cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125153.v1
title: Supplementary Material for: Clinically Relevant Effect of a New Intranasal Therapy (MP29-02) in Allergic Rhinitis Assessed by Responder Analysis

description: <b><i>Background:</i></b> It is unclear what constitutes a clinically meaningful response for allergic rhinitis (AR) outcomes. The objectives of these post hoc analyses were (1) to define a clinically meaningful response using novel efficacy analyses (including a responder analysis), and (2) to compare the efficacy of MP29-02 [a novel intranasal formulation of azelastine hydrochloride (AZE) and fluticasone propionate (FP)] with commercially available FP, AZE and placebo in seasonal AR (SAR) patients, using these novel analyses. <b><i>Methods:</i></b> 610 moderate-to-severe SAR patients (≥12 years old) were randomized into a double-blind, placebo-controlled, 14-day, parallel-group trial. Change from baseline in the reflective total nasal symptom score (rTNSS) over 14 days was the primary outcome. Post hoc endpoints included the sum of nasal and ocular symptoms (rT7SS), efficacy by disease severity and by predominant nasal symptom, and a set of responder analyses. <b><i>Results:</i></b> MP29-02 most effectively reduced rT7SS (relative greater improvement: 52% to FP; 56% to AZE) and both nasal and ocular symptoms irrespective of severity. More MP29-02 patients achieved a ≥30, ≥50, ≥60, ≥75 and ≥90% rTNSS reduction, which occurred days faster than with either active comparator; MP29-02 alone was superior to placebo at the ≥60% (or higher) threshold. One in 2 MP29-02 patients achieved a ≥50% rTNSS reduction and 1 in 6 achieved complete/near-to-complete response. Only MP29-02 was consistently superior to placebo for all patients, whatever their predominant symptom. <b><i>Conclusions:</i></b> MP29-02 provided faster and more complete symptom control than first-line therapies. It was consistently superior irrespective of severity, response criteria or patient-type, and may be considered the drug of choice for moderate-to-severe AR. These measures define a new standard for assessing relevance in AR.
DOI: 10.6084/m9.figshare.5125141
title: Supplementary Material for: Comparison of Immunosuppressive and Cytotoxic Cells in Angiosarcoma: Development of a Possible Supportive Therapy for Angiosarcoma

description: An imbalance of immunosuppressive and cytotoxic cells plays an important role in inhibiting the anti-tumor immune response of the tumor-bearing host. The purpose of this study was to elucidate the involvement of immunosuppressive cells, such as regulatory T cells and CD163+ M2 macrophages as well as cytotoxic cells, such as granulysin-bearing cells and TIA-1+ cells in cutaneous angiosarcoma (AS) by immunohistochemical staining. In addition we evaluated the potencies of bisphosphonate, which was previously reported to suppress the expression of matrix metalloproteinase 9 (MMP-9), as a supportive therapy for AS together with docetaxel in 6 cases of cutaneous AS. These findings suggest that a high number of immunosuppressive cells might be related to the prognosis of AS, and that a combination of docetaxel with bisphosphonate risedronate sodium might be effective for MMP-9-expressing AS.
DOI: 10.6084/m9.figshare.5125144
title: A systematic review of factors affecting driving and public transportation among youth and young adults with acquired brain injury

description: <i>Purpose</i>: Although many people with an acquired brain injury (ABI) encounter difficulties with executive functioning and memory which could negatively affect driving, few people are assessed for fitness to drive after injury. The purpose of this systematic review was to synthesize the literature on factors affecting driving and public transportation among youth and young adults with ABI, post injury. <i>Method</i>: Seven databases were systematically searched for articles from 1980 to 2016. Studies were screened independently by two researchers who performed the data extraction. Study quality was appraised using the Standard Quality Assessment Criteria (Kmet) for evaluating primary research from a variety of fields. <i>Results</i>: Of the 6577 studies identified in the search, 25 met the inclusion criteria, which involved 1527 participants with ABI (mean age = 25.1) across eight countries. Six studies focused on driving assessment and fitness to drive, ten on driving performance or risk of accidents and nine studies explored issues related to accessing or navigating public transportation. Quality assessment of the included studies ranged from 0.60 to 0.95. <i>Conclusions</i>: Our findings highlight several gaps in clinical practice and research along with a critical need for enhanced fitness to drive assessments and transportation-related training for young people with ABI.
DOI: 10.6084/m9.figshare.5125150.v1
title: Supplementary Material for: Endovascular Treatment of Distal Internal Carotid Artery Occlusions with Retrievable Stents

