cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14278509
title: Macronutrient dynamics in leaves and bunches of black pepper

description: Abstract: The objective of this work was to determine the macronutrient dynamics in leaves and bunches of black pepper (Piper nigrum) throughout the plant reproductive cycles. The experiment was carried out in a commercial field of 'Bragantina' black pepper. Leaves and bunches were sampled every 21 days for one year, during two crop cycles. The bunches were sampled from the twenty eighth day after the appearance of inflorescences until the complete fruit maturation. Samples of leaves and bunches were dried, and the contents of N, P, K, Ca, Mg, and S were determined. N, K, and Ca were the most common macronutrients found in the bunches and leaves of black pepper. The accumulation of dry matter in the bunches was similar for both cycles and it was adjusted to the linear and quadratic models. The accumulation and content of macronutrients followed the dry matter behavior trend. Macronutrient contents in leaves oscillate during the year, and K and Mg vary more than N, P, Ca, and S. The macronutrient contents in black pepper leaves and bunches depends on the plant vegetative stage, and this variation should be considered in the planning of the fertilization management.
DOI: 10.6084/m9.figshare.14278509.v1
title: Macronutrient dynamics in leaves and bunches of black pepper

description: Abstract: The objective of this work was to determine the macronutrient dynamics in leaves and bunches of black pepper (Piper nigrum) throughout the plant reproductive cycles. The experiment was carried out in a commercial field of 'Bragantina' black pepper. Leaves and bunches were sampled every 21 days for one year, during two crop cycles. The bunches were sampled from the twenty eighth day after the appearance of inflorescences until the complete fruit maturation. Samples of leaves and bunches were dried, and the contents of N, P, K, Ca, Mg, and S were determined. N, K, and Ca were the most common macronutrients found in the bunches and leaves of black pepper. The accumulation of dry matter in the bunches was similar for both cycles and it was adjusted to the linear and quadratic models. The accumulation and content of macronutrients followed the dry matter behavior trend. Macronutrient contents in leaves oscillate during the year, and K and Mg vary more than N, P, Ca, and S. The macronutrient contents in black pepper leaves and bunches depends on the plant vegetative stage, and this variation should be considered in the planning of the fertilization management.
DOI: 10.6084/m9.figshare.14278508.v1
title: Xanthosoma riedelianum starch for use in the food industry

description: Abstract: The objective of this work was to characterize the starch of Xanthosoma riedelianum, commonly known as “mangarito” in Brazil, and to evaluate its properties for the food industry. The starch was characterized as to its morphology and its thermal and technological properties. Morphology was evaluated by the analysis of granule size distribution, scanning electron microscopy, and X-ray diffraction. The thermal properties were examined by determining the initial, peak, and conclusion gelatinization temperatures, whereas the technological properties were obtained by analyzing viscosity, swelling power, solubility index, paste clarity, and syneresis. Although the extraction of X. riedelianum starch showed a low yield, the species is a source of starch with a high sticking temperature, mechanical stirring resistance, tendency to retrograde, and final viscosity. Therefore, this starch is ideal for products that require high viscosity, such as pie fillings, puddings, children’s foods, and bakery products, and its paste, which is opaque and viscous, can also be used in the formulation of broths.
DOI: 10.6084/m9.figshare.14278511
title: Carbon fractions in soil under no-tillage corn and cover crops in the Brazilian Cerrado

description: Abstract: The objective of this work was to evaluate soil carbon fractions under cover crops cultivated after corn (Zea mays), with or without nitrogen topdressing fertilization, in a long-term experiment in the Brazilian Cerrado. The experiment was carried out in a randomized complete block design, in split-plots with three replicates. The plots were represented by the cover crops, and the subplots, by the presence or absence of N topdressing for corn. The following cover crop species were planted after the harvest of the 30F53VYHR corn hybrid: 'BRS Mandarin' pigeonpea (Cajanus cajan), sunn hemp (Crotalaria juncea), oilseed radish (Raphanus sativus), and black mucuna (Mucuna aterrima). After the cutting of the cover crops, soil samples were collected at 0.0‒0.10 and 0.10‒0.20 m soil depths. After corn harvest, samples of its residues were taken. The cover crops alter the soil chemical and physical fractions, especially fulvic acid and soil particulate organic carbon. Nitrogen topdressing for corn decreases fulvic acid, but increases the humic acid/fulvic acid ratio and particulate organic carbon in the deeper soil layer.
DOI: 10.6084/m9.figshare.14278511.v1
title: Carbon fractions in soil under no-tillage corn and cover crops in the Brazilian Cerrado

description: Abstract: The objective of this work was to evaluate soil carbon fractions under cover crops cultivated after corn (Zea mays), with or without nitrogen topdressing fertilization, in a long-term experiment in the Brazilian Cerrado. The experiment was carried out in a randomized complete block design, in split-plots with three replicates. The plots were represented by the cover crops, and the subplots, by the presence or absence of N topdressing for corn. The following cover crop species were planted after the harvest of the 30F53VYHR corn hybrid: 'BRS Mandarin' pigeonpea (Cajanus cajan), sunn hemp (Crotalaria juncea), oilseed radish (Raphanus sativus), and black mucuna (Mucuna aterrima). After the cutting of the cover crops, soil samples were collected at 0.0‒0.10 and 0.10‒0.20 m soil depths. After corn harvest, samples of its residues were taken. The cover crops alter the soil chemical and physical fractions, especially fulvic acid and soil particulate organic carbon. Nitrogen topdressing for corn decreases fulvic acid, but increases the humic acid/fulvic acid ratio and particulate organic carbon in the deeper soil layer.
DOI: 10.6084/m9.figshare.14278514
title: Serum metabolites and body condition score associated with metritis, endometritis, ketosis, and mastitis in Holstein cows

description: Abstract: The objective of this work was to identify the serum metabolites and the body condition score (BCS) of Holstein cows associated with the occurrence of periparturient diseases, when under heat stress. Blood samples were collected from 181 cows one week after calving, and the BCS was recorded at calving. Cows with β-hydroxybutyrate (BHBA) concentration ≥ 0.8 mmol L-1 were 2.2 times more likely to develop metritis and 4.4 times more likely to develop clinical endometritis (CE). Cows with serum creatinine levels ≥ 2.0 mg dL-1 showed 2.2 and 4.5 greater risk (p ≤ 0.05) of suffering from metritis and CE, respectively, during the current lactation. The odds of metritis and CE occurrence were 2.7 and 4.6 times greater (p &lt; 0.01) in cows with serum total protein (TP) ≥ 5.0 mg dL-1. Cows with serum glucose levels ≤ 70 mg dL-1 and non-esterified fatty acids (NEFAs) ≥ 0.5 had 9.4 and 8.8 times greater odds of developing clinical ketosis, respectively, than cows with lower glucose and NEFA blood levels. The strategic use of metabolic tests to monitor transition Holstein cows, aiming to prevent some postpartum diseases due to heat stress, should focus on blood BHBA, NEFAs, glucose, creatinine, and TP. Additionally, the BCS ≤ 3.2 should be avoided to prevent endometritis.
DOI: 10.6084/m9.figshare.14278514.v1
title: Serum metabolites and body condition score associated with metritis, endometritis, ketosis, and mastitis in Holstein cows

description: Abstract: The objective of this work was to identify the serum metabolites and the body condition score (BCS) of Holstein cows associated with the occurrence of periparturient diseases, when under heat stress. Blood samples were collected from 181 cows one week after calving, and the BCS was recorded at calving. Cows with β-hydroxybutyrate (BHBA) concentration ≥ 0.8 mmol L-1 were 2.2 times more likely to develop metritis and 4.4 times more likely to develop clinical endometritis (CE). Cows with serum creatinine levels ≥ 2.0 mg dL-1 showed 2.2 and 4.5 greater risk (p ≤ 0.05) of suffering from metritis and CE, respectively, during the current lactation. The odds of metritis and CE occurrence were 2.7 and 4.6 times greater (p &lt; 0.01) in cows with serum total protein (TP) ≥ 5.0 mg dL-1. Cows with serum glucose levels ≤ 70 mg dL-1 and non-esterified fatty acids (NEFAs) ≥ 0.5 had 9.4 and 8.8 times greater odds of developing clinical ketosis, respectively, than cows with lower glucose and NEFA blood levels. The strategic use of metabolic tests to monitor transition Holstein cows, aiming to prevent some postpartum diseases due to heat stress, should focus on blood BHBA, NEFAs, glucose, creatinine, and TP. Additionally, the BCS ≤ 3.2 should be avoided to prevent endometritis.
DOI: 10.6084/m9.figshare.14278515
title: Maternal-offspring behavior of Guzerat beef cattle

description: Abstract: The objective of this work was to evaluate the characteristics of the maternal-offspring behavior of Guzerat bovines (Bos indicus) and the influence of this behavior on herd losses. A total of 73 gestating cows (multiparous and primiparous) and their respective calves were evaluated for the following behavioral traits: contact period between cow and calf (CPCC), cow age at calving, teat conditions, calf vigor at birth, need for human assistance (HA), and calf mortality until weaning. The mean weight of calves at birth was 29.12 kg. Vigor at birth was observed in 61.64% of calves; however, 27.4% of the calves required human assistance. Calf vigor was influenced by the CPCC, and calves without vigor needed more time with their mothers. Calves with low weight at birth required HA, whereas calves from cows with intermediate-sized teats did not. The absence of vigor at birth increased the mortality rate. The traits age of cows and vigor of calves at birth influence both the need for human assistance to calves in their first hours of life and herd losses.
DOI: 10.6084/m9.figshare.14278518
title: Recommendations for assessing earthworm populations in Brazilian ecosystems

description: Abstract: Earthworms are often related to fertile soils and are also frequently used as environmental quality indicators. However, to optimize their use as bioindicators, earthworm populations must be evaluated together with the environmental and anthropogenic variables regulating their communities. This review sought to identify the earthworm-sampling, soil chemical and physical, and environmental and anthropogenic attributes evaluated in 124 published studies that quantified earthworm abundance (&gt;7,300 samples) in 765 sites with different types of climate, soils, land use, and management systems in Brazil. Soil chemical and physical attributes (except pH) were less reported (≤50% of studies) than other environmental variables such as sampling date, altitude, temperature, precipitation, climate and soil type, and land use (&gt;50% of studies). Earthworms were rarely identified (24%) and few studies (31%) measured their biomass, although most provided adequate information on sampling protocol. Based on their importance in regulating earthworm populations, a set of variables is proposed to be evaluated when studying earthworm communities and other macrofauna groups. This should help guide future studies on earthworms in Brazil and other countries, optimize data collection and replicability, allow comparisons between different studies, and promote the use of earthworms as soil quality bioindicators.
DOI: 10.6084/m9.figshare.14278520
title: Body mass index, energy reserves, and tissue composition of cuts of Corriedale lambs

description: Abstract: The objective of this work was to identify relationships of the body mass index (BMI) with the body energy reserves and tissue composition of shoulder and leg cuts of Corriedale lambs. Twenty-two sheep with average age of 18 months were used. Linear regressions were determined between the studied characteristics. The mean body mass, body condition score (BCS), and BMI were 49.09±7.8 kg, 2.69±0.81, and 10.66±0.99, respectively. The BMI was correlated with the BCS (r = 0.51) and internal fat (r = 0.81). Multiple linear equations, involving BMI and BCS, yielded correlation coefficients between 0.50 and 0.76, with significant values for all studied characteristics. The body mass index allows estimating the body energy reserves of Corriedale sheep.
DOI: 10.6084/m9.figshare.14278520.v1
title: Body mass index, energy reserves, and tissue composition of cuts of Corriedale lambs

description: Abstract: The objective of this work was to identify relationships of the body mass index (BMI) with the body energy reserves and tissue composition of shoulder and leg cuts of Corriedale lambs. Twenty-two sheep with average age of 18 months were used. Linear regressions were determined between the studied characteristics. The mean body mass, body condition score (BCS), and BMI were 49.09±7.8 kg, 2.69±0.81, and 10.66±0.99, respectively. The BMI was correlated with the BCS (r = 0.51) and internal fat (r = 0.81). Multiple linear equations, involving BMI and BCS, yielded correlation coefficients between 0.50 and 0.76, with significant values for all studied characteristics. The body mass index allows estimating the body energy reserves of Corriedale sheep.
DOI: 10.6084/m9.figshare.14278515.v1
title: Maternal-offspring behavior of Guzerat beef cattle

description: Abstract: The objective of this work was to evaluate the characteristics of the maternal-offspring behavior of Guzerat bovines (Bos indicus) and the influence of this behavior on herd losses. A total of 73 gestating cows (multiparous and primiparous) and their respective calves were evaluated for the following behavioral traits: contact period between cow and calf (CPCC), cow age at calving, teat conditions, calf vigor at birth, need for human assistance (HA), and calf mortality until weaning. The mean weight of calves at birth was 29.12 kg. Vigor at birth was observed in 61.64% of calves; however, 27.4% of the calves required human assistance. Calf vigor was influenced by the CPCC, and calves without vigor needed more time with their mothers. Calves with low weight at birth required HA, whereas calves from cows with intermediate-sized teats did not. The absence of vigor at birth increased the mortality rate. The traits age of cows and vigor of calves at birth influence both the need for human assistance to calves in their first hours of life and herd losses.
DOI: 10.22002/7711x-nwv63
title: Staphylococcus aureus_WT

description: S. aureus WT cells grown in TSB media.
description: <strong>Tilt Series Date:</strong> 2017-07-21</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Staphylococcus aureus</p>
<strong>Strain:</strong> subsp. aureus str. Newman</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 240.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Tracy Palmer, University of Dundee. Data collected by Debnath Ghosal.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in TSA and in TSB  (Oxoid TSA and TSB from Thermo Fisher 10525943 & 10137562). Dilute an overnight culture 1/100 and grow for ~4 hr (to OD 2) then freeze.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 6 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-21-12/rawdata/</p>Saureus_WT_201707210012.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-21-12/rawdata/Saureus_WT_201707210012.mrc"
        > <i class="download icon"></i> Download </a></p>

        Saureus_WT_201707210012.rec,  Reconstruction (Pixel Size 1.56 nm), 890.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-21-12/3dimage_87428/Saureus_WT_201707210012.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/q9r7r-jjv47
title: Coxiella_burnetii_ wtACCMD_pH4d5

description: Coxiella burnetii Nine Mile phase II clone 4 (NMIIC4) strain. Wild-type cells day-5 culture. Cells grown in acidic media ACCMD and pH 4.75
description: <strong>Tilt Series Date:</strong> 2017-08-15</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Coxiella burnetii</p>
<strong>Strain:</strong> Nine Mile phase II clone 4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Robert Heinzen. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in Robert Heinzen's lab @NIAID and ~50 ul cells were sent to us.</p>
<strong>Sample Preparation:</strong> Refer to Heinzen lab. Freezing: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
  dga2017-08-15-29_slicer18744.jpg: cytoplasmic vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-15-29/rawdata/</p>Cb_20170816_Cb1pH4d50028.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-15-29/rawdata/Cb_20170816_Cb1pH4d50028.mrc"
        > <i class="download icon"></i> Download </a></p>

        Cb_20170816_Cb1pH4d50028_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-08-15-29/3dimage_88000/Cb_20170816_Cb1pH4d50028_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.yz3nnq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cenchrus setaceus",
 "Country is Fiji",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012064-250827131500795/datasets/export for details.
DOI: 10.22002/14yfv-bbt30
title: Agro_AD1408_GFP-VirB11

description: AD1408: pAdi16/A348dB11; Kanamycin 50; Functional GFP-VirB11 fusion.
description: <strong>Tilt Series Date:</strong> 2015-07-21</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Agrobacterium tumefaciens</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 121.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain constructed by Anath Das. Data collected and processed by Debnath Ghosal using Caltech tomography pipeline.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow culture in AB medium (pH 7) at 30C. For induction, use 375 µl of a decent ON culture to inoculate 5 ml AB mes pH 5.8 medium containing 100 µM Acetosyringone and antibiotic (Kan 50). Grow at 20C for 18 hr. Freeze cells.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-07-21-30/rawdata/</p>1408_atlas_20018.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2015-07-21-30/rawdata/1408_atlas_20018.mrc"
        > <i class="download icon"></i> Download </a></p>

        1408_atlas_20018_full.rec,  Reconstruction (Pixel Size 1.92 nm), 445.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gytbz-5wq86
title: V. cholerae RT4236 (refreshed)

description: Classical strain with ctxA deletionCell harbors pMT5 plasmid (inducible toxT)
description: <strong>Tilt Series Date:</strong> 2015-09-09</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> V. cholerae 0395-N1 pMT5 grown in 5ml LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin in glass tube shaking for overnight. After took the tube out from shaker, supernatant was removed and pellet was resuspended by gentle pipetting in 1ml fresh LB without IPTG nor ampicillin. Culture was incubated at room temperature for ~15 min before mixing with gold and freezing.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3.5 µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-09-09-9/3dimage_61191/</p>20150909_AK_pMT15_10009_full.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150909_AK_pMT15_10009.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-09-09-9/rawdata/20150909_AK_pMT15_10009.mrc"
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