cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7281/t1/ypueqt
title: Data associated with the publication: RNA compaction and iterative scanning for small RNA targets by the Hfq chaperone.

description: This dataset is related to a manuscript submitted to Nature Communications, describing a one-dimensional target search by small RNAs and Hfq, using single molecule total internal reflection fluorescence microscopy. RNA-guided enzymes must quickly search a vast sequence space for their targets. This search is aided by chaperones such as Hfq, a protein that mediates regulation by bacterial small RNAs (sRNAs). How RNA binding proteins enhance this search is little known. Using single-molecule Förster resonance energy transfer, we show that E. coli Hfq performs a one-dimensional scan in which compaction of the target RNA delivers sRNAs to sites distant from the location of Hfq recruitment. We also show that Hfq can transfer an sRNA between different target sites in a single mRNA, favoring the most stable duplex. We propose that compaction and segmental transfer, combined with repeated cycles of base pairing, enable the kinetic selection of optimal sRNA targets. Finally, we show that RNA compaction and sRNA transfer require conserved arginine patches. We suggest that arginine patches are a widespread strategy for enabling the movement of RNA across protein surfaces.
DOI: 10.7281/t18g8hm0
title: Data associated with An Improved Method for Interpretation of Riverine Concentration-Discharge Relationships Indicates Long-Term Shifts in Reservoir Sediment Trapping

description: Derived from river monitoring data, concentration-discharge (C-Q) relationships are powerful indicators of export dynamics. Proper interpretation of such relationships can be made complex, however, if the ln(C)~ln(Q) relationships are nonlinear or if the relationships change over time, season, or discharge. Methods of addressing these issues by ‘binning’ data can introduce artifacts that obscure underlying interactions among time, discharge, and season. Here we illustrate these issues and propose an alternative method that uses the regression coefficients of the recently-developed WRTDS (‘Weighted Regressions on Time, Discharge, and Season’) model for examining (C-Q) relationships in long-term, discretely-sampled data for various water-quality constituents, including their uncertainties. The method is applied to sediment concentration data from Susquehanna River at Conowingo Dam, Maryland to illustrate how the coefficients can be accessed and presented in ways that provide additional insights toward the interpretation of river water-quality data, which reaffirms the recently-documented decadal-scale decline in reservoir trapping performance.
DOI: 10.7281/t1x7hdoz
title: Data and code associated with the publication: Building RNA concentration fields

description: This repository contains all raw data, images, and code associated with our paper (available on https://chemrxiv.org/engage/chemrxiv/article-details/6758a1f6f9980725cfa766e7 ) and is scheduled for publication in a peer-reviewed journal. The scripts provided are used to analyze the raw data and generate all figures included in both the main manuscript and the supporting information. This repository primarily serves researchers in synthetic biology, biomolecular engineering, and chemical engineering, while also intersecting with materials science and molecular biology. The experimental and computational methods here span multiple disciplines, reflecting the broad applicability of programmable RNA concentration fields in areas like tissue engineering, self-assembly, and advanced materials design. This repository contains tabular data in text formats, images, .npy files for NumPy-based arrays, as well as Python scripts. The Python scripts read and process these datasets to perform analyses and generate publication-ready figures.
DOI: 10.34976/1j9g-f114
title: PMA Uganda Phase 1 Client Exit Interview Baseline Survey (2020)

description: Uganda Phase 1 Client Exit Interview Baseline Survey includes 122 enumeration areas (EAs) selected using a multi-stage stratified cluster design with urban-rural and region strata. The results representative at the national level and within urban/rural strata. The final sample included 2,397 clients which completed the interview. Data collection was conducted between September and October 2020. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/1hrp-p268
DOI: 10.34976/39y1-1055
title: PMA2020 India (Rajasthan) Round 3 Household Female Survey (2017)

