cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7418300
title: Chromosome instability in tumor cells due to defects in Aurora B mediated error correction at kinetochores

description: We characterized a panel of cancer cells and found that they exhibited chromosome instability (CIN) that was associated with high frequencies of aberrant kinetochore:microtubule attachments. Failure to resolve these defective attachments before anaphase onset can lead to missegregation of chromosomes. Aurora B kinase is concentrated at the inner centromere where it contributes to multiple kinetochore functions, one of which is in error-correction. Analysis of several CIN cell lines showed that many aspects of Aurora B kinase functions were normal. Furthermore, the amount and activity of Aurora B kinase was not reduced at the kinetochores of CIN cells that were examined. However, phosphorylation of a centromeric biosensor for Aurora B in OVCAR10, MCF7 and U2OS cells was consistently reduced relative to non CIN cells. This suggested a localized problem with Aurora B’s ability to phosphorylate substrates important for error correction. This possibility was supported by our ability to improve error correction and reduce the frequency of lagging chromosome in CIN cells by directing endogenous Aurora B to the region of centromere that was tested by the biosensor. Our studies suggest that the kinetochores of CIN cells have a defect that limits accessibility of Aurora B to substrates that are important for error-correction.
DOI: 10.7284/108018
title: Singlebeam Echosounder data collected during research cruise OC1205A using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418300.v2
title: Chromosome instability in tumor cells due to defects in Aurora B mediated error correction at kinetochores

description: We characterized a panel of cancer cells and found that they exhibited chromosome instability (CIN) that was associated with high frequencies of aberrant kinetochore:microtubule attachments. Failure to resolve these defective attachments before anaphase onset can lead to missegregation of chromosomes. Aurora B kinase is concentrated at the inner centromere where it contributes to multiple kinetochore functions, one of which is in error-correction. Analysis of several CIN cell lines showed that many aspects of Aurora B kinase functions were normal. Furthermore, the amount and activity of Aurora B kinase was not reduced at the kinetochores of CIN cells that were examined. However, phosphorylation of a centromeric biosensor for Aurora B in OVCAR10, MCF7 and U2OS cells was consistently reduced relative to non CIN cells. This suggested a localized problem with Aurora B’s ability to phosphorylate substrates important for error correction. This possibility was supported by our ability to improve error correction and reduce the frequency of lagging chromosome in CIN cells by directing endogenous Aurora B to the region of centromere that was tested by the biosensor. Our studies suggest that the kinetochores of CIN cells have a defect that limits accessibility of Aurora B to substrates that are important for error-correction.
DOI: 10.7284/108020
title: Singlebeam Echosounder data collected during research cruise OC1205A using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418273
title: Activated Tyrosine Kinases in Gastrointestinal Stromal Tumor with Loss of KIT Oncoprotein Expression

description: Oncogenic KIT or PDGFRA receptor tyrosine kinase (TK) mutations are compelling therapeutic targets in gastrointestinal stromal tumors (GISTs), and the KIT/PDGFRA kinase inhibitor, imatinib, is the standard of care for patients with metastatic GIST. However, approximately 10% of KIT-positive GIST metastases lose KIT expression at the time of clinical progression during imatinib therapy. In the present report, we performed TK-activation screens, using phosphotyrosine-TK double immunoaffinity purification and mass spectrometry, in GIST <i>in vitro</i> models lacking KIT expression. These studies demonstrated tyrosine-phosphorylated EGFR, AXL, and EPHA2 in four of six KIT-negative GIST lines (GIST62, GIST522, GIST54, GIST226, GIST48B, and GIST430B), and tyrosine-phosphorylated focal adhesion kinase (FAK) in each of the six KIT-negative lines. AXL expression was strong in KIT-negative or -weak clinical GIST samples that were obtained from progressing metastases during imatinib therapy. AXL knockdown inhibited viability in three KIT-negative GIST cell lines (GIST62, GIST54, and GIST522), but not in an AXL-negative, KIT-positive GIST control cell line (GIST430). AXL inhibition by R428, a specific AXL kinase inhibitor, reduced viability in AXL-activated GIST54. AXL knockdown in GIST62, GIST522, and GIST54 was accompanied by an increase in p21, p27, and p53 expression. By contrast, gefitinib-mediated EGFR inhibition, PF562271-mediated FAK inactivation, and shRNA-mediated knockdowns of EPHA2 and FAK had no effect on viability or colony formation of the KIT-negative GISTs. These findings highlight the potential relevance of AXL/p53 signaling as a therapeutic target in a subset of GISTs that have lost KIT oncoprotein expression.
DOI: 10.6084/m9.figshare.7418282
title: E. Popiel, A. Szewczuk - zadanie grupowe.docx

