cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25934/00005794
title: A Phase III, Open-Label, Multicenter, Randomized Study to Investigate the Efficacy and Safety of Atezolizumab (Anti-PD-L1 Antibody) Compared With Docetaxel in Patients With Non-Small Cell Lung Cancer After Failure With Platinum Containing Chemotherapy

description: This global, multicenter, open-label, randomized, controlled study evaluated the efficacy and safety of atezolizumab (an anti-programmed death−ligand 1 [anti-PD-L1] antibody)compared with docetaxel in participants with locally advanced or metastatic non-small cell lung cancer (NSCLC) after failure with platinum-containing chemotherapy. Participants were randomized 1:1 to receive either docetaxel or atezolizumab. Treatment may continue as long as participants experienced clinical benefit as assessed by the investigator, i.e., in the absence of unacceptable toxicity or symptomatic deterioration attributed to disease progression.
DOI: 10.25934/00005796
title: A Phase II, Multicenter, Single-Arm Study OF Atezolizumab In Patients With PD-L1-Positive Locally Advanced Or Metastatic Non-Small Cell Lung Cancer

description: This multicenter, single-arm study will evaluate the efficacy and safety of Atezolizumab in participants with PD-L1-positive locally advanced or metastatic non-small cell lung cancer (NSCLC). Participants will receive Atezolizumab 1200 milligrams (mg) intravenously every 3 weeks as long as participants are experiencing clinical benefit as assessed by the investigator, that is , in the absence of unacceptable toxicity or symptomatic deterioration attributed to disease progression.
DOI: 10.25934/00005804
title: A Phase II, Multicenter, Single-Arm Study of Atezolizumab in Patients With Locally Advanced or Metastatic Urothelial Bladder Cancer

description: This Phase II, single-arm study is designed to evaluate the effect of atezolizumab treatment in participants with locally advanced or metastatic urothelial bladder cancer. Participants will be enrolled into 1 of 2 cohorts. Cohort 1 (reported here) will consist of participants who are treatment-naïve and ineligible for cisplatin-containing chemotherapy. Cohort 2 will contain participants who have progressed during or following a prior platinum-based chemotherapy regimen. The results of the second cohort are reported separately (NCT02108652). Participants in both cohorts will be given a 1200 milligrams (mg) intravenous (IV) dose of atezolizumab on Day 1 of 21-day cycles. Treatment of participants in Cohort 1 will continue until disease progression per Response Evaluation Criteria in Solid Tumors Version 1.1 (RECIST v1.1) or unmanageable toxicity. Treatment of participants in Cohort 2 will continue until loss of clinical benefit or unmanageable toxicity.
DOI: 10.25934/00005997
title: A Phase III, Open-Label, Randomized Study of Atezolizumab (Anti-PD-L1 Antibody) in Combination With Bevacizumab Versus Sunitinib in Patients With Untreated Advanced Renal Cell Carcinoma

description: This multi-center, randomized, open-label study will evaluate the efficacy and safety of atezolizumab plus bevacizumab versus sunitinib in participants with inoperable, locally advanced, or metastatic RCC who have not received prior systemic active or experimental therapy, either in the adjuvant or metastatic setting.
DOI: 10.25934/00007372
title: A Phase III, Open-Label, Randomized Study of Atezolizumab in Combination With Bevacizumab Compared With Sorafenib in Patients With Untreated Locally Advanced or Metastatic Hepatocellular Carcinoma

description: This study will evaluate the efficacy and safety of atezolizumab in combination with bevacizumab compared with sorafenib in participants with locally advanced or metastatic Hepatocellular Carcinoma (HCC) who have received no prior systemic treatment.
DOI: 10.5061/dryad.bb61h6h
title: Data from: Plant water uptake along a diversity gradient provides evidence for complementarity in hydrological niches

