cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22346989
title: Supplementary Material for: A Proposed Human Structural Brain Connectivity Matrix in the Center for Morphometric Analysis Harvard-Oxford Atlas Framework: A historical perspective and future direction for enhancing the precision of human structural connectivity with a novel neuroanatomical typology.

description: A complete structural definition of the human nervous system must include delineation of its wiring diagram (e.g., [1]). The complete formulation of the human brain circuit diagram (BCD; [2]) has been hampered by an inability to determine connections in their entirety (i.e., not only pathway stems, but also origins and terminations). From a structural point of view, a neuroanatomic formulation of the BCD should include the origins and terminations of each fiber tract as well as the topographic course of the fiber tract in three dimensions. Classic neuroanatomical studies have provided trajectory information for pathway stems and their speculative origins and terminations [3–7]. We have summarized these studies previously [7] and present them here in a macroscale-level human cerebral structural connectivity matrix. A matrix in the present context is an organizational construct that embodies anatomical knowledge about cortical areas and their connections. This is represented in relation to parcellation units according to the Harvard-Oxford Atlas neuroanatomical framework established by the Center for Morphometric Analysis at Massachusetts General Hospital in the early 2000s, which is based on the MRI volumetrics paradigm of Dr. Verne Caviness and colleagues [8]. This is a classic connectional matrix based mainly on data predating the advent of DTI tractography, which we refer to as the "pre-DTI era" human structural connectivity matrix. In addition, we present representative examples that incorporate validated structural connectivity information from non-human primates and more recent information on human structural connectivity emerging from DTI tractography studies. We refer to this as the "DTI era" human structural connectivity matrix. This newer matrix represents a work in progress and is necessarily incomplete due to the lack of validated human connectivity findings on origins and terminations as well as pathway stems. Importantly, we use a neuroanatomical typology to characterize different types of connections in the human brain, which is critical for organizing the matrices and the prospective database. Although substantial in detail, the present matrices may be assumed to be only partially complete because the sources of data relating to human fiber system organization are limited largely to inferences from gross dissections of anatomic specimens or extrapolations of pathway tracing information from non-human primate experiments [2,9,10]. These matrices, which embody a systematic description of cerebral connectivity, can be used in cognitive and clinical studies in neuroscience and, importantly, to guide research efforts for further elucidating, validating and completing the human brain circuit diagram [2].
DOI: 10.6084/m9.figshare.22348537
title: Supplementary Material for: Soy Gly m 8 sIgE has limited value in the diagnosis of Soy Allergy in Peanut Ara h 2 Sensitised Adults

description: Background: Recently, specific IgE (sIgE) sensitization against Gly m 8 (soy 2S albumin) has been described as a good diagnostic marker for soy allergy (SA). The aim of this study is to evaluate the diagnostic value of Gly m 8 by determining the sensitization profiles based on the homologues soy allergens Bet v 1, Ara h 1, Ara h 2 and Ara h 3. Methods: Thirty soy allergic adults were included, sIgE to total soy extract, Gly m 8, Gly m 4, Gly m 5, Gly m 6, Bet v 1, Ara h 1, Ara h 2 and Ara h 3 were determined. Sensitization patterns were analyzed and determined. The clinical relevance of sIgE of Gly m 8 sensitization was measured by assessing its capacity to degranulate basophils in Gly m8 sensitized patients by an indirect Basophil Activation Test (iBAT). Results: Based on the sIgE patterns of sensitization two groups of SA patients were identified. (i) Peanut-associated SA group (all patients were sensitized to one or more of the peanut compounds) and (ii) Non-Peanut/PR-10-associated SA group (22 patients were sensitized to Gly m 4 and Bet v 1 but not to any of the peanut compounds). A high and significant correlation between total soy extract and Gly m 6 (R2 =0.97), Gly m 5 (R2 =0.85) and Gly m 8 (R2 =0.78) was observed. A non-significant correlation was observed between the levels of sIgE of Gly m 8 vs Ara h2. The iBAT results showed that Gly m 8 did not induce basophil degranulation in any of the Peanut-associated patients; indicating that the Gly m8 sensitizations were not clinically relevant. Conclusions: Gly m 8 was not a major allergen in the selected soy allergic population. The iBAT results indicated that Gly m 8 was not able to induce basophil degranulation in sIgE Gly m 8 sensitized soy allergic patients. Thus, Gly m 8 would have no added value in the diagnosis of SA in the present study population.
DOI: 10.6084/m9.figshare.22692553
title: Supplementary Material for: IL-1β derived Th17 immune responses are a critical factor for neutrophilic-eosinophilic airway inflammation on psychological stress-induced immune tolerance breakdown in mice

description: Introduction: Asthma is an inflammatory reaction mediated by type 2 helper T (Th2) cells and is known to increase eosinophil levels. Our previous study showed that stress-related asthma can cause neutrophilic and eosinophilic airway inflammation by suppressing immune tolerance. However, the mechanism of stress-induced neutrophilic and eosinophilic airway inflammation remains unclear. Therefore, to elucidate the cause of neutrophilic and eosinophilic inflammation, we investigated the immune response during the induction of airway inflammation. In addition, we focused on the relationship between immune response modulation immediately after stress exposure and the development of airway inflammation. Methods: Asthmatic mice were induced by three phases using Female BALB/c mice. During the first phase, the mice were made to inhale ovalbumin (OVA) to induce immune tolerance before sensitization. Some mice were exposed to restraint stress during the induction of immune tolerance. In the second phase, the mice were sensitized with OVA/alum intraperitoneal injections. In the final phase, onset of asthma was induced through OVA exposure. Asthma development was evaluated based on airway inflammation and T-cell differentiation. Microarray and qPCR analyses were used to enumerate candidate factors to investigate the starting point of immunological modification immediately after stress exposure. Furthermore, we focused on interleukin-1β (IL-1β), which initiates these immune modifications, and performed experiments using its receptor blocker interleukin-1 receptor antagonist (IL-1RA). Results: Stress exposure during immune tolerance induction increased eosinophil and neutrophil airway infiltration. This inflammation was associated with decreased T regulatory cell levels and increased Th2 and Th17 levels in bronchial lymph node cells. Microarray and qPCR analyses showed that the initiation of Th17 differentiation might be triggered by stress exposure during tolerance induction. IL-1RA administration during stress exposure suppressed neutrophilic and eosinophilic airway inflammation via Th17 reduction and Treg increase. Discussion/Conclusions: Our results show that psychological stress causes both eosinophilic and neutrophilic inflammatory responses due to the breakdown of immune tolerance. Furthermore, stress-induced inflammation can be abolished using IL-1RA.
DOI: 10.6084/m9.figshare.22819868
title: Supplementary Material for: Association between serum Klotho and kidney stones in US middle-aged and older individuals with diabetes mellitus: Results from 2007–2016 National Health and Nutrition Survey

description: Introduction: Kidney stones (KSs) are associated with hematuria and renal failure and pose a signiﬁcant clinical and public health concern. Diabetes is associated with a higher risk of KSs. In addition, α-Klotho (Klotho), as a novel anti-aging protein, is associated with kidney disease, diabetes, and complications and may participate in the pathological mechanism of KSs. However, studies that used large population-based database research are limited. Therefore, this study aimed to investigate whether or not KS prevalence is associated with serum Klotho levels in diabetic adults in the United States. Methods: This nationally representative cross-sectional study used data on diabetic adults in the US aged 40–79 years from the National Health and Nutrition Examination Survey 2007–2016 cycles. Multivariate logistic regression models were used to calculate the association between Klotho and KS. Restricted cubic splines were used to further test for linearity and explore the shape of the dose-response association. Moreover, we performed stratiﬁed and interaction analyses to see if the relationship was stable in diﬀerent subgroups. Results: Among the 3,537 diabetic patients included in this study (mean age of 61.4 years, consisting of 51.3% males), 543 participants (15.4%) suffered from KS. In the fully adjusted model, Klotho was negatively associated with KS (OR = 0.72; 95% CI: 0.54–0.96; p = 0.027). A negative relationship was observed between the occurrence of KS and Klotho (nonlinear: p = 0.560). Some differences in the association between Klotho and KS were found in stratified analyses, however, these differences lacked statistical significance. Conclusions: Serum Klotho was negatively associated with the incidence of KS, when ln-transformed Klotho concentration increased by 1 unit, the risk of KS was 28% lower.
DOI: 10.6084/m9.figshare.23301884
title: Supplementary Material for: Supporting Children who are English Language Learners Succeed in Their Early Literacy Development.

description: Abstract Introduction The Better Start Literacy Approach [1] is an example of a Multi-Tiered System of Support (MTSS) framework to facilitate children’s early literacy success. It is set within a strengths-based and culturally responsive framework to literacy teaching and is being implemented in over 800 English medium schools across New Zealand. This report focuses on how bilingual children identified at school entry as English Language Learners (ELL) responded to the Better Start Literacy Approach during their first year at school. Method Using a novel matched-control design, the growth in phoneme awareness, phoneme-grapheme knowledge and oral narrative skills for 1,853 ELL was compared to a cohort of 1,853 non-ELL. The cohorts were matched for ethnicity (mostly Asian, 46% and Pacific, 26%), age (M = 65months), gender (53% male) and socio-economic deprivation index (82% in areas of mid to high deprivation). Results Data analyses indicated similar positive growth rates for ELL and non-ELL from baseline to the first monitoring assessment following 10 weeks of Tier 1 (universal/ class level) teaching. Despite demonstrating lower phoneme awareness skills at baseline, following 10 weeks of teaching, the ELL cohort performed similarly to non-ELL in non-word reading and spelling tasks. Predictors of growth analyses indicated that ELL from areas of low socio-economic deprivation, who used a greater number of different words in their English story retells at the baseline assessment, and females made the most growth in their phonic and phoneme awareness development. Following the 10-week monitoring assessment, 11% of the ELL and 13% of the non-ELL cohorts received supplementary Tier 2 (targeted small group) teaching. At the next monitoring assessment (20 weeks post baseline assessment) the ELL cohort showed accelerated growth in listening comprehension, phoneme-grapheme matching and phoneme blending skills, catching up to their non-ELL peers. Discussion Despite limitations of the data set available, it provides one of the few insights into the response of ELL to Tier 1 and Tier 2 teaching in their first year at school. The data suggest that the Better Start Literacy Approach, which includes high quality professional learning and development for teachers, literacy specialists and speech-language therapists, is an effective approach towards developing foundational literacy skills for English Language Learners. The important role speech-language therapists have in collaborating with class teachers to support children’s early literacy success within MTSS frameworks is discussed.
DOI: 10.6084/m9.figshare.23508495
title: Supplementary Material for: A Giant Urachal Accessory Spleen: Case Report

description: Accessory spleen (AS) refers to single or multiple splenic tissues which appear outside the relative normal spleen position results from embryonic dysplasia similar in structure and function to the spleen. AS is frequently observed in the splenic hilus and or adjacent to the tail of pancreas, and only a few cases occurred in the pelvic cavity. We present an extremely rare AS case in urachus, which was initially considered as an urachal neoplasm revealed on CT images with big mass. However, the postoperative pathology confirmed it was an AS that had not been reported at urachal before. Urachal AS can be misdiagnosed as a tumor, so it is vital to make an accurate imaging preoperative diagnosis to avoid unnecessary biopsy and surgery.
DOI: 10.13026/c25c73
title: Squid Giant Axon Membrane Potential

description: The SGAMP database contains single-unit neuronal recordings of North Atlantic squid (Loligo pealei) giant axons in response to stimulus currents. The membrane potential and stimulus current are given for a total of 170 trials across 8 different axons.
DOI: 10.17188/1208213
title: Materials Data on Ca by Materials Project

description: Ca is Copper structured and crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Ca is bonded to twelve equivalent Ca atoms to form a mixture of corner, edge, and face-sharing CaCa12 cuboctahedra. There are eight shorter (3.87 Å) and four longer (3.94 Å) Ca–Ca bond lengths.
DOI: 10.17632/j28vhs37n8.1
title: MATLAB scripts for processing and post-processing experimental data for "Crystallization and jamming in narrow fluidized beds"

description: This data presents MATLAB scripts and data in order to reproduce the figures and videos obtained for the article "Crystallization and jamming in narrow fluidized beds"
DOI: 10.3886/e114850v1
title: Replication data for: Optimal Taxation of Top Labor Incomes: A Tale of Three Elasticities