description: <b>Streszczenie:</b> Podejmowanie decyzji to proces, który ma na celu wybór najkorzystniejszego rozwiązania. Obejmuje on grupę operacji myślowych oraz obliczeniowych. Aby ulepszyć procesy decyzyjne wykorzystuje się różne metody i techniki oparte na dziedzinie matematycznej i statystycznej. Podejmowanie decyzji jest podstawowym warunkiem rozwiązywania większości problemów występujących w przedsiębiorstwie. W każdym przypadku analiza różnych decyzji wymaga porównania korzyści i kosztów różnych sposobów postępowania. Istnieją różne definicje ryzyka finansowego. Jedna z nich mówi, że jest to rodzaj ryzyka, związane ze strukturą kapitałową kredytobiorcy. Jeżeli podmiot gospodarczy finansuje swój majątek kapitałami obcymi, to istnieje ryzyko, że odsetki będą na tyle wysokie, że znajdzie się on w trudnej sytuacji ekonomicznej i nie będzie on w stanie dokonać spłaty kredytu lub wykupu obligacji. Ryzyko to jest tym wyższe, im wyższy jest udział kapitałów obcych w strukturze kapitałów kredytobiorcy oraz im wyższe są koszty jego pozyskania. <i> </i> <b><i>Abstract:</i></b> <i>Making decisions is a process that aims to choose the best solution. It includes a group of thought and computational operations. To improve the decision-making processes, various methods and techniques based on the mathematical and statistical field are used. Decision making is a basic condition for solving most problems occurring in the enterprise. In each case, the analysis of the various decisions requires a comparison of the benefits and costs of the different procedures.</i> <i>The definition says that the financial risk is related to the borrower's capital structure. If an economic entity finances its assets with external capital, there is a risk that interest will be so high that it will be in a difficult economic situation and will not be able to repay the loan or redeem the bonds. The higher the risk is, the higher the share of foreign capital in the capital structure of the borrower and the higher the costs of its acquisition.</i>
DOI: 10.6084/m9.figshare.7418264
title: Manuscript submission data and R code archive for: An experimental evaluation of the impact of a Payment for Environmental Services programme on deforestation, submitted to Conservation Science and Practice.

description: Detailed description in README file. These are the R code and data files used to produce the submission.<br>
DOI: 10.6084/m9.figshare.7418282.v2
title: E. Popiel, A. Szewczuk - zadanie grupowe.docx

description: <b>Streszczenie:</b> Podejmowanie decyzji to proces, który ma na celu wybór najkorzystniejszego rozwiązania. Obejmuje on grupę operacji myślowych oraz obliczeniowych. Aby ulepszyć procesy decyzyjne wykorzystuje się różne metody i techniki oparte na dziedzinie matematycznej i statystycznej. Podejmowanie decyzji jest podstawowym warunkiem rozwiązywania większości problemów występujących w przedsiębiorstwie. W każdym przypadku analiza różnych decyzji wymaga porównania korzyści i kosztów różnych sposobów postępowania. Istnieją różne definicje ryzyka finansowego. Jedna z nich mówi, że jest to rodzaj ryzyka, związane ze strukturą kapitałową kredytobiorcy. Jeżeli podmiot gospodarczy finansuje swój majątek kapitałami obcymi, to istnieje ryzyko, że odsetki będą na tyle wysokie, że znajdzie się on w trudnej sytuacji ekonomicznej i nie będzie on w stanie dokonać spłaty kredytu lub wykupu obligacji. Ryzyko to jest tym wyższe, im wyższy jest udział kapitałów obcych w strukturze kapitałów kredytobiorcy oraz im wyższe są koszty jego pozyskania. <i> </i> <b><i>Abstract:</i></b> <i>Making decisions is a process that aims to choose the best solution. It includes a group of thought and computational operations. To improve the decision-making processes, various methods and techniques based on the mathematical and statistical field are used. Decision making is a basic condition for solving most problems occurring in the enterprise. In each case, the analysis of the various decisions requires a comparison of the benefits and costs of the different procedures.</i> <i>The definition says that the financial risk is related to the borrower's capital structure. If an economic entity finances its assets with external capital, there is a risk that interest will be so high that it will be in a difficult economic situation and will not be able to repay the loan or redeem the bonds. The higher the risk is, the higher the share of foreign capital in the capital structure of the borrower and the higher the costs of its acquisition.</i>
DOI: 10.7284/108030
title: Water Temperature data collected during research cruise OC1205A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418264.v1
title: Manuscript submission data and R code archive for: An experimental evaluation of the impact of a Payment for Environmental Services programme on deforestation, submitted to Conservation Science and Practice.

