cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2c9p4j
title: CCDC 2184047: Experimental Crystal Structure Determination

description: Related Article: Alexandre N. Sobolev, Christopher B. Smith, Colin L. Raston|2022|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: 10.5517/ccdc.csd.cc2c9p5k
title: CCDC 2184048: Experimental Crystal Structure Determination

description: Related Article: Alexandre N. Sobolev, Christopher B. Smith, Colin L. Raston|2022|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: 10.25377/sussex.21263289.v1
title: Research data for paper Molecular and functional characterization of an evolutionarily conserved CREB-binding protein in the Lymnaea CNS

description: Research data for paper Molecular and functional characterization of an evolutionarily conserved CREB-binding protein in the <em>Lymnaea</em> CNS (FASEB Journal October 2022). <br> This dataset consists of two Excel spreadsheets containing molecular biological and electrophysiological data, respectively. <br> The data used for Figure 2 was obtained by measuring the expression levels of the CBP mRNA in different tissues of <em>Lymnaea</em> by using qRT-PCR. The data used for the graph and associated statistical analysis show that the expression level is highest in the central nervous system (CNS). <br> The data used for Figure 6F was obtained by intracellular microelectrophysiology to measure the amplitude of the monosynaptic EPSP evoked in the motoneuron B1 by the electrical stimulation of the Cerebral Giant Cell (CGC) under different experimental conditions. The data used for the graph and associated statistical analysis show that injection of cAMP into the CGC cell body increased EPSP amplitude in the B1 motoneuron, but pre-treatment with either of the three HAT inhibitors prevented the cAMP-induced increase of EPSP. It also shows that 5'AMP that was used as a control for cAMP did not increase the amplitude of the B1 EPSP.
DOI: 10.25377/sussex.21263289
title: Research data for paper Molecular and functional characterization of an evolutionarily conserved CREB-binding protein in the Lymnaea CNS

description: Research data for paper Molecular and functional characterization of an evolutionarily conserved CREB-binding protein in the <em>Lymnaea</em> CNS (FASEB Journal October 2022). <br> This dataset consists of two Excel spreadsheets containing molecular biological and electrophysiological data, respectively. <br> The data used for Figure 2 was obtained by measuring the expression levels of the CBP mRNA in different tissues of <em>Lymnaea</em> by using qRT-PCR. The data used for the graph and associated statistical analysis show that the expression level is highest in the central nervous system (CNS). <br> The data used for Figure 6F was obtained by intracellular microelectrophysiology to measure the amplitude of the monosynaptic EPSP evoked in the motoneuron B1 by the electrical stimulation of the Cerebral Giant Cell (CGC) under different experimental conditions. The data used for the graph and associated statistical analysis show that injection of cAMP into the CGC cell body increased EPSP amplitude in the B1 motoneuron, but pre-treatment with either of the three HAT inhibitors prevented the cAMP-induced increase of EPSP. It also shows that 5'AMP that was used as a control for cAMP did not increase the amplitude of the B1 EPSP.
DOI: 10.17632/vphzykvvf2.1
title: ana_cont: Python package for analytic continuation

description: We present the Python package ana_cont for the analytic continuation of fermionic and bosonic many-body Green's functions by means of either the Padé approximants or the maximum entropy method. The determination of hyperparameters and the implementation are described in detail. The code is publicly available on GitHub, where also documentation and learning resources are provided.
DOI: 10.17632/p5nbm6s32v.1
title: Hedgerow Soil Carbon to 1 meter (California)