description: <b><i>Background:</i></b> Acute stroke due to distal intracranial internal carotid artery (ICA) occlusion has a poor natural history. Outcome in patients who receive intravenous tissue plasminogen activator (tPA) is also unsatisfactory. The objective of this study is to evaluate the effectiveness and safety of endovascular treatment with retrievable stents in these patients. <b><i>Methods:</i></b> Data from a prospective register of patients with acute stroke treated with an endovascular procedure in a single centre were analysed. <b><i>Results:</i></b> A total of 20 patients with distal ICA occlusion were collected. Mean baseline National Institutes of Health Stroke Scale score was 18. Eight cases (40%) had received previous intravenous tPA. Mean time from stroke to recanalization was 393 min. Retrievable stents with proximal occlusion and aspiration were used in all cases. In 3 patients, 2 retrievable stents were used simultaneously. Complete recanalization (thrombolysis in cerebral infarction 2b/3) was accomplished in 85% of cases. A favourable clinical outcome (modified Rankin Scale score 0-2) was achieved in 13 patients (65%). Mortality occurred in 2 cases (10%). <b><i>Conclusions:</i></b> Endovascular treatment of patients with distal ICA occlusion seems safe and effective. Retrievable stents may be the treatment of choice, although randomized clinical trials are necessary. The use of 2 retrievable stents at the same time could be an alternative technique useful in thrombi of larger size.
DOI: 10.6084/m9.figshare.5125135
title: Supplementary Material for: Which Social Network or Support Factors are Associated with Cognitive Abilities in Old Age?

description: <b><i>Background:</i></b> Social networks and support have been proposed as cognitively protective in old age. As studies often consider these social factors in isolation the question of which characteristics of the social environment are beneficial remains. <b><i>Objective:</i></b> The current study examined associations between measures of social networks (including contact with friends/family, marital status and living arrangement), feelings of loneliness and social support, and a range of cognitive outcomes. <b><i>Methods:</i></b> Social network, loneliness and support data were available in the Lothian Birth Cohort 1936 (LBC1936, n = 1,091) at age 70. Participants completed a battery of cognitive tests, and factor scores were available for general cognitive ability, and the cognitive domains of processing speed and memory. Childhood cognitive ability data from age 11 were also available. <b><i>Results:</i></b> When examined in separate ANCOVAs, lower loneliness and more social support were significantly associated with better cognitive abilities at age 70, though not memory (independently of age, sex, childhood cognitive ability and social class), accounting for about 0.5-1.5% of the variance. When the social factors were considered simultaneously, higher loneliness remained associated with lower general cognitive ability (η<sub>p</sub><sup>2</sup> = 0.005, p = 0.046), and those living alone (η<sub>p</sub><sup>2</sup> = 0.007, p = 0.014) or with less social support (η<sub>p</sub><sup>2</sup> = 0.007, p = 0.016) had slower processing speed. When these final models were repeated including a depression symptoms score as a covariate, the associations between loneliness and general cognitive ability, and social support and processing speed, were no longer significant. However, the association between living alone and processing speed remained (η<sub>p</sub><sup>2</sup> = 0.006, p = 0.031). <b><i>Conclusions:</i></b> Of the social factors considered, loneliness, social support and living arrangement were most consistently associated with aspects of cognitive ability in older people, and these associations appeared to be partly, though not wholly, accounted for by symptoms of depression. Although longitudinal follow-up is required to examine the causal direction of the effects more definitively, it may be beneficial to promote the development of interventions to reduce loneliness and social isolation, and to increase social support.
DOI: 10.6084/m9.figshare.5125138
title: Supplementary Material for: Comparative Organization and Gene Expression Profiles of the Porcine Pseudoautosomal Region

description: The pseudoautosomal region (PAR) has important biological functions in spermatogenesis, male fertility and early development. Even though pig (<i>Sus scrofa</i>, SSC) is an agriculturally and biomedically important species, and its genome is sequenced, current knowledge about the porcine PAR is sparse. Here we defined the PAR in SSCXp/Yp by demarcating the sequence of the pseudoautosomal boundary at X:6,743,567 bp in intron 3-4 of <i>SHROOM2</i> and showed that <i>SHROOM2</i> is truncated in SSCY. Cytogenetic mapping of 20 BAC clones containing 15 PAR and X-specific genes revealed that the pig PAR is largely collinear with other mammalian PARs or Xp terminal regions. The results improved the current SSCX sequence assembly and facilitated distinction between the PAR and X-specific genes to study their expression in adult and embryonic tissues. A pilot analysis showed that the PAR genes are expressed at higher levels than X-specific genes during early development, whereas the expression of PAR genes was higher at day 60 compared to day 26, and higher in embryonic tissues compared to placenta. The findings advance the knowledge about the comparative organization of the PAR in mammals and suggest that the region might have important functions in early development in pigs.
DOI: 10.6084/m9.figshare.5125144.v1
title: A systematic review of factors affecting driving and public transportation among youth and young adults with acquired brain injury