description: Detailed description in README file. These are the R code and data files used to produce the submission.<br>
DOI: 10.6084/m9.figshare.7418282.v1
title: E. Popiel, A. Szewczuk - zadanie grupowe.docx

description: <b>Streszczenie:</b> Podejmowanie decyzji to proces, który ma na celu wybór najkorzystniejszego rozwiązania. Obejmuje on grupę operacji myślowych oraz obliczeniowych. Aby ulepszyć procesy decyzyjne wykorzystuje się różne metody i techniki oparte na dziedzinie matematycznej i statystycznej. Podejmowanie decyzji jest podstawowym warunkiem rozwiązywania większości problemów występujących w przedsiębiorstwie. W każdym przypadku analiza różnych decyzji wymaga porównania korzyści i kosztów różnych sposobów postępowania. Istnieją różne definicje ryzyka finansowego. Jedna z nich mówi, że jest to rodzaj ryzyka, związane ze strukturą kapitałową kredytobiorcy. Jeżeli podmiot gospodarczy finansuje swój majątek kapitałami obcymi, to istnieje ryzyko, że odsetki będą na tyle wysokie, że znajdzie się on w trudnej sytuacji ekonomicznej i nie będzie on w stanie dokonać spłaty kredytu lub wykupu obligacji. Ryzyko to jest tym wyższe, im wyższy jest udział kapitałów obcych w strukturze kapitałów kredytobiorcy oraz im wyższe są koszty jego pozyskania. <i> </i> <b><i>Abstract:</i></b> <i>Making decisions is a process that aims to choose the best solution. It includes a group of thought and computational operations. To improve the decision-making processes, various methods and techniques based on the mathematical and statistical field are used. Decision making is a basic condition for solving most problems occurring in the enterprise. In each case, the analysis of the various decisions requires a comparison of the benefits and costs of the different procedures.</i> <i>The definition says that the financial risk is related to the borrower's capital structure. If an economic entity finances its assets with external capital, there is a risk that interest will be so high that it will be in a difficult economic situation and will not be able to repay the loan or redeem the bonds. The higher the risk is, the higher the share of foreign capital in the capital structure of the borrower and the higher the costs of its acquisition.</i>
DOI: 10.6084/m9.figshare.7418273.v2
title: Activated Tyrosine Kinases in Gastrointestinal Stromal Tumor with Loss of KIT Oncoprotein Expression

description: Oncogenic KIT or PDGFRA receptor tyrosine kinase (TK) mutations are compelling therapeutic targets in gastrointestinal stromal tumors (GISTs), and the KIT/PDGFRA kinase inhibitor, imatinib, is the standard of care for patients with metastatic GIST. However, approximately 10% of KIT-positive GIST metastases lose KIT expression at the time of clinical progression during imatinib therapy. In the present report, we performed TK-activation screens, using phosphotyrosine-TK double immunoaffinity purification and mass spectrometry, in GIST <i>in vitro</i> models lacking KIT expression. These studies demonstrated tyrosine-phosphorylated EGFR, AXL, and EPHA2 in four of six KIT-negative GIST lines (GIST62, GIST522, GIST54, GIST226, GIST48B, and GIST430B), and tyrosine-phosphorylated focal adhesion kinase (FAK) in each of the six KIT-negative lines. AXL expression was strong in KIT-negative or -weak clinical GIST samples that were obtained from progressing metastases during imatinib therapy. AXL knockdown inhibited viability in three KIT-negative GIST cell lines (GIST62, GIST54, and GIST522), but not in an AXL-negative, KIT-positive GIST control cell line (GIST430). AXL inhibition by R428, a specific AXL kinase inhibitor, reduced viability in AXL-activated GIST54. AXL knockdown in GIST62, GIST522, and GIST54 was accompanied by an increase in p21, p27, and p53 expression. By contrast, gefitinib-mediated EGFR inhibition, PF562271-mediated FAK inactivation, and shRNA-mediated knockdowns of EPHA2 and FAK had no effect on viability or colony formation of the KIT-negative GISTs. These findings highlight the potential relevance of AXL/p53 signaling as a therapeutic target in a subset of GISTs that have lost KIT oncoprotein expression.
DOI: 10.6084/m9.figshare.7418273.v1
title: Activated tyrosine kinases in gastrointestinal stromal tumor with loss of KIT oncoprotein expression

