cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5104897
title: Factor 11 single-nucleotide variants in women with heavy menstrual bleeding

description: In a previous study it was shown that lower factor XI (FXI) levels in women with heavy menstrual bleeding (HMB). Our aim was to determine the single-nucleotide variants (SNVs) in the <i>F11</i> gene in women with HMB. In addition, an extensive literature search was performed to determine the clinical significance of each SNV. Patients referred for HMB (PBAC-score &gt;100) were included. With direct sequencing analysis of all 15 exons and flanking introns of the <i>F11</i> gene, 29 different non-structural SNVs were detected in 49 patients with HMB. Interestingly, most of these SNVs have previously been associated with venous thrombosis instead of bleeding. These findings have not helped to elucidate the molecular basis of HMB. They also question the specificity of previously reported <i>F11</i> variations in patients with thrombosis. More studies are needed to explain the lower FXI levels seen in patients with HMB.IMPACT STATEMENTWomen with mild deficiencies of factor XI (FXI) (In light of these findings, we performed <i>F11</i> gene analysis to determine the single-nucleotide variants (SNVs) in women with HMB and performed an extensive literature search to determine the clinical significance of each SNV. By direct sequencing analysis of the <i>F11</i> gene we found 29 different non-structural SNVs in 49 women with heavy menstrual bleeding. Remarkably, a number of these SNVs have previously been implicated in thrombosis.These findings have not helped to elucidate the molecular basis of lower FXI levels in HMB. They also question the specificity of previously reported <i>F11</i> variations in patients with thrombosis. More studies are needed to explain the lower FXI levels seen in patients with HMB. Women with mild deficiencies of factor XI (FXI) ( In light of these findings, we performed <i>F11</i> gene analysis to determine the single-nucleotide variants (SNVs) in women with HMB and performed an extensive literature search to determine the clinical significance of each SNV. By direct sequencing analysis of the <i>F11</i> gene we found 29 different non-structural SNVs in 49 women with heavy menstrual bleeding. Remarkably, a number of these SNVs have previously been implicated in thrombosis. These findings have not helped to elucidate the molecular basis of lower FXI levels in HMB. They also question the specificity of previously reported <i>F11</i> variations in patients with thrombosis. More studies are needed to explain the lower FXI levels seen in patients with HMB.
DOI: 10.6084/m9.figshare.5104927.v2
title: HDR brachytherapy decreases proliferation rate and cellular progression of a radioresistant human squamous cell carcinoma in vitro

description: <b>Purpose:</b> To investigate the effects of high dose rate (HDR) brachytherapy on cellular progression of a radioresistant human squamous cell carcinoma in vitro, based on clinical parameters. <b>Materials and methods:</b> An acrylic platform was designed to attach tissue culture flasks and assure source positioning during irradiation. At exponential phase, A431cells, a human squamous cell carcinoma, were irradiated twice up to 1100 cGy. Cellular proliferation was assessed by Trypan blue exclusion assay and survival fraction was calculated by clonogenic assay. DNA content analysis and cell cycle phases were assessed by flow cytometry and gel electrophoresis, respectively. Cellular death patterns were measured by HOPI double-staining method. <b>Results:</b> Significant decreasing cellular proliferation rate (<i>p</i> p 2/M phase (32.3 ± 1.5%) in the irradiated group as compared with untreated cells (8.22 ± 1.2%) was detected. Also, a significant (<i>p</i> <b>Conclusion:</b> HDR brachytherapy led to a decreased proliferation rate and cell survival and also hampered cellular progression to mitosis suggesting that tumor cell death mainly occurred due to mitotic death and G<sub>2</sub>/M cell cycle arrest.
DOI: 10.6084/m9.figshare.5104888
title: New type of progressive provisioning as a characteristic parental behaviour of the crabronid wasp <i>Pemphredon fabricii</i> (Hymenoptera Crabronidae)