description: Biodiversity enhances a variety of ecosystem processes, and yet the
 underlying mechanisms through which these relationships occur remain a
 critical knowledge gap. Here, we used the natural abundance of stable
 isotopes to measure depth of water uptake in five common grassland species
 (Asclepias tuberosa, Lespedeza capitata, Liatris aspera, Schizachyrium
 scoparium, and Sorghastrum nutans) growing across an experimental
 grassland diversity gradient. Using this approach, we addressed the
 following questions: (1) Does the depth-specific provenance of water
 uptake differ among species and/or do interspecific differences in water
 source manifest with increasing community diversity? (2) Does the isotopic
 niche space occupied by plants change with increasing diversity? (3) Is
 plasticity in water uptake depth across a diversity gradient associated
 with functional plant responses? We found that the depth of soil water
 used by plants was inherently different among species when grown in
 monocultures. All species used less shallow soil water and more
 intermediate-depth soil water in mixed assemblages than in monocultures,
 resulting in similar interspecific differences in water source across the
 diversity gradient. However, plasticity in the locations of water used
 were positively associated with increases in plant growth in higher
 diversity treatments. These results indicate that plasticity in water-use
 may contribute to positive biodiversity-productivity relationships
 commonly observed in temperate grasslands.
description: OKeefe_et_al_2019_dataThis folder contains all data files and analysis code associated with: O’Keefe K, Nippert JB, McCulloh KA. 2019. Plant water uptake along a diversity gradient provides evidence for complementarity in hydrological niches. Oikos 10.1111/oik.06529
DOI: 10.5061/dryad.th8334d
title: Data from: Evolutionary signatures of photoreceptor transmutation in geckos reveal potential adaptation and convergence with snakes

description: Most vertebrates use a combination of rod and cone photoreceptors to
 enable vision in conditions ranging from starlight to direct sunlight.
 Nocturnal geckos, however, have simplex retinas that contain only rods in
 terms of morphology and physiology, but these rods are thought to be
 derived from cones through an evolutionary process known as photoreceptor
 transmutation. To investigate this, we generated eye transcriptomes and
 analyzed patterns of phototransduction gene evolution in geckos in
 comparison to other reptiles. We confirm that geckos have lost several
 major components of the rod phototransduction pathway, including rod opsin
 (RH1), which we identified as a pseudogene in multiple genomes. We also
 identified a partial rod transducin transcript, but found no evidence of
 the protein in retinal sections. However, we find that geckos express
 several complete rod phototransduction transcripts in the eye, which may
 contribute to the rod-like physiology of nocturnal gecko photoreceptors.
 Finally, we found surprising evidence that even though photoreceptor
 transmutation evolved independently in geckos and snakes, they have
 experienced parallel shifts in selective constraint on phototransduction
 genes. These results implicate convergent adaptive change in the
 underlying molecular machinery of visual transduction, in addition to the
 more obvious changes to cellular morphology, during photoreceptor
 transmutation.
description: AlignmentsMultiple sequence alignment fasta files for each of the phototransduction gene analyzed in the studyPAML FilesInput files for each PAML analysisPAML Results TablesDetailed result tables in excel format for each of the PAML analysesFDR ControlInput and output files of the FDR control analyses, as well a results summary table in excel formatTranscriptome and Expression DataData associated with the transcriptome and expression analyses including the de novo Trinity assembly, reference files, read counts, and results summary table in excel format.
DOI: 10.5061/dryad.4433sp2
title: Data from: Urban areas affect flight altitudes of nocturnally migrating birds

description: 1. Urban areas affect terrestrial ecological processes and local weather,
 but we know little about their effect on aerial ecological processes. 2.
 Here, we identify urban from non-urban areas based on the intensity of
 artificial light at night (ALAN) in the landscape, and, along with weather
 covariates, evaluate the effect of urbanization on flight altitudes of
 nocturnally migrating birds. 3. Birds are attracted to ALAN, hence we
 predicted that altitudes would be lower over urban than over non-urban
 areas. However, other factors associated with urbanization may also affect
 flight altitudes. For example, surface temperature and terrain roughness
 are higher in urban areas, increasing air turbulence, height of the
 boundary layer, and affecting local winds. 4. We used data from nine
 weather surveillance radars in the eastern US to estimate altitudes at
 five quantiles of the vertical distribution of birds migrating at night
 over urban and non-urban areas during five consecutive spring and autumn
 migration seasons. We fit generalized linear mixed models by season for
 each of the five quantiles of bird flight altitude and their differences
 between urban and non-urban areas. 5. After controlling for other
 environmental variables and contrary to our prediction, we found that
 birds generally fly higher over urban areas compared to rural areas in
 spring, and marginally higher at the mid layers of the vertical
 distribution in autumn. We also identified a small interaction effect
 between urbanization and crosswind speed, and between urbanization and
 surface air temperature, on flight altitudes. We also found that the
 difference in flight altitudes of nocturnally migrating birds between
 urban and non-urban areas varied among radars and seasons, but were
 consistently higher over urban areas throughout the years sampled. 6. Our
 results suggest that the effects of urbanization on wildlife extend into
 the aerosphere, and are complex, stressing the need of understanding the
 influence of anthropogenic factors on airspace habitat.
description: Flight altitudes by
 quantileCSV file contains data
 used for modeling flight altitudes of nocturnal bird migration in relation
 to urban areas and weather variables.Cabrera-Cruz_flight_altitude_by_quantile.csvDifferences between flight altitudes, by quantileCSV file contains data used for modeling the difference in flight altitudes of nocturnal bird migration over urban bright and non-urban dark areas in relation to weather variables.Cabrera-Cruz_flight_altitude_differences_by_quantile.csv
DOI: 10.5061/dryad.777461k
title: Data from: Species-specific effects of phosphorus addition on tropical tree seedling response to elevated CO2

description: 1. Tropical forest productivity is often thought to be limited by soil
 phosphorus (P) availability. Phosphorus availability might therefore
 constrain potential increases in growth as the atmospheric CO2
 concentration increases, yet there is little experimental evidence with
 which to evaluate this hypothesis. We hypothesized that while all species
 would respond more strongly to elevated CO2 when supplied with extra P,
 individual species’ responses would also depend on their habitat
 associations with either high- or low-P soils. We further hypothesized
 that this effect would be exacerbated by a reduction in transpiration rate
 under elevated CO2, as transpiration may aid in P acquisition. 2. We used
 a pot experiment to test the effects of P addition on the physiological
 and growth response to elevated CO2 of eight tropical tree species with
 contrasting distributions across a soil P gradient in Panamanian lowland
 forests. Seedlings were grown in an ambient (400 ppm) or elevated (800
 ppm) CO2-controlled glasshouse in either a high or low P treatment to
 quantify the effects of P limitation on relative growth rate,
 transpiration, maximum photosynthetic rate, and foliar nutrients. 3. We
 found evidence of limitation by P and CO2 on growth, photosynthesis,
 foliar nutrients, and transpiration. However, species’ P affinities did
 not predict relative growth rate or transpiration responses to elevated
 CO2 in either the low P or high P treatments. 4. Transpiration rates
 decreased under elevated CO2, but foliar P was greater for some species
 under elevated CO2, suggesting a greater capacity for upregulation of P
 acquisition in species associated with low P soils. 5. Our results show
 that tropical forest responses to elevated CO2 will be species-specific
 and not necessarily explained by P affinities based on distribution, which
 poses challenges for predictions of community-wide responses.
description: Tropical tree response
 data_elevated CO2 and phosphorusPhysiological responses
 data of 8 tropical tree seedlings to various CO2 and soil phosphorus
 treatments.Thompson_etal_PCO2.csv
DOI: 10.5061/dryad.gj34813
title: Data from: Echolocation and roosting ecology determine sensitivity of forest-dependent bats to coffee agriculture

description: Species differ in vulnerability to anthropogenic landuse changes.
 Knowledge of the mechanisms driving differential sensitivity can inform
 conservation strategies but is generally lacking for species-rich taxa in
 the tropics. The diverse bat fauna of Southeast Asia is threatened by
 rapid loss of forest and expanding agricultural activities, but the
 associations between species, traits, vulnerability to agriculture and the
 underlying drivers have yet to be elucidated. We studied the responses of
 speciose insectivorous bat assemblages to robusta coffee cultivation in
 Sumatra, Indonesia. We compared abundance, species richness and assemblage
 structures of bats between forests and coffee farms based on trapping data
 and evaluated the influence of vegetation complexity on assemblage
 composition and species-level reactions. Bat abundance and species
 richness were significantly lower in coffee farms than in forests. Bat
 assemblage structure differed between landuses, and the overall variation
 can be largely explained by vegetation simplification. Species sensitive
 to coffee agriculture were associated with more complex vegetation
 structure, whereas tolerant species were associated with simpler
 vegetation structure. Sensitive and tolerant species differed in the type,
 frequency, and bandwidth of echolocation calls and roost use. Species
 sensitive to coffee use broadband and high-pitched frequency-modulated
 calls, which are efficient at detecting insects in complex vegetation, and
 roost in plant structures that may be lost as vegetation is simplified. In
 contrast, tolerant species used lower-pitched constant frequency calls and
 roost in caves. We advocate for greater use of trait analyses in studies
 seeking to clarify the influence of agriculture on diverse tropical bat
 faunas.
description: insectivorousBat_Capture_BBS_Sumatra_Indonesia_2011_2012Species occurrence data by harp trap and mist net in coffee plantations and forests Bukit Barisan Selatan Landscape from 2011 to 2012.vegetationMeasuresat_BatTrapPoints_BBS_Sumatra_Indoneisa_2011_2012Presence-absence data of vegetation strata at all trap points of harp trap and mist nets at 9 study sites in Bukit Barisan Selatan Landscape, Sumatra, Indonesia, from 2011 to 2012.
DOI: 10.5061/dryad.82gn3m6
title: Data from: The complete genome sequence of the thermophilic bacterium Laceyella sacchari FBKL4.010 reveals the basis for tetramethylpyrazine biosynthesis in Moutai‐flavor Daqu

description: The genus Laceyella consists of a thermophilic filamentous bacteria. The
 pure isolate of Laceyella sacchari FBKL4.010 was isolated from
 Moutai‐flavor Daqu, Guizhou Province, China. In this study, the whole
 genome was sequenced and analyzed. The complete genome consists of one
 3,374,379‐bp circular chromosome with 3,145 coding sequences (CDSs), seven
 clustered regularly interspaced short palindromic repeat (CRISPR) regions
 of 12 CRISPRs. Moreover, we identified that the genome contains genes
 encoding key enzymes such as proteases, peptidases, and acetolactate
 synthase (ALS) of the tetramethylpyrazine metabolic pathway. Metabolic
 pathways relevant to tetramethylpyrazine synthesis were also reconstructed
 based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) PATHWAY
 database. Annotation and syntenic analyses using antiSMASH 4.0 also
 revealed the presence of two gene clusters in this strain that differ from
 known tetramethylpyrazine synthesis clusters, with one encoding amino acid
 dehydrogenase (ADH) and the other encoding transaminase in
 tetramethylpyrazine metabolism. The results of this study provide flavor
 and genomic references for further research on the flavor‐producing
 functions of strain FBKL4.010 in the Moutai liquor‐making process.
description: Figure
 A1FIGURE A1 The
 reconstructed acetoin metabolic pathway in the strain FBKL4.010 based on
 the KEGG PATHWAY database. EMP represent Embden-Meyerhof pathway. Red
 marked genes represent genes related with tetramethylpyrazine synthesis on
 FBKL4.010 genome. The locus tags of marked genes and the ANI value with
 the most similar genes were shown next to the marked
 genes.TABLE
 A1TABLE A1 | Protein
 sequences relevant to tetramethylpyrazine metabolism in Laceyella sacchari
 FBKL4.010.Figure
 A2FIGURE A2 The
 reconstructed result of the ammonium metabolic pathway in the strain
 FBKL4.010 based on the KEGG PATHWAY database. Red marked genes represent
 genes related with tetramethylpyrazine synthesis on FBKL4.010 genome. The
 locus tags of marked genes and the ANI value with the most similar genes
 were shown next to the marked genes.Figure
 A3FIGURE A3 The
 reconstructed result of the ammonium metabolic pathway in the strain
 FBKL4.010 based on the KEGG PATHWAY database. Red marked genes represent
 genes related with tetramethylpyrazine synthesis on FBKL4.010 genome. The
 locus tags of marked genes and the ANI value with the most similar genes
 were shown next to the marked genes.
DOI: 10.5061/dryad.93h3dk2
title: Data from: Salting-out assisted liquid-liquid extraction coupled with high performance liquid chromatography for the determination of vitamin D3 in milk samples