description: Oncogenic KIT or PDGFRA receptor tyrosine kinase (TK) mutations are compelling therapeutic targets in gastrointestinal stromal tumors (GISTs), and the KIT/PDGFRA kinase inhibitor, imatinib, is the standard of care for patients with metastatic GIST. However, approximately 10% of KIT-positive GIST metastases lose KIT expression at the time of clinical progression during imatinib therapy. In the present report, we performed TK-activation screens, using phosphotyrosine-TK double immunoaffinity purification and mass spectrometry, in GIST <i>in vitro</i> models lacking KIT expression. These studies demonstrated tyrosine-phosphorylated EGFR, AXL, and EPHA2 in four of six KIT-negative GIST lines (GIST62, GIST522, GIST54, GIST226, GIST48B, and GIST430B), and tyrosine-phosphorylated focal adhesion kinase (FAK) in each of the six KIT-negative lines. AXL expression was strong in KIT-negative or -weak clinical GIST samples that were obtained from progressing metastases during imatinib therapy. AXL knockdown inhibited viability in three KIT-negative GIST cell lines (GIST62, GIST54, and GIST522), but not in an AXL-negative, KIT-positive GIST control cell line (GIST430). AXL inhibition by R428, a specific AXL kinase inhibitor, reduced viability in AXL-activated GIST54. AXL knockdown in GIST62, GIST522, and GIST54 was accompanied by an increase in p21, p27, and p53 expression. By contrast, gefitinib-mediated EGFR inhibition, PF562271-mediated FAK inactivation, and shRNA-mediated knockdowns of EPHA2 and FAK had no effect on viability or colony formation of the KIT-negative GISTs. These findings highlight the potential relevance of AXL/p53 signaling as a therapeutic target in a subset of GISTs that have lost KIT oncoprotein expression.
DOI: 10.7284/108031
title: Water Temperature data collected during research cruise OC1205A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418225
title: LGMD2E is the most common type of sarcoglycanopathies in the Iranian population

description: Sarcoglycanopathies (SGCs) which are caused by mutations in <i>SGCA</i>, <i>SGCB</i>, <i>SGCG</i> or <i>SGCD</i> genes are a subgroup of autosomal-recessive limb-girdle-muscular-dystrophies (LGMD2). Although frequencies of mutations in these genes are different among populations, mutations in <i>SGCA</i> and <i>SGCD</i>, respectively, have the highest and lowest frequencies in most populations. Here, we report the proportion of mutations in SGC genes among a group of Iranian SGCs patients. Clinical features and results of SGC genes screening of 25 SGCs probands are presented. Large deletion mutations are confirmed with MLPA assays. In total, 15 candidate disease causing mutations were observed in the <i>SGCA</i>, <i>SGCB</i>, <i>SGCG</i> and <i>SGCD</i> genes; ten were novel. Fourteen (56%), seven (28%), three (12%) and one (4%) patient, respectively, carried mutations in <i>SGCB</i>, <i>SGCG</i>, <i>SGCD</i> and <i>SGCA</i>. The findings suggest that LGMD2E is the most common form of SGCs in the Iranian population and that LGMD2D is the rarest. Twelve LGMD2E cases carried the same mutation. To the best of knowledge, the mutation spectrum in SGCs is being reported for the first time in Iranian population. The finding will be beneficial for screening and genetic-counseling of SGCs patients in Iran.
DOI: 10.7284/108032
title: Transmissometer data collected during research cruise OC1205A using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418225.v1
title: LGMD2E is the most common type of sarcoglycanopathies in the Iranian population