description: Bees and stinging wasps (Hymenoptera Aculeata) are well known for the great variety of their nesting resources, which include cavities such as empty reed galls. The majority of the species are mass provisioners, and they do not take any care of their brood after provisioning of the nest. <i>Pemphredon fabricii</i> (Crabronidae) nests in abandoned reed galls of <i>Lipara</i> (Diptera Chloropidae) frit flies. However, <i>P. fabricii</i> uses a different type of late progressive provisioning, described here. Nesting females do not make separate chambers for larvae, but instead fill the interior space of the gall with paralysed aphids and lay a single egg at the body surface of one to eight aphids out of the total number of aphids provisioned. Larvae are polyphagous, and are provisioned with at least 21 aphid species. <i>Hyalopterus pruni</i> is the most common prey, since it feeds on common reed in summer. Before pupation, the larvae sort in the cavity from the biggest (turning to females) at the base to the smallest (turning to males) at the apex. In about 20% of nests, the nesting female brings fresh aphids to feed the smallest larvae at the apex of the nest, while the bigger larvae at the bottom reach maturity much earlier. Similar care for larvae at the end of their development has never been reported in any other insect species. Nests of <i>P. fabricii</i> are commonly attacked by two predator beetle and 14 parasitoid species. All these parasites are generalists, and <i>P. fabricii</i> serves as their satellite host.
DOI: 10.6084/m9.figshare.5104897.v1
title: Factor 11 single-nucleotide variants in women with heavy menstrual bleeding

description: In a previous study it was shown that lower factor XI (FXI) levels in women with heavy menstrual bleeding (HMB). Our aim was to determine the single-nucleotide variants (SNVs) in the <i>F11</i> gene in women with HMB. In addition, an extensive literature search was performed to determine the clinical significance of each SNV. Patients referred for HMB (PBAC-score &gt;100) were included. With direct sequencing analysis of all 15 exons and flanking introns of the <i>F11</i> gene, 29 different non-structural SNVs were detected in 49 patients with HMB. Interestingly, most of these SNVs have previously been associated with venous thrombosis instead of bleeding. These findings have not helped to elucidate the molecular basis of HMB. They also question the specificity of previously reported <i>F11</i> variations in patients with thrombosis. More studies are needed to explain the lower FXI levels seen in patients with HMB.IMPACT STATEMENTWomen with mild deficiencies of factor XI (FXI) (In light of these findings, we performed <i>F11</i> gene analysis to determine the single-nucleotide variants (SNVs) in women with HMB and performed an extensive literature search to determine the clinical significance of each SNV. By direct sequencing analysis of the <i>F11</i> gene we found 29 different non-structural SNVs in 49 women with heavy menstrual bleeding. Remarkably, a number of these SNVs have previously been implicated in thrombosis.These findings have not helped to elucidate the molecular basis of lower FXI levels in HMB. They also question the specificity of previously reported <i>F11</i> variations in patients with thrombosis. More studies are needed to explain the lower FXI levels seen in patients with HMB. Women with mild deficiencies of factor XI (FXI) ( In light of these findings, we performed <i>F11</i> gene analysis to determine the single-nucleotide variants (SNVs) in women with HMB and performed an extensive literature search to determine the clinical significance of each SNV. By direct sequencing analysis of the <i>F11</i> gene we found 29 different non-structural SNVs in 49 women with heavy menstrual bleeding. Remarkably, a number of these SNVs have previously been implicated in thrombosis. These findings have not helped to elucidate the molecular basis of lower FXI levels in HMB. They also question the specificity of previously reported <i>F11</i> variations in patients with thrombosis. More studies are needed to explain the lower FXI levels seen in patients with HMB.
DOI: 10.6084/m9.figshare.5104888.v1
title: New type of progressive provisioning as a characteristic parental behaviour of the crabronid wasp <i>Pemphredon fabricii</i> (Hymenoptera Crabronidae)