description: India Round 3 (Rajasthan) Household and Female (HQFQ) survey used a two-stage cluster design. A sample of 147 enumeration areas (EAs) was drawn by the International Institute for Population Sciences from a master sampling frame. Each EA was listed and mapped; 35 households were randomly selected. Occupants in selected households were enumerated and eligible females of reproductive age (15-49) were contacted and consented for interview. Data collection was conducted between November and December, 2014. The final completed sample included 4,892 household interviews and 6,095 female interviews. Data collection was conducted between August to October 2017. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/b88s-zx32
DOI: 10.34976/a7q7-bm91
title: PMA Côte d’Ivoire Phase 1 Service Delivery Point Survey (2020)

description: PMA Côte d’Ivoire Phase 1 Service Delivery Point Survey includes 122 enumeration areas (EAs) selected using a multi-stage stratified cluster design with urban-rural and region strata. The results are representative at the national level and within urban/rural strata. The final sample included 215 facilities which completed the interview. Data collection was conducted between September and November 2020. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/f0vf-qd73
DOI: 10.34976/bev9-rc94
title: PMA Nigeria (Kano, Lagos) Covid-19 Female Follow-up Survey (2020)

description: PMA Nigeria (Kano) COVID-19 Female Follow-up (FQFU) phone survey (June 2020) was conducted among females age 15-49 at the time of the COVID-19 Survey who were interviewed at the baseline survey between December 2019 and January 2020, consented to follow-up, and own or had access to a phone (33.6% of the baseline population). Of the 429 eligible respondents, 8.2% were not reached. Of those reached, 98.7% completed the survey for a response rate of 90.7% among contacted women.PMA Nigeria (Lagos) COVID-19 Female Follow-up (FQFU) phone survey was conducted in July 2020 among females age 15-49 at the time of the COVID-19 survey who were interviewed at the baseline survey between December 2019 and January 2020, consented to follow-up, and own or had access to a phone (82.6% of the baseline population). Of the 1174 eligible respondents, 15.6% were not reached. Of those reached, 96.6% completed the survey for a response rate of 81.5% among contacted women
DOI: 10.34976/f3xs-sa70
title: PMA2020 Democratic Republic of Congo (Kinshasa, Kongo Central) Round 5 Household Female Survey (2016)

description: Democratic Republic of Congo (Kinshasa) Round 5 Household and Female (HQFQ) survey included a sample of 58 enumeration areas (EA) was drawn (PPS) in Kinshasa. Each EA was listed and mapped; 33 households were randomly selected. Occupants in selected households were enumerated and eligible females of reproductive age (15-49) were contacted and consented for interview. The final sample included 1,841 completed households, and 2,595 completed female surveys. Data collection was conducted between July and September, 2016.Democratic Republic of Congo (Kongo Central) Round 5 Household and Female (HQFQ) survey included a sample of 52 enumeration areas (EA) was drawn (PPS) in Kongo Central. Each EA was listed and mapped; 33 households were randomly selected. Occupants in selected households were enumerated and eligible females of reproductive age (15-49) were contacted and consented for interview. The final sample included 1,575 completed households, and 1,697 completed female surveys. Data collection was conducted between July and September, 2016. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/b88s-zx32
DOI: 10.34976/he9w-wz04
title: PMA Kenya Phase 2 Household and Female Survey (2020)

description: PMA Kenya Phase 2 (KEP2) Household and Female survey collects national and county level representative data on knowledge, practice, and coverage of family planning services in 103 enumeration areas (EAs) using a multi-stage stratified cluster design with urban-rural strata. The final sample included 9,727 households and 9,323 de facto females who completed the interview for the cross-sectional sample. Data collection was conducted between November and December 2020.Phase 2 panel data collection was conducted among females aged 15-49 at the time of the Phase 2 survey who were interviewed at the baseline survey between October and December 2019 and consented to follow-up. Of the 8797 eligible respondents, 19.5% were not reached for follow-up. Of those reached, 7018 (79.7%) completed the survey, for a response rate of 99% among contacted women. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/cjvx-z226
DOI: 10.34976/j5rf-8736
title: PMA Ethiopia Panel (2021-2023) Cohort 2: 6-week Follow-up Survey