description: Sarcoglycanopathies (SGCs) which are caused by mutations in <i>SGCA</i>, <i>SGCB</i>, <i>SGCG</i> or <i>SGCD</i> genes are a subgroup of autosomal-recessive limb-girdle-muscular-dystrophies (LGMD2). Although frequencies of mutations in these genes are different among populations, mutations in <i>SGCA</i> and <i>SGCD</i>, respectively, have the highest and lowest frequencies in most populations. Here, we report the proportion of mutations in SGC genes among a group of Iranian SGCs patients. Clinical features and results of SGC genes screening of 25 SGCs probands are presented. Large deletion mutations are confirmed with MLPA assays. In total, 15 candidate disease causing mutations were observed in the <i>SGCA</i>, <i>SGCB</i>, <i>SGCG</i> and <i>SGCD</i> genes; ten were novel. Fourteen (56%), seven (28%), three (12%) and one (4%) patient, respectively, carried mutations in <i>SGCB</i>, <i>SGCG</i>, <i>SGCD</i> and <i>SGCA</i>. The findings suggest that LGMD2E is the most common form of SGCs in the Iranian population and that LGMD2D is the rarest. Twelve LGMD2E cases carried the same mutation. To the best of knowledge, the mutation spectrum in SGCs is being reported for the first time in Iranian population. The finding will be beneficial for screening and genetic-counseling of SGCs patients in Iran.
DOI: 10.7284/108033
title: TSG (Thermosalinograph) data collected during research cruise OC1205A using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418198
title: A systematic review and combined analysis of therapeutic drug monitoring studies for long-acting paliperidone

description: <b>Introduction</b>: This is a combined analysis of therapeutic drug monitoring (TDM) studies of long-acting injectable paliperidone formulations: monthly (PP1M) and three-month (PP3M) injections. <b>Areas covered</b>: Fourteen PP1M articles and one PP3M article were identified. Using the paliperidone concentration/dose (C/D) ratio as a measure of clearance provided a weighted mean of 7.7 ng/ml per mg/day among 69 patients from three steady-state PP1M studies (twice as high as oral paliperidone). C/D ratios were: 1) higher by a factor of 1.26 in 12 geriatric patients, 2) lower in obese patients, and 3) 50% lower in three patients taking carbamazepine. No clinically meaningful PP3M pharmacokinetic data have been published. <b>Expert commentary</b>: Half-life studies and more TDM PP1M studies using steady state are urgently needed. Early TDM studies may help orient PP1M dosing but steady state may not be reached until after the ninth injection (8 months). PP3M may take &gt; 1 year to reach steady state. Any clinician considering switching patients to PP1M: 1) should switch from oral risperidone to PP1M rather than from oral paliperidone to PP1M, and 2) become proficient in paliperidone TDM to use during switches. TDM is highly recommended for patients with abnormal clearance (from obesity, geriatric age, or potent inducers).
DOI: 10.7284/108210
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1206A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7418198.v1
title: A systematic review and combined analysis of therapeutic drug monitoring studies for long-acting paliperidone

description: <b>Introduction</b>: This is a combined analysis of therapeutic drug monitoring (TDM) studies of long-acting injectable paliperidone formulations: monthly (PP1M) and three-month (PP3M) injections. <b>Areas covered</b>: Fourteen PP1M articles and one PP3M article were identified. Using the paliperidone concentration/dose (C/D) ratio as a measure of clearance provided a weighted mean of 7.7 ng/ml per mg/day among 69 patients from three steady-state PP1M studies (twice as high as oral paliperidone). C/D ratios were: 1) higher by a factor of 1.26 in 12 geriatric patients, 2) lower in obese patients, and 3) 50% lower in three patients taking carbamazepine. No clinically meaningful PP3M pharmacokinetic data have been published. <b>Expert commentary</b>: Half-life studies and more TDM PP1M studies using steady state are urgently needed. Early TDM studies may help orient PP1M dosing but steady state may not be reached until after the ninth injection (8 months). PP3M may take &gt; 1 year to reach steady state. Any clinician considering switching patients to PP1M: 1) should switch from oral risperidone to PP1M rather than from oral paliperidone to PP1M, and 2) become proficient in paliperidone TDM to use during switches. TDM is highly recommended for patients with abnormal clearance (from obesity, geriatric age, or potent inducers).
DOI: 10.7284/108200
title: Anemometer data collected during research cruise OC1206A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111553
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise OC1206A using a Sea-Bird SBE-911+ instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108202
title: Fluorometer data collected during research cruise OC1206A using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition