cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21541864.v1
title: Additional file 10 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

description: Additional file 10 Supplementary Table 2. The identity and frequency of all types of fingerprints in mouse KRAB-ZFP-associated ZnFs (information for Supplementary Fig. 3).
DOI: 10.6084/m9.figshare.21541870.v1
title: Additional file 11 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

description: Additional file 11 Supplementary Table 3. High frequency ZnFs in clusters 3–5 (additional information for Fig. 1C).
DOI: 10.6084/m9.figshare.17871800.v1
title: Mitochondrial genome sequencing with short overlapping amplicons on MiSeq FGx system

description: With the development and maturation of massively parallel sequencing (MPS) technology, the mitochondrial genome (mitogenome) sequencing is increasingly applied in the forensic field. In this study, we employed the strategy of short overlapping amplicons for the whole mitogenome, library preparation with tagmentation using the Nextera® XT DNA Library Preparation Kit, sequencing on the MiSeq FGx<sup>TM</sup> Forensic Genomics System and analyzing data using the mitochondrial(mtDNA) MSR Plug-in and the mtDNA Variant Analyzer. A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3, respectively. Results showed more than 1800 × of averaged depth of coverage (DoC) at each position. Concordant haplotypes of 9947 A and 2800 M were obtained at 32 variants. Cross-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily distinguished. Full and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference profiles. More than 86% variants were detected from ≥200-bp degraded samples but its haplotype was assigned to more ancestral haplogroup. Further, a total of 3 962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to transversions. Two new transversions (C13735A and A14755C) and two tri-alleles at nps 9824 and 16092 were identified. There were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 haplogroups. Haplogroup D was the preponderant top-level haplogroup in Xibe followed by F, B, M, A, N, G, C, Z, Y, HV and J. Random match probability (RMP) and haplotype diversity (HD) of the whole mitogenome was calculated as 0.0097 and 1.0000, respectively. Compared with HVS-I only, RMP decreased 33.56%, while the number of haplotypes and HD increased 15.73% and 0.49%, respectively. Principal component analysis (PCA) showed that Xibe was clustered to East and Southeast Asian. As a whole, this MPS strategy is suitable for the whole mitogenome sequencing especially for degraded samples and can facilitate generating mitogenome data to support the routine application in forensic sciences. EMP00726 is the first whole mitogenome dataset from Xibe contributed to the EMPOP. Supplemental data for this article are available online at.
DOI: 10.6084/m9.figshare.21541882
title: Additional file 13 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

description: Additional file 13 Supplementary Table 5. sgRNA efficiency test in reporter system (raw data for Fig. 4B and D).
DOI: 10.6084/m9.figshare.7385873
title: Additional file 6: of Intramuscular preadipocytes impede differentiation and promote lipid deposition of muscle satellite cells in chickens

description: Table S6. The enriched pathways based on 1653 DEG. (XLSX 16Â kb)
DOI: 10.6073/pasta/fd89fe2e352567e6671fe6ed54a1ec83
title: North Temperate Lakes LTER: Fish Species Richness 1981 - current