description: Bees and stinging wasps (Hymenoptera Aculeata) are well known for the great variety of their nesting resources, which include cavities such as empty reed galls. The majority of the species are mass provisioners, and they do not take any care of their brood after provisioning of the nest. <i>Pemphredon fabricii</i> (Crabronidae) nests in abandoned reed galls of <i>Lipara</i> (Diptera Chloropidae) frit flies. However, <i>P. fabricii</i> uses a different type of late progressive provisioning, described here. Nesting females do not make separate chambers for larvae, but instead fill the interior space of the gall with paralysed aphids and lay a single egg at the body surface of one to eight aphids out of the total number of aphids provisioned. Larvae are polyphagous, and are provisioned with at least 21 aphid species. <i>Hyalopterus pruni</i> is the most common prey, since it feeds on common reed in summer. Before pupation, the larvae sort in the cavity from the biggest (turning to females) at the base to the smallest (turning to males) at the apex. In about 20% of nests, the nesting female brings fresh aphids to feed the smallest larvae at the apex of the nest, while the bigger larvae at the bottom reach maturity much earlier. Similar care for larvae at the end of their development has never been reported in any other insect species. Nests of <i>P. fabricii</i> are commonly attacked by two predator beetle and 14 parasitoid species. All these parasites are generalists, and <i>P. fabricii</i> serves as their satellite host.
DOI: 10.6084/m9.figshare.5104873
title: Chemical reactions from US patents (1976-Sep2016)

description: Reactions extracted by text-mining from United States patents published between 1976 and September 2016. The reactions are available as CML or reaction SMILES. Note that the reactions SMILES are derived from the CML. The files can be unzipped using a program like 7-Zip.<br><br>The reactions were extracted using an enhanced version of the reaction extraction code described in https://www.repository.cam.ac.uk/handle/1810/244727<br>with LeadMine (https://www.nextmovesoftware.com/leadmine.html) used for chemical entity recognition.<br><br>General tips:<br>Duplicate reactions are frequent due to the same or highly similar text occurring in multiple patents, this is especially true when combining the applications and grant datasets, many reactions from applications will later appear in patent grants.<br>Paragraph numbers are only present for 2005+ patent grants and patent applications.<br>Multiple reactions can be extracted from the same paragraph.<br>Atom maps in the reactions SMILES are derived using Epam's Indigo toolkit. While typically correct, the atom-maps are wrong in many cases and hence should not be entirely relied on.<br><br>The reactions have been filtered to remove common cases of incorrectly extracted reactions:<br>All product atoms must be accounted for by the atom-mapping<br>The product(s) must have &gt;8 heavy atoms<br>The product must not be charged if it is a single component<br>The number of products must be &lt;5 and number of reactants+agents &lt;16<br><br>CML:<br>A schema for the CML is present in cml_xsd.zip<br><br>Reaction SMILES<br>For convenience the reaction SMILES includes tab delimited columns for:<br>PatentNumber, ParagraphNum, Year, TextMinedYield, CalculatedYield<br>All of this information is also present in the CML (year is inferred from the folders)<br><br><br><br><br>
DOI: 10.6084/m9.figshare.5104846
title: When moles became diggers: <i>Tegulariscaptor</i> gen. nov., from the early Oligocene of south Germany, and the evolution of talpid fossoriality

description: The systematics of <i>Geotrypus</i> is among the most debated within Talpidae, but the recent development of quantitative methods for shape analyses allows us to provide a thorough reconsideration of <i>Geotrypus</i> spp. In the present study, we perform a systematic revision of the species <i>Geotrypus minor</i> from the early Oligocene of Germany using two-dimensional geometric morphometrics on the humerus, and cladistic analyses using two different character matrices. Our results suggest a distinct generic allocation for this species based on its unique humeral shape. Cladistic analyses reveal that <i>G. minor</i> has closer phylogenetic relationships with urotrichine shrew-moles than with other <i>Geotrypus</i> species or highly fossorial moles. Quantitative methods applied in this study support qualitative observations and fully justify a new generic allocation. In light of these results, Tegulariscaptor gen. nov. is proposed to encompass the material previously assigned to <i>G. minor</i>. http://zoobank.org/urn:lsid:zoobank.org:pub:8A839F1E-0EC8-4799-B3AE-1A4E54A95F0E
DOI: 10.6084/m9.figshare.5104837
title: PRIORITY EFFECTS CAUSED BY PLANT ORDER OF ARRIVAL AFFECT BELOWGROUND PRODUCTIVITY