description: PMA Ethiopia Panel Cohort 2: 6-week Follow-up survey followed women who were enrolled into the Panel Cohort 2 Baseline Survey. Women who were 5-9 weeks postpartum at baseline who consented to the baseline survey, women 0-4 weeks postpartum at baseline who consented to the baseline and consented to follow-up, and women pregnant at baseline who consented to the baseline and consented to follow-up were eligible for the 6-week follow-up survey. Women (n=273) who were 5-9 weeks postpartum at baseline received the 6-week follow-up survey at the same time as their baseline interview, conducted between November 2021 and January 2022. Women (n=2,024) 0-4 weeks postpartum or pregnant at baseline received a 6-week follow-up survey approximately 6-week after the delivery. A total of 2,072 women completed the 6-weeks follow-up survey conducted between November 2021 and October 2022. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/zvvy-x402
DOI: 10.34976/vfbp-bz42
title: PMA2020 (2013-2019) Service Delivery Point Master Codebook

description: PMA2020 (2013-2019) Service Delivery Point Survey Master Codebook contains Service Delivery Point surveys conducted between 2013 and 2019 as part of the PMA2020 grant.
DOI: 10.34976/wvw9-pe08
title: PMA2020 Ghana Round 1 Service Delivery Point Survey (2013)

description: Ghana Round 1 Service Delivery Point (SQ) survey used a two-stage cluster design with urban and rural, major ecological zones as the strata. A sample of 100 enumeration areas (EAs) was drawn by the Ghana Statistical Service from its master sampling frame. Each EA was listed and mapped. Public facilities were included if a selected EA fell within the catchment area. Private facilities were included if they fell within the boundaries of the EA. Data collection was conducted between September and October, 2013. The final completed sample in Ghana Round 1 was 138 SDPs. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/vfbp-bz42
DOI: 10.34976/x3bk-0w75
title: PMA Democratic Republic of Congo (Kinshasa, Kongo Central) Phase 1 Household and Female Survey (2020)

description: PMA Democratic Republic of Congo (Kinshasa Kongo Central) Phase 1 Household and Female (HQFQ) Survey includes 58 enumeration areas (EAs) in Kinshasa and 52 EAs in Kongo Central. The EAs were drawn using the stratified cluster design from the master sampling frame using probabilities proportional to size. The results are representative at province level. The final sample included 1,968 (97.0%) households and 2,611 (95.3%) de facto women in Kinshasa, and 1,965 (98.5%) households and 1,950 (98.8%) de facto women in Kongo Central, which completed the interviews. Data collection was conducted between December 2019 and January 2020. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/cjvx-z226
DOI: 10.7281/t1/3lvnv0
title: Data associated with the publication: Increased static charge-induced threshold voltage shifts and memristor activity in pentacene OFETs comprising polystyrene-based gate dielectrics containing electroactive small molecule crystallites

description: Device electronic data and micrographs, organized by the figure numbers in the manuscripts
DOI: 10.7281/t1/7ws8ad
title: Data associated with the publication: Evaluation of underweight status may improve identification of the highest-risk patients during outpatient evaluation for pulmonary tuberculosis

description: This dataset is an anonymized subset of the data collected by the STOMP-TB study (A Comprehensive Snapshot of Tuberculosis Transmission in an Urban Ugandan Community). The included records are from patients who were diagnosed with pulmonary TB through routine care at one of four health facilities in Kampala, Uganda, or control patients who underwent TB evaluation with a negative result at the same facilities. The included variables were used for analysis of underweight status, characteristic TB symptoms, and probability of bacteriologically-confirmed TB in the publication “Evaluation of underweight status may improve identification of the highest-risk patients during outpatient evaluation for pulmonary tuberculosis” by PJ Kitonsa et al. (Plos One, accepted December 2020).
DOI: 10.7281/t1/aotrd6
title: Data associated with the publication: Dendritic cell activation by iron oxide nanoparticles depends on the extracellular environment