description: This data set is a derived data set based on fish catch data. Data are collected annually to enable us to track the fish assemblages of eleven primary lakes (Allequash, Big Muskellunge, Crystal, Sparkling, Trout, bog lakes 27-02 [Crystal Bog] and 12-15 [Trout Bog], Mendota, Monona, Wingra and Fish). Sampling on Lakes Monona, Wingra, and Fish started in 1995; sampling on other lakes started in 1981. Sampling is done at six littoral zone sites per lake with seine, minnow or crayfish traps, and fyke nets; a boat-mounted electrofishing system samples three littoral transects. Vertically hung gill nets are used to obtain two pelagic samples per lake from the deepest point. A trammel net samples across the thermocline at two sites per lake. In the bog lakes only fyke nets and minnow traps are deployed. Parameters measured include species-level identification and lengths for all fish caught, and weight and scale samples from a subset. Derived data sets include species richness, catch per unit effort, and size distribution by species, lake, and year. Species richness for a lake is the number of fish species caught in that lake during the annual fish sampling. Hybrids captured are only included in the richness value if neither of the two hybridized species are caught in the lake that year. Fish identified only to genus or higher taxonomic level are not included if any fish identified to species within that genus or higher taxonomic level are caught. E.g., Unidentified Chub would be only included in the richness value if no other chub is caught in that lake that year. Sampling Frequency: annually. Number of sites: 11
 Notes: Beach seining was discontinued after 2019. 2020 data does not exist due to insufficient sampling. In 2021, sampling in Fish Lake was suspended due to significant lake level changes. Data is missing for the two bogs in 2022.
 Please consult NTL's website for information on experimental lake manipulations and the DNR's website for management activities
DOI: 10.6084/m9.figshare.21541872
title: Additional file 4 of ERF49 mediates brassinosteroid regulation of heat stress tolerance in Arabidopsis thaliana

description: Additional file 4. Detailed information of genes upregulated after BR treatment.
DOI: 10.6084/m9.figshare.21541891
title: Additional file 15 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

description: Additional file 15 Supplementary Table 7. Primers used in Fig. 5.
DOI: 10.48577/jpl.hlb3ug
title: Applying an Uncrewed Surface Vehicle to Measure Under-Pier Bathymetry

description: This paper describes a simple and cost-effective solution developed to map generalized bathymetry underneath Navy piers. This challenging environment is constrained by tides, ship movements, varying pier architectures, and sporadic or non-existent GPS signals. We used a small, remotely operated surface vessel with an integrated single-beam sonar system (for depth, z measurements) and geographic positioning system (GPS; for some latitude/longitude, x,y positions) and also used an ultra short baseline (USBL) acoustic positioning system to determine x,y positions when GPS was denied under the pier. This manuscript presents the methods developed, including the approach used to combine these different data streams, to allow other researchers to collect and process similar datasets in constrained environments.
DOI: 10.48577/jpl.96lkft
title: Double Asteroid Redirection Test (DART): Navigating to Obliteration

description: DART is NASA’s demonstration of an asteroid deflection using a kinetic impactor. The spacecraft launched aboard a SpaceX’s Falcon 9 on November 24th 2021, on a direct collision with the binary asteroid system Didymos planned for September 26th 2022. By impacting the small moon, Dimorphos, DART’s objective was to alter the moon’s orbit about the larger asteroid by several minutes. The navigation of a ballistic mission is usually relatively simple. Other than heading to a violent demise, this mission had a number of unconventional aspects which gave the navigation team interesting challenges: a tight propellant budget for part of the mission, no reaction wheels which resulted in a noisy spacecraft with the Nav team having to rely heavily on Delta Differential Oneway Ranging measurements to identify off line-of-sight Delta-V, and critical operations in the last 30 days of the mission under a new thrusting control mode regime. Optical navigation was a critical element in the success of this mission, contributing to the determination of the spacecraft and target ephemerides for refined targeting maneuvers. After strategic decisions in the final weeks of the missions, DART could have comfortably hit the larger asteroid, Didymos, which increased the probably of impact with its moon Dimorphos.
DOI: 10.48577/jpl.hyylyd
title: The magnetic field in the Flame nebula