description: Using a regional survey on intensively managed farms, soil organic carbon (SOC) concentrations and stocks (0–100 cm) were evaluated in a pairwise comparison of long-term (10+ years) woody hedgerow plantings and adjacent crop fields in Yolo County, CA, USA. Twenty-one paired sites were selected to represent four soil types (Yolo silt loam, Brentwood clay loam, Capay silty clay, and Corning loam), with textures ranging from 16% to 51% clay. We hypothesized that SOC will be greater under hedgerows than cultivated fields, in both the surface and the subsurface, but that the difference and distribution will vary by soil type and/or silt and clay content. Soil C was higher in the upper 100 cm under hedgerows (14.4 kg m−2) relative to cultivated fields (10.6 kg m−2) and at all depths (0–10, 10–20, 20–50, 50–75, and 75–100 cm). The difference in SOC (3.8 kg m−2) did not vary by soil type, suggesting a broad potential for hedgerows to increase SOC stocks. Assuming adoption rates of 50 to 80% across California for hypothetical field edges of average-size farms, and an identical SOC sequestration potential across soil types, hedgerows could sequester 10.8 to 17.3 MMT CO2e, or 7 to 12% of California’s annual greenhouse gas reduction goals. Data includes soil physicochemical properties (i.e. carbon, nitrogen bulk density, % sand, % clay, and pH), morphological characteristics (i.e. topsoil depth, rooting depth), and site/management information (i.e. hedgerow age, compost application, cover crop).
DOI: 10.17632/x54bnz5vxk.1
title: DeePKS-kit: A package for developing machine learning-based chemically accurate energy and density functional models

description: We introduce DeePKS-kit, an open-source software package for developing machine learning based energy and density functional models. DeePKS-kit is interfaced with PyTorch, an open-source machine learning library, and PySCF, an ab initio computational chemistry program that provides simple and customized tools for developing quantum chemistry codes. It supports the DeePHF and DeePKS methods. In addition to explaining the details in the methodology and the software, we also provide an example of developing a chemically accurate model for water clusters.
DOI: 10.17632/7yy2s724yx.1
title: PEDESTRIAN SPEED DATA UNDER DIFFERENT CLOTHES ATTIRE

description: little is known about pedestrian facility design standards based on clothing characteristics, despite the fact that pedestrians are observed walking differently when they are on different attires.  For example an Arabian man on long jallabiya is always finding it difficult to have a longer pacing distance; an African men wearing flowing gown known as babbar-riga most a time hinder other facility users while trying to redress his attire. Similarly an African woman wearing headscarf known as gyale obstructs flow of other pedestrians whenever she is redressing the gyale.
DOI: 10.17632/c8x3wxz97c.1
title: Perceptual hearing sensitivity during vocal production_Original code

description: The folder, 2-AFC setup, is the custom-made app in Figure S6.  Bat training and detection threshold estimates for the bats in all three detection tasks were all achieved with this app. 
The folder, Data analyse, is used to organized the detection thresholds and call parameters.
DOI: 10.17632/swp88cvpwb.1
title: Permafrost modelling with OpenFOAM®: New advancements of the permaFoam solver

description: Permafrost, i.e., soil that is year-round frozen in depth, is covering a quarter of the continents of the northern hemisphere. It currently experiences fast changes due to climate change at global scale and technogenic perturbations at local scale, and the assessment and anticipation of these changes are of primary importance for many environmental and engineering applications in cold regions. To these ends, permafrost modelling is required, while the strong couplings and non-linearities involved in the physics at stake make it highly challenging, especially from a computational point of view. In this work we present a new solver for permafrost hydrology developed in the framework of OpenFOAM®, allowing to benefit from its advanced high-performance computing capabilities. The solver is tested for realistic, field-based cases, and its parallel performances are characterized up to ∼16 000 cores on IRENE supercomputer (TGCC, CEA).
DOI: 10.17632/ptc9t46xyn.1
title: tapir: A tool for topologies, amplitudes, partial fraction decomposition and input for reductions

description: The demand for precision predictions in the field of high energy physics has dramatically increased over recent years. Experiments conducted at the LHC, as well as precision measurements at the intensity frontier such as Belle II require equally precise theoretical predictions to make full use of the acquired data. To match the experimental precision, second-, third- and, for certain quantities, even higher-order calculations in perturbative quantum field theory are required.