description: This dataset contains all raw data associated with the study elucidating the mechanisms of nanoparticle-mediated activation of dendritic cells (DCs) when they were exposed to hydroxyethyl starch-coated bionized nanoferrite IONPs (BP) in vitro and in vivo. We observed no evidence of toxicity at doses up to 25 mg Fe/mouse, five-fold higher than those used in subsequent in vivo experiments. Although DCs cultured with BP revealed high levels of nanoparticle uptake, neither JAWSII dendritic cells nor bone marrow derived cells (BMDCs) showed significant changes in marker expression. To assess whether BP interactions in vivo produced different effects, we analyzed CD80, CD86, and MHC II expression of DCs recovered from the livers, spleens, bone marrows, and lymph nodes of mice injected once with BP (5 mg Fe). Interestingly, only DCs in spleens and bone marrows responded to BP exposure. DCs recovered from other tissues and organs showed no evidence of increased activation. These findings highlight complex effects with systemic exposure to nanoparticles, and their potential to mediate specific and selective activation of innate immune cells, which depends on the tissue site and features of the extracellular environment. Our study also emphasize that results obtained from in vitro experiments must be interpreted with caution as they may not faithfully represent responses in living systems.
DOI: 10.7281/t1/avoeqr
title: Data associated with the publication: Cholinergic reinforcement signaling is impaired by amyloidosis prior to its synaptic loss.

description: Alzheimer's Disease (AD) is associated with amyloidosis and dysfunction of the cholinergic system which is crucial for learning and memory. However, the nature of acetylcholine signaling within regions of cholinergic-dependent plasticity and how it changes with experience is poorly understood, much less the impact of amyloidosis on this signaling. Therefore, we optically measure the release profile of acetylcholine to unexpected, predicted, and predictive events in visual cortex (VC)—a site of known cholinergic-dependent plasticity—in a preclinical mouse model of AD that develops amyloidosis. We find that acetylcholine exhibits reinforcement signaling qualities, reporting behaviorally-relevant outcomes and displaying release profiles to predictive and predicted events that change as a consequence of experience. We identify three stages of amyloidosis occurring prior to the degeneration of cholinergic synapses within VC and observe that cholinergic responses in amyloid-bearing mice become impaired over these stages, diverging progressively from age- and sex-matched littermate controls. In particular, amyloidosis degrades signaling of unexpected rewards and punishments, and attenuates the experience-dependent 1) increase of cholinergic responses to outcome predictive visual cues, and 2) decrease of cholinergic responses to predicted outcomes. Hyperactive spontaneous acetylcholine release occurring transiently at the onset of impaired cholinergic signaling is also observed, further implicating disrupted cholinergic activity as an early functional biomarker in AD. Our findings suggest that acetylcholine acts as a reinforcement signal that is impaired by amyloidosis prior to pathological degeneration of the cholinergic system, providing a deeper understanding of the effects of amyloidosis on acetylcholine signaling and informing future interventions for AD.
DOI: 10.7281/t1/iwovkd
title: Data associated with the publication: Variations in ocean deoxygenation across Earth System Models: Isolating the role of parametrized lateral mixing

description: Examines the impact of changing the lateral mixing coefficient within a single Earth System Model on oxygen distribution under global warming. Results from six simulations are shown, four with constant values of mixing coefficient and two with spatially varying values of mixing coefficient.
DOI: 10.7281/t1/ntwjar
title: Data associated with the publication: An expanded neurogenetic toolkit to decode olfaction in the African malaria mosquito Anopheles gambiae.