description: Context. Star formation drives the evolution of galaxies and the cycling of matter between different phases of the interstellar medium and stars. The support of interstellar clouds against gravitational collapse by magnetic fields has been proposed as a possible explanation for the low observed star formation efficiency in galaxies and the Milky Way. The Planck satellite provided the first all-sky map of the magnetic field geometry in the diffuse interstellar medium on angular scales of 5-15′. However, higher spatial resolution observations are required to understand the transition from diffuse, subcritical gas to dense, gravitationally unstable filaments. Aims. NGC 2024, also known as the Flame Nebula, is located in the nearby Orion B molecular cloud. It contains a young, expanding HII region and a dense supercritical filament. This filament harbors embedded protostellar objects and is likely not supported by the magnetic field against gravitational collapse. Therefore, NGC 2024 provides an excellent opportunity to study the role of magnetic fields in the formation, evolution, and collapse of dense filaments, the dynamics of young HII regions, and the effects of mechanical and radiative feedback from massive stars on the surrounding molecular gas. Methods. We combine new 154 and 216 μm dust polarization measurements carried out using the HAWC+ instrument aboard SOFIA with molecular line observations of 12CN(1–0) and HCO+(1–0) from the IRAM 30-meter telescope to determine the magnetic field geometry, and to estimate the plane of the sky magnetic field strength across the NGC 2024 HII region and the surrounding molecular cloud. Results. The HAWC+ observations show an ordered magnetic field geometry in NGC 2024 that follows the morphology of the expanding HII region and the direction of the main dense filament. The derived plane of the sky magnetic field strength is moderate, ranging from 30 to 80 μG. The strongest magnetic field is found at the northern west edge of the HII region, characterized by the highest gas densities and molecular line widths. In contrast, the weakest field is found toward the main, dense filament in NGC 2024. Conclusions. We find that the magnetic field has a non negligible influence on the gas stability at the edges of the expanding HII shell (gas impacted by the stellar feedback) and the filament (site of the current star formation).
DOI: 10.48577/jpl.3aju3r
title: The High Energy X-ray Probe (HEX-P): The Future of Hard X-ray Dual AGN Science

description: A fundamental goal of modern-day astrophysics is to understand the connection between supermassive black hole (SMBH) growth and galaxy evolution. Merging galaxies offer one of the most dramatic channels for galaxy evolution known, capable of driving inflows of gas into galactic nuclei, potentially fueling both star formation and central SMBH activity. Dual active galactic nuclei (dual AGNs) in late-stage mergers with nuclear pair separations &lt;10 kpc are thus ideal candidates to study SMBH growth along the merger sequence since they coincide with the most transformative period for galaxies. However, dual AGNs can be extremely difficult to confirm and study. Hard X-ray (&gt;10 keV) studies offer a relatively contamination-free tool for probing the dense obscuring environments predicted to surround the majority of dual AGN in late-stage mergers. To date, only a handful of the brightest and closest systems have been studied at these energies due to the demanding instrumental requirements involved. We demonstrate the unique capabilities of HEX-P to spatially resolve the soft and - for the first time - hard X-ray counterparts of closely-separated (~2-5 arcsec) dual AGNs in the local Universe. By incorporating state-of-the-art physical torus models, we reproduce realistic broadband X-ray spectra expected for deeply embedded accreting SMBHs. Hard X-ray spatially resolved observations of dual AGNs – accessible only to HEX-P – will hence transform our understanding of dual AGN in the nearby Universe.
DOI: 10.6084/m9.figshare.7385987
title: MOESM5 of Exploration of methylation-driven genes for monitoring and prognosis of patients with lung adenocarcinoma

description: Additional file 5. All relevant methylated sites of the five methylation-driven genes obtained from the TCGA database. (1–16) methylated sites of the gene CCDC181; (17–33) methylated sites of the gene ELF3; (34–47) methylated sites of the gene KLHDC9; (48) methylated site of the gene PLAU; (49–57) methylated sites of the gene S1PR1.
DOI: 10.48577/jpl.rb73rv
title: OCO-2/3: Unique Challenges of Trace Gas Spectrometers

