizhou Tujia ethnic minority and the phylogenetic relationships with 22 other populations

description: Short tandem repeats (STR) are highly polymorphic DNA markers utilised in forensic personal identification and human population genetic research. Guizhou Tujia is one of the ancient minority groups in southwest China, however, the population has not been studied using the highly discriminating 23 STR Huaxia Platinum Kit. To obtain genetic data from 23 autosomal STRs in Guizhou Tujia and examine the population’s relationship with others. A total of 480 individuals from the Guizhou Tujia population were analysed using 23 STR loci of Huaxia Platinum Kit. Allele frequencies and forensic parameters were estimated. Population genetic relationships were calculated by Nei’s genetic distances and visualised using a variety of biostatistical methods. A total of 264 alleles were found, with allelic frequencies ranging from 0.0010 to 0.5104. The combined discrimination power (CDP) and the combined probability of paternity (CPE) of 23 STR loci were 0.9999999999999999999999999996 and 0.999999999710422, respectively. Guizhou Tujia showed closer genetic relationships with Hubei Tujia, Guizhou Gelao, and Guizhou Miao than with other populations. We first obtained the population genetic data of Guizhou Tujia using the 23 STR system and demonstrated its value in forensic applications. Comprehensive population comparisons showed an evident genetic affinity pattern between populations that are geographically, ethnically and linguistically related.
DOI: 10.6084/m9.figshare.22224864
title: Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China

description: Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. This investigation intends to provide light on Qingdao’s paternal genetic diversity and its evolutionary connections to other Han subgroups. The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID<sup>®</sup> PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.
DOI: 10.6084/m9.figshare.22224864.v1
title: Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China

description: Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. This investigation intends to provide light on Qingdao’s paternal genetic diversity and its evolutionary connections to other Han subgroups. The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID<sup>®</sup> PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.
DOI: 10.6084/m9.figshare.23622819.v1
title: Sex-dependent association of DNA methylation in the coding region of the corticotropin-releasing hormone gene and schizophrenia spectrum disorder

description: Schizophrenia spectrum disorder (SSD) is a common mental disorder causing severe and chronic disability. Epigenetic changes in genes related to the hypothalamic–pituitary–adrenal (HPA) axis are believed to play an important role in SSD pathogenesis. The methylation status of the corticotropin-releasing hormone (<i>CRH</i>) gene, which is central to the HPA axis, has not been investigated in patients with SSD. We investigated the methylation status of the coding region of the <i>CRH</i> gene (hereafter, <i>CRH</i> methylation) using peripheral blood samples from patients with SSD. We used sodium bisulphite and MethylTarget to determine <i>CRH</i> methylation after collecting peripheral blood samples from 70 patients with SSD who had positive symptoms and 68 healthy controls. <i>CRH</i> methylation was significantly increased in patients with SSD, especially in male patients. Differences in <i>CRH</i> methylation were detectable in the peripheral blood of patients with SSD. Epigenetic abnormalities in the <i>CRH</i> gene were closely related to positive symptoms of SSD, suggesting that epigenetic processes may mediate the pathophysiology of SSD.
DOI: 10.6084/m9.figshare.22039337.v1
title: Genetic polymorphisms of 19 X-STRs in populations of Hubei Han and Guangxi Zhuang and their comparisons with 13 other Chinese populations

description: A prerequisite for applying short tandem repeat (STR) kits is obtaining population allele and/or haplotype frequencies and forensic parameters. Firstly, we aimed to investigate the population data of 19 X-chromosomal STRs (X-STRs) included in the AGCU X19 STR kit in the Han people residing in Hubei Province, Central China, and the Zhuang people residing in the Guangxi Zhuang Autonomous Region of South China. Furthermore, we compared these population data with those for other Chinese populations. In total, 509 unrelated Han males and 266 unrelated Zhuang males were genotyped using the AGCU X19 STR kit. Allele frequencies, haplotype frequencies, and forensic parameters were computed, and genetic differences among 15 Chinese populations were analysed. The 19 X-STRs showed a high power of discrimination and high mean chance of exclusion, whether calculated using allele or haplotype frequencies. Major differences were found between Han and Oroqen, Uyghur, Mongolian, Tibetan, Li, and Yi populations. Aberrant biallelic patterns at DXS10159, DXS10134, and DXS10079 and allelic dropouts at DXS10164 were observed. The 19 X-STRs were highly polymorphic in the Hubei Han and Guangxi Zhuang populations, and the AGCU X19 STR kit was shown to be suitable for forensic casework.
DOI: 10.6084/m9.figshare.22225191
title: Forensic efficiency evaluation of a novel multiplex panel of InDels and STRs in the Guizhou Han population and its phylogenetic relationships with other reference populations

description: Insertion/deletion polymorphism (InDel), as the third genetic marker, has been given a lot of attention by forensic geneticists since it has the advantages of extensive distributions in the human genome, small amplicon, and low mutation rate. However, the extant InDel panels were only viewed as supplemental tools for kinship analyses. In addition, these panels were not conductive to mixture deconvolution because InDels in these panels mainly displayed two alleles. The purpose of this study is to investigate genetic distributions of a novel panel of InDels and STRs in the Guizhou Han population; assess the forensic application value of the panel; and conduct population genetic analyses of the Guizhou Han and other reference populations based on the overlapping loci. The bloodstain samples of 209 Guizhou Han were gathered and genotyped by the novel panel. Allelic frequencies and forensic parameters of two miniSTRs and 59 InDels in the panel were estimated. In addition, we assessed phylogenetic relationships among the Guizhou Han and other reference populations by principal component analysis, <i>D<sub>A</sub></i> genetic distance, and neighbor-joining tree. A total of 139 alleles of 61 loci could be observed in the Guizhou Han population. Polymorphic information content values of 59 InDels were greater than 0.3 in the Guizhou Han population. The cumulative power of discrimination and probability of exclusion of two miniSTRs and 59 InDels in the Guizhou Han population were 0.999999999999999999999999997984 and 0.9999986, respectively. Principal component analysis of 14 populations showed that the Guizhou Han population located closer to Hunan Han and Southern Han Chinese (CHS) populations. Similar results were also discerned from <i>D<sub>A</sub></i> genetic distances and the neighbor-joining tree. To sum up, the novel panel could be employed for forensic personal identification and paternity testing in the Guizhou Han population as a promising independent tool. Besides, the principal component analysis and phylogenetic tree of the Guizhou Han and other compared populations revealed that the Guizhou Han population possesses close genetic affinities with Hunan Han, CHS, and Han Chinese in Beijing (CHB) populations.