description: This archive contains raw calcium imaging .tif stacks and confocal images in .czi format used in the publication.
DOI: 10.7281/t1/pyd0pg
title: Data associated with the publication: Global protein dynamics as communication sensors in peptide synthetase domains

description: Data accompanying “Global protein dynamics as communication sensors in peptide synthetase domains.” The data was used to demonstrate the function of protein dynamics in molecular recognition and allostery. We used the Yersiniabactin Synthetase cyclization domain Cy1 as a model system and predominantly employed NMR. The data was used to determine the solution structure of Cy1. For wild-type and the mutant D391N, the data was used to monitor the molecular response of Cy1 when presented to its partner carrier protein ArCP as ArCP is modified from holo to substrate-loaded form. Other data was used to describe Cy1 dynamics through relaxation dispersion and Hahn-Echo, assess its stability through thermal melts, and compare Cy1 wild-type and mutant data.
DOI: 10.7281/t1/rpcqp5
title: Data and code associated with the publication: Direct measurements simplified models of interfacial colloidal interactions diffusion with adsorbed macromolecules

description: Data for this paper, including: raw videos (.seq files), custom analysis codes (FORTRAN and MatLab) and analyzed values (.txt files).
DOI: 10.7281/t1/u5guv3
title: Data associated with the publication: Stability of N-Heterocyclic carbene monolayers under continuous voltammetric interrogation

description: N-Heterocyclic carbenes (NHCs) are promising monolayer-forming ligands that can overcome limitations of thiol-based monolayers in terms of stability, surface functionality and reactivity across a variety of transition metal surfaces. Recent publications have reported the ability of NHCs to support biomolecular receptors on gold substrates for sensing applications, and improved tolerance to prolonged biofluid exposure relative to thiols. However, important questions remain regarding the stability of these monolayers when subjected to voltage perturbations, which is needed for applications with electrochemical platforms. Here, we investigate the ability of two NHCs, 1,3-diisopropylbenzimidazole and 5-(ethoxycarbonyl)-1,3-diisopropylbenzimidazole, to form monolayers via self-assembly from methanolic solutions of their trifluoromethanesulfonate salts. We compare the electrochemical behavior of the resulting monolayers relative to that of benchmark mercaptohexanol monolayers in phosphate-buffered saline. Within the -0.15 to 0.25 V vs Ag|AgCl voltage window, NHC monolayers are stable on gold surfaces, wherein they electrochemically perform like thiol-based monolayers and undergo similar reorganization kinetics, displaying long-term stability under incubation in buffered media and under continuous voltammetric interrogation. At negative voltages, NHC monolayers cathodically desorb from the electrode surface at lower bias (-0.1 V) than thiol-based monolayers (-0.5 V). At voltages more positive than 0.25 V, NHC monolayers anodically desorb from electrode surfaces at similar voltages to thiol-based monolayers. These results highlight new limitations to NHC monolayer stability imposed by electrochemical interrogation of the underlying gold electrodes. Our results serve as a framework for future optimization of NHC monolayers on gold for electrochemical applications, as well as structure-functionality studies of NHCs on gold.
DOI: 10.7281/t1/uijlzo
title: Data associated with the publication: Selective detection of functionalized carbon particles based on polymer semiconducting and conducting devices as potential particulate matter sensors

description: This file contains original instrument data for differential scanning calorimetry, gel permeation chromatography, transistor parameters, electron microscopy, and x-ray diffraction. Files with .rar extension can be read with 7-zip.
DOI: 10.7281/t1/uzit7c
title: Data associated with the publication: Microphysical simulations of Titan’s south polar HCN cloud during southern fall using TitanCARMA.

description: TitanCARMA model output from all of the simulations described in the associated paper.
DOI: 10.34976/27yd-pf57
title: PMA2020 Ethiopia Round 1 Service Delivery Point Survey (2014)

description: Ethiopia Round 1 Service Delivery Point (SQ) survey used a two-stage cluster design with urban and rural, major regions as strata. A sample of 200 enumeration areas (EAs) was drawn by the Central Statistical Agency from its master sampling frame. Each EA was listed and mapped. Public facilities were included if a selected EA fell within the catchment area. Private facilities were included if they fell within the boundaries of the EA. Data collection was conducted between January and March, 2014. The final completed sample in Ethiopia Round 1 was 389 SDPs. More information about this dataset can be found in the corresponding codebook, accessible at https://doi.org/10.34976/vfbp-bz42