description: Raw data Weidlich et al. 2017_Journal of Ecology: Root lenght density 2012 and 2014, Root dry weigth 2014, Soil data
DOI: 10.6084/m9.figshare.5104837.v1
title: PRIORITY EFFECTS CAUSED BY PLANT ORDER OF ARRIVAL AFFECT BELOWGROUND PRODUCTIVITY

description: Raw data Weidlich et al. 2017_Journal of Ecology: Root lenght density 2012 and 2014, Root dry weigth 2014, Soil data
DOI: 10.6084/m9.figshare.5104783
title: Methanol formation

description: Enthalpies and Gibbs free energies of the chemical routes yielding methanol (in gas phase) in the ISM at different temperatures and pressures.
DOI: 10.6084/m9.figshare.5104783.v1
title: Methanol formation

description: Enthalpies and Gibbs free energies of the chemical routes yielding methanol (in gas phase) in the ISM at different temperatures and pressures.
DOI: 10.6084/m9.figshare.5104741
title: Computational analysis GeCKO v2 library (human)

description: <b>Table 1 - Non-specific sgRNAs GeCKO v2 (human).</b> This table represents the total of 5664 sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) that recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. For the analysis, sgRNA target sites were aligned against the human reference genome (GRCh38/hg19 – primary assembly) using BLAT (v36) after optimisation of the algorithm for short length queries (-tileSize=6, -stepSize=3). The resulted alignments were further filtered to only include perfect matches and unique targets (exclusion of hits on alternative assemblies). Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.<br><b>Table 2 - Flagged genes GeCKO v2 (human).</b> This table represents the total of 775 genes for which more than half the corresponding sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) are non-specific, i.e. recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. A threshold of &gt;50% non-specific sgRNAs per gene (e.g. 4 out of 6 for protein coding genes; 3 out of 4 for miRNA genes) was set in order to flag a group of sgRNAs. Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.
DOI: 10.6084/m9.figshare.5104744
title: Grades from a course on C programming

description: This dataset contains the grades obtained by the students of the subject "Programming I", taught during the first course of the Degree in Telecommunication Technology and Service Engineering. This degree is one of the three degrees offered by the Escuela Politécnica Superior of the Universidad Autónoma de Madrid, Spain. <br>The data comes from the following courses: 2014, 2015 and 2016. Students were examined on an almost weekly basis: 13 exams in 2014, 12 exams in 2015 and 10 exams in 2015. Each exercise was scored between 0 and 10. The final or total grade was calculated as a weighted average of the individual grades. <br>Each course, a different collection of weights was used. The formula for 2015 was an arithmetic average. However, in 2014 and 2016, the weights increased as the examination got closer to the end of the term, with a more pronounced effect in 2016. These data have been used to study the adaptation of the students to the different grading schemes.
DOI: 10.6084/m9.figshare.5104726
title: Supplementary Material for: Metaanalysen als Königsweg für die Formulierung von Therapieleitlinien?