To facilitate such calculations, computer software automating as many steps as possible is required. Yet, each calculation poses different challenges and thus, a high level of configurability is required. In this context we present tapir: a tool for identification, manipulation and minimization of Feynman integral families. It is designed to integrate in toolchains based on the computer algebra system FORM, the use of which is common practice in the field. tapir can be used to reduce the complexity of multi-loop problems with cut-filters, topology mapping, partial fraction decomposition and alike.
DOI: 10.17632/2f39h7tr5t.1
title: The macrophage-associated lncRNA MALR facilitates ILF3 liquid-liquid phase separation to promote HIF1α signaling in esophageal cancer

description: original WB
DOI: 10.17632/nxdrvfphzz.1
title: Composition of Cell-Derived Matrices from Acomys cahirinus and Mus musculus - Label Free Quantitative Proteomics

description: The Spiny Mouse (Acomys) is gaining popularity as a research organism due to its phenomenal regenerative capabilities. However, access to Acomys colonies is limited and primary fibroblasts can only be maintained in culture for a limited time. To address these obstacles, we generated two immortalized Acomys dermal fibroblast lines. AcoSV40 fibroblasts were generated through lentiviral transfection with the SV40 Large T antigen. AcoSI fibroblasts were generated through spontaneous immortalization during prolonged subculture. 

To demonstrate functional similarity between the two cell lines and primary Acomys fibroblasts (pAFs), we assessed deposited ECM proteins. Primary Mus fibroblasts and NIH3T3 fibroblasts were included as a comparison because NIH3T3 fibroblasts are a commonly used substitute for primary Mus fibroblasts. We made cell derived matrices (CDMs) with each of the 5 cell types by culturing them on collagen functionalized PDMS substrates for 7-28 days in media containing 25mg/mL Ficoll-400. Three sets of CDMs from each cell type were made. The CDMs were decellularized with a Triton X-100 and ammonium hydroxide solution, followed by a DNase treatment. Decellularized CDMs were then homogenized, acetone precipitated, and sent to the UF Mass Spectrometry Research and Education Center for label-free quantitative proteomics. Nano-liquid chromatography tandem mass spectrometry (Nano-LC/MS/MS) was performed on a Thermo Scientific Q Exactive HF Orbitrap mass spectrometer equipped with an EASY Spray nanospray source (Thermo Scientific) operated in positive ion mode.  The LC system was an UltiMate™ 3000 RSLCnano system from Thermo Scientific. Precursor ion intensity label free quantitation was done using Proteome Discoverer (Thermo Fisher Scientific vs 2.4.0.305). The spreadsheets provided are the identified protein IDs found in each of the sample groups (Acomys, AcoSV40, AcoSI, Mus, NIH3T3). Three replicates are grouped into each result file. 

Using these outputs, we performed the following comparisons : Acomys vs. AcoSV40, Acomys vs. AcoSI, and Mus vs. NIH3T3 in Proteome Discoverer.  No significant differences in CDM composition were found between pAFs and AcoSV40 fibroblasts. AcoSI-1 CDMs shared 88% of proteins identified with pAFs. The proteins that differed between the two samples were involved in biological processes related to metabolism and translation, based on a GO enrichment analysis. In comparison, NIH3T3s, a commonly used substitute for Mus musculus cells, only shared 75% of proteins with their counterpart. Based on these results, AcoSV40 and AcoSI-1 should be representative of pAFs in experiments related to ECM deposition.
DOI: 10.17632/vz4gdfnxxf.1
title: Dry (Wet) -Cold (Warm) Trend in the Huang-Huai-Hai Plain of China: Using a Compound Trend Identification Method

description: The impact of climate change on the human living environment cannot be underestimated. It not only leads to frequent extreme climate events but also changes the dry-wet and cold-warm structures in various regions. As a critical grain-producing area in China, it is essential to analyze the changes in climatic conditions in Huang-Huai-Hai Plain. 
In this work, we mainly designed a method to determine the compound dry-wet and cold-warm structural changes and constructed an index to quantify this change. The compound trend characteristics of this period were analyzed using the remote sensing precipitation data and temperature reanalysis data from 2001 to 2021 in the Huang-Huai-Hai region. 
The results show that: the study area gradually changed from drying-cooling to wetting-warming during 2006-2016. Although some areas of the Huang River Basin (especially the southern part of the Huang River) align with this trend, there is still a phenomenon of drying on the whole.
DOI: 10.6084/m9.figshare.21071251
title: Biomechanical effects of a halo orthotic on a pediatric anthropomorphic test device in a simulated frontal motor vehicle collision

description: <b>Objective:</b> Cervical spine injuries in children under 10 frequently involve the craniocervical junction. In patients too small for conventional spinal instrumentation, treatment may involve placement of a halo orthotic, and these patients will frequently be discharged home in a halo orthotic. To date, little research has been done on the biomechanics of motor vehicle collisions involving young children in halo orthotics. To better understand possible safety concerns, we applied a halo orthotic to an appropriately sized anthropomorphic test device (ATD, or crash test dummy) on an acceleration sled to simulate a frontal motor vehicle collision. <b>Methods:</b> For the tests, a Hybrid III 3-year-old ATD was instrumented with head and chest accelerometers, head angular rate sensors, a six-axis upper neck load cell, and a chest linear potentiometer. Four tests were conducted on an acceleration sled, and kinematics were recorded with high speed video. Testing variables included 1) with or without a halo orthotic and 2) with a standard booster seat or a commercially available harness vest. <b>Results:</b> The halo orthotic reduced flexion and extension but was associated with increased rotation, especially in the condition of a halo orthotic with a standard booster seat. Increased cervical distraction was noted with the halo orthotic, and this was especially increased in the condition of a halo orthotic with the harness vest. <b>Conclusions:</b> The biomechanics of a child involved in a motor vehicular collision may be dramatically altered with a halo orthotic, as modeled by an acceleration sled test. While cervical spine flexion and extension are reduced with the halo orthotic, rotation appears to increase. Immobilization from a halo orthotic also appears to increase cervical distraction, especially when used in conjunction with a harness vest. Further testing is needed to determine the safest restraints for this small, but at-risk, population.
DOI: 10.6084/m9.figshare.21071251.v1
title: Biomechanical effects of a halo orthotic on a pediatric anthropomorphic test device in a simulated frontal motor vehicle collision

description: <b>Objective:</b> Cervical spine injuries in children under 10 frequently involve the craniocervical junction. In patients too small for conventional spinal instrumentation, treatment may involve placement of a halo orthotic, and these patients will frequently be discharged home in a halo orthotic. To date, little research has been done on the biomechanics of motor vehicle collisions involving young children in halo orthotics. To better understand possible safety concerns, we applied a halo orthotic to an appropriately sized anthropomorphic test device (ATD, or crash test dummy) on an acceleration sled to simulate a frontal motor vehicle collision. <b>Methods:</b> For the tests, a Hybrid III 3-year-old ATD was instrumented with head and chest accelerometers, head angular rate sensors, a six-axis upper neck load cell, and a chest linear potentiometer. Four tests were conducted on an acceleration sled, and kinematics were recorded with high speed video. Testing variables included 1) with or without a halo orthotic and 2) with a standard booster seat or a commercially available harness vest. <b>Results:</b> The halo orthotic reduced flexion and extension but was associated with increased rotation, especially in the condition of a halo orthotic with a standard booster seat. Increased cervical distraction was noted with the halo orthotic, and this was especially increased in the condition of a halo orthotic with the harness vest. <b>Conclusions:</b> The biomechanics of a child involved in a motor vehicular collision may be dramatically altered with a halo orthotic, as modeled by an acceleration sled test. While cervical spine flexion and extension are reduced with the halo orthotic, rotation appears to increase. Immobilization from a halo orthotic also appears to increase cervical distraction, especially when used in conjunction with a harness vest. Further testing is needed to determine the safest restraints for this small, but at-risk, population.
DOI: 10.6084/m9.figshare.20715627.v1
title: Body mass index influence on lap belt position and abdominal injury in frontal motor vehicle crashes