description: No abstract available.
DOI: 10.6084/m9.figshare.13153010
title: Additional file 3 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 3. Table S3. Immunohistochemical data of four risk ARGs.
DOI: 10.6084/m9.figshare.13153007.v1
title: Additional file 2 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 2. Table S2.Gene ontology enrichment analysis of the differentially expressed ARGs in the TCGA dataset.
DOI: 10.6084/m9.figshare.13153016.v1
title: Additional file 5 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 5. Table S5. COX analysis of age, histological type, FIGO stage and risk score.
DOI: 10.6084/m9.figshare.13153004
title: Additional file 1 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 1. Table S1. List of differentially expressed ARGs between EC tissue and normal endometrial tissue in the TCGA dataset.
DOI: 10.6084/m9.figshare.13153010.v1
title: Additional file 3 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 3. Table S3. Immunohistochemical data of four risk ARGs.
DOI: 10.6084/m9.figshare.13153013.v1
title: Additional file 4 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 4. Table S4. Clinical and pathological characteristics of high and low risk patients.
DOI: 10.6084/m9.figshare.21541879
title: Additional file 12 of Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9

description: Additional file 12 Supplementary Table 4. Expression profile for mouse KRAB-Zfps in various types and tissue types (information for Fig. 2).
DOI: 10.6084/m9.figshare.13153007
title: Additional file 2 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 2. Table S2.Gene ontology enrichment analysis of the differentially expressed ARGs in the TCGA dataset.
DOI: 10.6084/m9.figshare.13153013
title: Additional file 4 of An integrated autophagy-related gene signature predicts prognosis in human endometrial Cancer

description: Additional file 4. Table S4. Clinical and pathological characteristics of high and low risk patients.
DOI: 10.6084/m9.figshare.13677499
title: Evaluating Misclassification Effects on Single Sequential Treatment in Sequential Multiple Assignment Randomized Trial (SMART) Designs

description: Sequential multiple assignment randomized trial designs tailor individual treatment by rerandomizing participants to subsequent therapies based on their response to initial treatment. Misclassification of participant responses to initial treatment can lead to inappropriate treatment assignment and thus impact the final outcome. The aim of this study is to derive a series of formulas for quantifying potential misclassification effects on the mean, variance, and statistical inference of a single sequential treatment (SST) effect with continuous outcome. Relative bias is expressed as a function of sensitivity, specificity, and the probability of being true responders. Results show that misclassification can introduce bias to the estimated treatment effect. Though the magnitude of bias varies, there are a few general conclusions: (1) for any fixed sensitivity (or specificity) the relative bias of the mean of responders (or nonresponders) always approaches 0 in a monotonic nonlinear pattern as specificity (or sensitivity) increases; (2) the relative bias of SST variance always has nonmonotone nonlinear relationship with sensitivity or specificity; (3) the SST variance under misclassification is always over-estimated. Furthermore, the results show that misclassification can affect statistical inference, with power exhibiting either monotonic or nonmonotonic patterns and resulting in either under- or over-estimation.
DOI: 10.6084/m9.figshare.21541866.v1
title: Additional file 2 of ERF49 mediates brassinosteroid regulation of heat stress tolerance in Arabidopsis thaliana

description: Additional file 2. Detailed information of genes downregulated in ERF49 overexpression lines after heat treatment.
DOI: 10.6084/m9.figshare.21541869
title: Additional file 3 of ERF49 mediates brassinosteroid regulation of heat stress tolerance in Arabidopsis thaliana

description: Additional file 3. Detailed information of genes upregulated after heat treatment.
DOI: 10.6084/m9.figshare.13677499.v1
title: Evaluating Misclassification Effects on Single Sequential Treatment in Sequential Multiple Assignment Randomized Trial (SMART) Designs

description: Sequential multiple assignment randomized trial designs tailor individual treatment by rerandomizing participants to subsequent therapies based on their response to initial treatment. Misclassification of participant responses to initial treatment can lead to inappropriate treatment assignment and thus impact the final outcome. The aim of this study is to derive a series of formulas for quantifying potential misclassification effects on the mean, variance, and statistical inference of a single sequential treatment (SST) effect with continuous outcome. Relative bias is expressed as a function of sensitivity, specificity, and the probability of being true responders. Results show that misclassification can introduce bias to the estimated treatment effect. Though the magnitude of bias varies, there are a few general conclusions: (1) for any fixed sensitivity (or specificity) the relative bias of the mean of responders (or nonresponders) always approaches 0 in a monotonic nonlinear pattern as specificity (or sensitivity) increases; (2) the relative bias of SST variance always has nonmonotone nonlinear relationship with sensitivity or specificity; (3) the SST variance under misclassification is always over-estimated. Furthermore, the results show that misclassification can affect statistical inference, with power exhibiting either monotonic or nonmonotonic patterns and resulting in either under- or over-estimation.
DOI: 10.6084/m9.figshare.21541875.v1
title: Additional file 5 of ERF49 mediates brassinosteroid regulation of heat stress tolerance in Arabidopsis thaliana