description: In this study, salting-out assisted liquid-liquid extraction (SALLE) as a
 simple and efficient extraction technique followed by high performance
 liquid chromatography was employed for the determination of vitamin D3 in
 milk samples. The sample treatment is based on the use of water-miscible
 acetonitrile as the extractant and acetonitrile phase separation under
 high-salt conditions. Under the optimum conditions, acetonitrile and
 ammonium sulfate was used as the extraction solvent and salting-out agent,
 respectively. The vitamin D3 extract was separated using Hypersil ODS (250
 x i.d 4.6 mm, 5 µm) high performance liquid chromatography column that was
 coupled with diode array detector (HPLC-DAD). Vitamin D2 was used as
 internal standard (IS) to offset any variations in chromatographic
 conditions. The vitamin D3 and the IS were eluted in 18 minutes. Good
 linearity (r2 &gt; 0.993) was obtained within the range of 0.025 –
 60.0 µg g-1 with the limit of detection (LOD) of 0.015 µg g-1 and limit of
 quantification (LOQ) of 0.025 µg g-1. The validated method was applied for
 the determination of vitamin D3 in milk samples. The recoveries for spiked
 samples were from 94.4 – 113.5 %.
description: N.H. Sazali et
 alThe
 data were collected for the salting-out liquid liquid extraction for the
 determination of vitamin D3 in milk samples
DOI: 10.5061/dryad.595718c
title: FragSAD: A database of diversity and species abundance distributions from habitat fragments

description: Habitat destruction is the single greatest anthropogenic threat to
 biodiversity. Decades of research on this issue have led to the
 accumulation of hundreds of data sets comparing species assemblages in
 larger, intact, habitats to smaller, more fragmented, habitats. Despite
 this, little synthesis or consensus has been achieved, primarily because
 of non‐standardized sampling methodology and analyses of notoriously
 scale‐dependent response variables (i.e., species richness). To be able to
 compare and contrast the results of habitat fragmentation on species'
 assemblages, it is necessary to have the underlying data on species
 abundances and sampling intensity, so that standardization can be
 achieved. To accomplish this, we systematically searched the literature
 for studies where abundances of species in assemblages (of any taxa) were
 sampled from many habitat patches that varied in size. From these, we
 extracted data from several studies, and contacted authors of studies
 where appropriate data were collected but not published, giving us 117
 studies that compared species assemblages among habitat fragments that
 varied in area. Less than half (41) of studies came from tropical forests
 of Central and South America, but there were many studies from temperate
 forests and grasslands from all continents except Antarctica. Fifty‐four
 of the studies were on invertebrates (mostly insects), but there were
 several studies on plants (15), birds (16), mammals (19), and reptiles and
 amphibians (13). We also collected qualitative information on the length
 of time since fragmentation. With data on total and relative abundances
 (and identities) of species, sampling effort, and affiliated meta‐data
 about the study sites, these data can be used to more definitively test
 hypotheses about the role of habitat fragmentation in altering patterns of
 biodiversity.
description: metadata_utf8abundances_utf8
DOI: 10.5061/dryad.360k8v0
title: Data from: Spatial insurance in multi-trophic metacommunities

description: Metacommunity theory suggests that dispersal is a key driver of diversity
 and ecosystem functioning in changing environments. The capacity of
 dispersal to mitigate effects of environmental change might vary among
 trophic groups, potentially resulting in changes in trophic interactions
 and food web structure. In a mesocosm experiment, we compared the
 compositional response of bacteria, phyto- and zooplankton to a factorial
 manipulation of acidification and dispersal. We found that the buffering
 capacity of dispersal varied among trophic groups: dispersal alleviated
 the negative effect of acidification on phytoplankton diversity
 mid-experiment, but had no effect on the diversity of zooplankton and
 bacteria. Likewise, trophic groups differed in whether dispersal
 facilitated compositional change. Dispersal accelerated changes in
 phytoplankton composition under acidification, possibly mediated by
 changes in trophic interactions, but had no effect on the composition of
 zooplankton and bacteria. Overall, our results suggest that the potential
 for spatial insurance can vary among trophic groups.
description: Diversity, biomass, and
 size structurediversity_biomass.csvZooplankton compositionzooplankton_composition.csvPhytoplankton compositionphytoplankton_composition.csvComposition of bacterial communitybacteria_composition.csv