description: This paper derives optimal top tax rate formulas in a model where top earners respond to taxes through three channels: labor supply, tax avoidance, and compensation bargaining. The optimal top tax rate increases when there are zero-sum compensation-bargaining effects. We present empirical evidence consistent with bargaining effects. Top tax rate cuts are associated with top one percent pretax income shares increases but not higher economic growth. US CEO "pay for luck" is quantitatively more prevalent when top tax rates are low. International CEO pay levels are negatively correlated with top tax rates, even controlling for firms' characteristics and performance.
DOI: 10.5067/glossac-l3-v1.0
title: GloSSAC Level 3 netCDF file - Version 1
DOI: 10.5281/zenodo.3676882
title: Dataset/Development of a novel calorimetry setup based on metallic paramagnetic temperature sensors

description: Dataset related to the publication "Development of a novel calorimetry setup based on metallic paramagnetic temperature sensors" submitted to Review of Scientific Instruments.
DOI: 10.5284/1046750
title: Origins of agriculture: archaeobotanical database

description: Scope
This database compiles, from published sources, the sample records of archaeobotanical (plant) remains from archaeological sites located in southwest Asia, central Anatolia and Cyprus dated to the Pre-Pottery Neolithic or earlier.

Research
The database contributes directly to the following publication, and users are referred to that article for further information on the development and intended use of the database:

Wallace, M., Jones, G., Charles, M., Forster, E., Stillman, E., Bonhomme, V., Livarda, A., Osborne, C., Rees, M., Frenck, G., Preece, C. (submitted). Re-analysis of archaeobotanical remains from pre- and early agricultural sites provides no evidence for a narrowing of the wild plant food spectrum during the origins of agriculture in southwest Asia. Vegetation History and Archaeobotany.

Funding
This database was developed during two projects based at the University of Sheffield, funded by a European Research Council (ERC) grant 'The Evolutionary Origins of Agriculture' (grant no. 269830-EOA, PI Glynis Jones, University of Sheffield) and a Natural Environment Research Council (NERC) grant 'Origins of Agriculture: an Ecological Perspective on Crop Domestication' (grant no. NE/H022716/1, PI Colin Osborne, University of Sheffield). The database builds on an earlier database compiled by Sue Colledge during 'The Origin and Spread of Neolithic Plant Economies in the Near East and Europe' project (AHRB, PIs Stephen Shennan and James Conolly, University College London) and the 'Domestication of Europe' project (NERC, PI Terry Brown, University of Manchester).

Citation
When using data included in this database the original publication(s) of the data should be cited. Original publications can be identified in the tables '4_Records (samples)' and '5_References'. The authors would be grateful if this database is cited in addition to the original publication(s).

Disclaimer
This database is a compilation of data as presented by other researchers. Inclusion in this database does not constitute an endorsement of the data or the researchers. The authors of the database do not take responsibility for any adverse outcome due to transcription or other errors introduced in the creation of this database. When using the database the original source of data should be checked to ensure the accuracy and integrity of the data included in the database
DOI: 10.5286/isis.e.rb1810217
title: Homogeneous nucleation in phosphate-based glassy precursors to fast-ion conducting glass-ceramic electrolytes

description: The structure of the phosphate materials Na_{1+x}Ge_{2-x}Al_x(PO_4)_3 with x = 0, 0.4 and 0.8 will be investigated using high real-space resolution neutron diffraction. In the crystalline phases with x = 0.4 and 0.8, fast-sodium ion conductivity occurs. These solid electrolyte materials are best prepared via the glass-ceramic route, which indicates a homogeneous nucleation mechanism. The objectives are (1) to understand the structural relationship between an ion-conducting glass ceramic and its precursor glass, and (2) to monitor the structural rearrangements that may occur during the early stages of crystallization. The latter is of general scientific interest for any glass undergoing homogeneous nucleation, and has never been explored in non-siliceous systems. The experiments will reveal the Ge coordination environment, which is inaccessible from spectroscopic methods.
DOI: 10.5291/ill-data.6-05-988
title: Structure of magnesium aluminosilicate glass
DOI: 10.5517/ccdc.csd.cc20lv0h
title: CCDC 1865146: Experimental Crystal Structure Determination

description: Related Article: Bernhard Herrschaft|2018|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.11876364
title: Data set with ab initio CH3Cl potential energy surface

description: The data set with <i>ab initio</i> CH<sub>3</sub>Cl potential energy surface used in [P. O. Dral, A. Owens, A. Dral, G. Csányi, Hierarchical Machine Learning of Potential Energy Surfaces. J. Chem. Phys. 2020, 152, 204110]. <br><br>Original publication describing most of this data set is [A. Owens, S. N. Yurchenko, A. Yachmenev, J. Tennyson, W. Thiel, Accurate ab initio vibrational energies of methyl chloride. J. Chem. Phys. 2015, 142, 244306].<br><br>Files in CH3Cl_PES.zip:geom.dat - geometries of CH3Cl in internal coordinatesxyz.dat - geometries of CH3Cl in Cartesian coordinates (in Angstrom)<br>MP2.dat - energies at MP2/aug-cc-pVQZVTZ.dat - energies at CCSD(T)-F12b/cc-pVTZ-F12VQZ.dat - energies at CCSD(T)-F12b/cc-pVQZ-F12CBS.dat - energies at CCSD(T)-F12b/CBS<br>SR.dat - scalar relativistic (SR) effects<br>CV.dat - energy corrections to account for core-valence electron correlation<br>HO.dat - higher-order coupled cluster terms beyond perturbative triples<br>DBOC.dat - diagonal Born-Oppenheimer corrections<br>TBE.dat - theoretical best estimate of ab initio energies<br>Every file contains data for 44819 geometries given in the same order.Every line of geom.dat defines one geometry in internal coordinates given in the order r(C-Cl), r(C-H1), r(C-H2), r(C-H3), beta(Cl-C-H1), beta(Cl-C-H2), beta(Cl-C-H3), teta<sub>12</sub>, teta13. r denotes internuclear distance (in Angstrom), beta denotes bond angles (in degrees), teta<sub>ij </sub> denotes dihedral angle (in degrees) between adjacent planes containing HiCCl and HjCCl. See also [A. Owens, S. N. Yurchenko, A. Yachmenev, J. Tennyson, W. Thiel, Accurate ab initio vibrational energies of methyl chloride. J. Chem. Phys. 2015, 142, 244306] for definitions.<br><br>As a near-equilibrium geometry used for generating molecular descriptors in [P. O. Dral, A. Owens, A. Dral, G. Csányi, Hierarchical Machine Learning of Potential Energy Surfaces. J. Chem. Phys., 152, 204110] as described in [P. O. Dral, A. Owens, S. N. Yurchenko, W. Thiel, J. Chem. Phys. 2017, 146, 244108] and [P. O. Dral, J. Comput. Chem. 2019, 40, 2339–2347], the C<sub>3v</sub> symmetrical geometry of CH<sub>3</sub>Cl was used with r(C-Cl) = 1.7773 A, r(C-H) = 1.0839 A, beta = 108.49 degrees, teta = 120.00 degrees.
DOI: 10.6084/m9.figshare.21878247
title: Supplementary Material for: Somatic variants and exon-level copy number changes in five hyperplastic-stage oral leukoplakias.

description: Oral leukoplakia (OL), an oral potentially malignant disorder begins with a hyperplastic/hyperkeratotic stage at which no genome-scale somatic single nucleotide variant profiles have been described so far. We performed exome sequencing of five cases at this stage with no evidence of dysplasia to identify genetic alterations (exon-level copy number alterations, indels, and single nucleotide variants), their association with transcript levels and relationship with oral cancer susceptibility. Pathway enrichment analysis of genes associated with tobacco chewing and age-related mutation signatures, transcripts with variants predicted to be functionally damaging and those with significantly altered levels have all indicated the involvement of focal adhesion, ECM–receptor interactions, regulation of cytoskeleton and DNA repair. Two novel mutations identified in FAT1 tumor suppressor gene were associated with decreased transcript levels. In addition, 16 expressed cancer driver genes contained functionally damaging variants. Many of the affected genes were also reported in dysplastic OL lesions. The presence of variants in cancer driver genes and those shared with oral dysplasias possibly provide a basis for further progression and increased susceptibility to oral cancer.