description: As obesity rates climb, it is important to study its effects on motor vehicle safety due to differences in restraint interaction and biomechanics. Previous studies have shown that an abdominal seatbelt sign (referred hereafter as seatbelt sign) sustained from motor vehicle crashes (MVCs) is associated with abdominal trauma when located above the anterior superior iliac spine (ASIS). This study investigates whether placement of the lap belt causing a seatbelt sign is associated with abdominal organ injury in occupants with increased body mass index (BMI). We hypothesized that higher BMI would be associated with a higher incidence of superior placement of the lap belt to the ASIS level, and a higher incidence of abdominal organ injury. A retrospective data analysis was performed using 230 cases that met inclusion criteria (belted occupant in a frontal collision that sustained at least one abdominal injury) from the Crash Injury Research and Engineering Network (CIREN) database. Computed tomography (CT) scans were rendered to visualize fat stranding to determine the presence of a seatbelt sign. 146 positive seatbelt signs were visualized. ASIS level was measured by adjusting the transverse slice of the CT to the visualized ASIS level, which was used to determine seatbelt sign location as superior, on, or inferior to the ASIS. Obese occupants had a significantly higher incidence of superior belt placement (52%) vs on-ASIS placement (24%) compared to their normal (27% vs 67%) BMI counterparts (p &lt; 0.001). Notable trends included obese occupants with superior placement having less abdominal organ injury incidence than those with on-ASIS belt placement (42% superior placement vs 55% on-ASIS). In non-obese occupants, there was a higher incidence of abdominal organ injury with superior lap belt placement compared to on-ASIS placement counterparts (Normal BMI: 62% vs 41%, Overweight: 57% vs 43%). In CIREN occupants with abdominal injury, those with obesity are more prone to positioning the lap belt superior to the ASIS, though the impact on abdominal injury incidence remains a key point for continued exploration into how occupant BMI affects crash safety and belt design.
DOI: 10.6084/m9.figshare.20715627
title: Body mass index influence on lap belt position and abdominal injury in frontal motor vehicle crashes

description: As obesity rates climb, it is important to study its effects on motor vehicle safety due to differences in restraint interaction and biomechanics. Previous studies have shown that an abdominal seatbelt sign (referred hereafter as seatbelt sign) sustained from motor vehicle crashes (MVCs) is associated with abdominal trauma when located above the anterior superior iliac spine (ASIS). This study investigates whether placement of the lap belt causing a seatbelt sign is associated with abdominal organ injury in occupants with increased body mass index (BMI). We hypothesized that higher BMI would be associated with a higher incidence of superior placement of the lap belt to the ASIS level, and a higher incidence of abdominal organ injury. A retrospective data analysis was performed using 230 cases that met inclusion criteria (belted occupant in a frontal collision that sustained at least one abdominal injury) from the Crash Injury Research and Engineering Network (CIREN) database. Computed tomography (CT) scans were rendered to visualize fat stranding to determine the presence of a seatbelt sign. 146 positive seatbelt signs were visualized. ASIS level was measured by adjusting the transverse slice of the CT to the visualized ASIS level, which was used to determine seatbelt sign location as superior, on, or inferior to the ASIS. Obese occupants had a significantly higher incidence of superior belt placement (52%) vs on-ASIS placement (24%) compared to their normal (27% vs 67%) BMI counterparts (p &lt; 0.001). Notable trends included obese occupants with superior placement having less abdominal organ injury incidence than those with on-ASIS belt placement (42% superior placement vs 55% on-ASIS). In non-obese occupants, there was a higher incidence of abdominal organ injury with superior lap belt placement compared to on-ASIS placement counterparts (Normal BMI: 62% vs 41%, Overweight: 57% vs 43%). In CIREN occupants with abdominal injury, those with obesity are more prone to positioning the lap belt superior to the ASIS, though the impact on abdominal injury incidence remains a key point for continued exploration into how occupant BMI affects crash safety and belt design.