description: Additional file 5. Detailed information of 30 overlap genes downregulated in ERF49 overexpression lines and upregulated after heat and BR treatment.
DOI: 10.48577/jpl.pkskzq
title: Considerations for Detecting Organic Indicators of Metabolism on Enceladus

description: Enceladus is of interest to astrobiology and the search for life since it is thought to host active hydrothermal activity and habitable conditions. It is also possible that the organics detected on Enceladus may indicate an active prebiotic or biotic system; in particular, the conditions on Enceladus may favor mineral-driven proto-metabolic reactions. When including metabolism-related biosignatures in Enceladus mission concepts, it is necessary to base these in a clearer understanding of how these signatures could also be produced prebiotically. In addition, postulating which biological metabolisms to look for on Enceladus requires a non Earth-centric approach, since the details of biological metabolic pathways are heavily shaped by adaptation to geochemical conditions over the planet’s history. Creating metabolism-related organic detection objectives for Enceladus missions therefore requires consideration of how metabolic systems may operate differently on another world, while basing these speculations on observed Earth-specific microbial processes. In addition, advances in origin of life research can play a critical role in distinguishing between interpretations of any future organic detections on Enceladus, and discovery of an extant prebiotic system would be a transformative astrobiological event in its own right.
DOI: 10.48577/jpl.phybor
title: Measuring the vertical profile of atmospheric turbulence with the Laser Communication Relay Demonstration at Table Mountain Facility, California

description: No abstract available.
DOI: 10.6084/m9.figshare.16823257
title: Viromes and surveys of RNA viruses in camel-derived ticks revealing transmission patterns of novel tick-borne viral pathogens in Kenya

description: Tick-borne viruses (TBVs) capable of transmitting between ticks and hosts have been increasingly recognized as a global public health concern. In this study, <i>Hyalomma</i> ticks and serum samples from camels were collected using recorded sampling correlations in eastern Kenya. Viromes of pooled ticks were profiled by metagenomic sequencing, revealing a diverse community of viruses related to at least 11 families. Five highly abundant viruses, including three novel viruses (Iftin tick virus, Mbalambala tick virus [MATV], and Bangali torovirus [BanToV]) and new strains of previously identified viruses (Bole tick virus 4 [BLTV4] and Liman tick virus [LMTV]), were characterized in terms of genome sequences, organizations, and phylogeny, and their molecular prevalence was investigated in individual ticks. Moreover, viremia and antibody responses to these viruses have been investigated in camels. MATV, BLTV4, LMTV, and BanToV were identified as viral pathogens that can potentially cause zoonotic diseases. The transmission patterns of these viruses were summarized, suggesting three different types according to the sampling relationships between viral RNA-positive ticks and camels positive for viral RNA and/or antibodies. They also revealed the frequent transmission of BanToV and limited but effective transmission of other viruses between ticks and camels. Furthermore, follow-up surveys on TBVs from tick, animal, and human samples with definite sampling relationships are suggested. The findings revealed substantial threats from the emerging TBVs and may guide the prevention and control of TBV-related zoonotic diseases in Kenya and in other African countries.
DOI: 10.6084/m9.figshare.7385933
title: MOESM1 of Exploration of methylation-driven genes for monitoring and prognosis of patients with lung adenocarcinoma

description: Additional file 1. Methylation levels of 118 driver genes.