description: Effects of Distraction and Relaxation Training in Chronic Tinnitus and Impact of Individual Case Complexity. <i>Background</i>: In the case of complex chronic tinnitus many experts recommend inpatient rather than outpatient psychological treatment. Severe tinnitus-related distress and psychopathology are supposed to make treatment success difficult and are to be compensated by increased treatment efforts. Yet, evidence for the impact of case complexity on treatment effects is weak or equivocal. <i>Patients and Methods</i>: In a prospective randomized controlled trial with 139 tinnitus patients we investigated if previous findings on the effectiveness of an outpatient computer-aided and machine-assisted distraction and relaxation training (DRT) can be corroborated and to what extent case complexity is relevant for the short- to long-term success of the training. Treatment success was assessed by use of reliable and valid instruments for tinnitus-related distress, tinnitus coping and emotional distress not related to tinnitus. Furthermore, we analyzed whether outpatient DRT is also effective in patients with similarly complex tinnitus as in most of the inpatient population. The effect of DRT in these outpatients was contrasted with that of inpatient treatment. <i>Results</i>: DRT yielded a longlasting reduction of tinnitus-related distress and increased utilization of self-encouragement, relaxation, and attention diversion to cope with tinnitus. Intervention-specific changes in emotional distress not related to tinnitus were non-certifiable. There was no evidence that increased case complexity curtailed treatment success. The contrast of the effects of inpatient treatment and DRT indicated no advantage of the former. <i>Conclusions</i>: Recommending different therapeutic approaches according to tinnitus complexity seems rather eminence- than evidence-based. Further research on differential treatment indication and on dose-response relationship is required.
DOI: 10.6084/m9.figshare.5104741.v2
title: Computational analysis GeCKO v2 library (human)

description: <b>Table 1 - Non-specific sgRNAs GeCKO v2 (human).</b> This table represents the total of 5664 sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) that recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. For the analysis, sgRNA target sites were aligned against the human reference genome (GRCh38/hg19 – primary assembly) using BLAT (v36) after optimisation of the algorithm for short length queries (-tileSize=6, -stepSize=3). The resulted alignments were further filtered to only include perfect matches and unique targets (exclusion of hits on alternative assemblies). Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.<br><b>Table 2 - Flagged genes GeCKO v2 (human).</b> This table represents the total of 775 genes for which more than half the corresponding sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) are non-specific, i.e. recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. A threshold of &gt;50% non-specific sgRNAs per gene (e.g. 4 out of 6 for protein coding genes; 3 out of 4 for miRNA genes) was set in order to flag a group of sgRNAs. Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.
DOI: 10.6084/m9.figshare.5104723
title: Supplementary Material for: Maternal Footprints of Southeast Asians in North India

description: We have analyzed 7,137 samples from 125 different caste, tribal and religious groups of India and 99 samples from three populations of Nepal for the length variation in the COII/tRNA<sup>Lys</sup> region of mtDNA. Samples showing length variation were subjected to detailed phylogenetic analysis based on HVS-I and informative coding region sequence variation. The overall frequencies of the 9-bp deletion and insertion variants in South Asia were 1.9 and 0.6%, respectively. We have also defined a novel deep-rooting haplogroup M43 and identified the rare haplogroup H14 in Indian populations carrying the 9-bp deletion by complete mtDNA sequencing. Moreover, we redefined haplogroup M6 and dissected it into two well-defined subclades. The presence of haplogroups F1 and B5a in Uttar Pradesh suggests minor maternal contribution from Southeast Asia to Northern India. The occurrence of haplogroup F1 in the Nepalese sample implies that Nepal might have served as a bridge for the flow of eastern lineages to India. The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal.
DOI: 10.6084/m9.figshare.5104720
title: Supplementary Material for: Residual Perception of Moving Objects: Dissociation of Moving and Static Objects in a Case of Posterior Cortical Atrophy

description: <i>Background/Aims:</i> Several studies have reported specific cognitive deficits of posterior cortical atrophy (PCA) starting in the early stage; however, these characteristics have not been demonstrated as arising in the middle or late stage of the disease. We report a patient with PCA who exhibited atypical symptoms after the middle stage. <i>Methods:</i> We observed and examined the patient for more than 10 years in clinical and everyday situations. <i>Results:</i> With increasing symptoms, the patient gradually showed blind-like behavior. He could not find a static object even when it was in front of him, but he could see and catch a tossed ball very well. In addition, he could walk and pick up scattered golf balls without colliding with obstacles. Magnetic resonance imaging and single photon emission computed tomography indicated severe degeneration in the white matter of the parietal lobe and lateral occipital region, whereas the primary visual cortex was relatively intact. <i>Conclusion:</i> Several studies have reported specific cognitive deficits in PCA; however, the present results support the conclusion that not only the initial stage but also the middle and late stages of the disease have the potential to disturb specific cognitive systems.