description: <i>Purpose</i>: Although many people with an acquired brain injury (ABI) encounter difficulties with executive functioning and memory which could negatively affect driving, few people are assessed for fitness to drive after injury. The purpose of this systematic review was to synthesize the literature on factors affecting driving and public transportation among youth and young adults with ABI, post injury. <i>Method</i>: Seven databases were systematically searched for articles from 1980 to 2016. Studies were screened independently by two researchers who performed the data extraction. Study quality was appraised using the Standard Quality Assessment Criteria (Kmet) for evaluating primary research from a variety of fields. <i>Results</i>: Of the 6577 studies identified in the search, 25 met the inclusion criteria, which involved 1527 participants with ABI (mean age = 25.1) across eight countries. Six studies focused on driving assessment and fitness to drive, ten on driving performance or risk of accidents and nine studies explored issues related to accessing or navigating public transportation. Quality assessment of the included studies ranged from 0.60 to 0.95. <i>Conclusions</i>: Our findings highlight several gaps in clinical practice and research along with a critical need for enhanced fitness to drive assessments and transportation-related training for young people with ABI.
DOI: 10.6084/m9.figshare.5125129
title: Supplementary Material for: Complex Three-Way Translocation Involving <b><i>MLL</i></b>, <b><i>ELL</i></b>, <b><i>RREB1</i></b>, and <b><i>CMAHP </i></b>Genes in an Infant with Acute Myeloid Leukemia and t(6;19;11)(p22.2;p13.1;q23.3)

description: Rearrangements affecting the <i>MLL </i>gene in hematological malignancies are associated with poor prognosis. Most often they are reciprocal translocations and more rarely complex forms involving at least 3 chromosomes. We describe an unusual case with cutaneous leukemic infiltrates that waxed and waned until progression to acute myeloid leukemia, AML-M5. The leukemic cells harbored a novel apparent 3-way translocation t(6;19;11)(p22.2;p13.1;q23.3). We utilized advanced molecular cytogenetic methods including 24-color karyotyping, high-resolution array comparative genomic hybridization (aCGH) and DNA sequencing to characterize the genomic complement in the leukemic cells from aspirated bone marrow cells at AML diagnosis. Karyotyping showed 47,XY,t(6;19;11)(p22;p13;q23),+der(6)t(6;11)(p22;q23)[17]/48,sl,+8[3]/48,sl,+8,der(12)t(1;12)(q11;p13)[3]/ 48,sdl,der(Y)t(Y;1)(q12;q11),+8[7] conferring <i>MLL-ELL</i> fusion. Oligo-aCGH analysis confirmed gains of 6p22qter and 11q23.3qter involving the <i>CMAHP</i> and <i>MLL </i>genes, respectively. DNA sequencing disclosed an additional breakpoint at 6p24.3 (at <i>RREB1</i> gene). Retrospective fluorescence in situ hybridization revealed presence of the <i>MLL</i>-involving rearrangement in the initial stages of disease before clear morphological signs of bone marrow involvement. The patient responded well to therapy and remains in remission &gt;6 years from diagnosis. This apparent 3-way translocation is remarkable because of its rarity and presentation with myeloid sarcoma, and may, as more cases are characterized, further our understanding onto how such complex translocations contribute to promote leukemogenesis and respond to therapy.
DOI: 10.6084/m9.figshare.5125132
title: Supplementary Material for: Clinical Benefit for Patients with Non-Small Cell Lung Cancer Enrolled in Phase I Trials

description: <b><i>Aim: </i></b>To analyze the clinical features and outcomes of advanced non-small cell lung cancer (NSCLC) patients treated in phase I trials. <b><i>Patients and Methods: </i></b>The clinical characteristics, efficacy and toxicity data of 70 pretreated NSCLC patients enrolled in 17 phase I trials between January 2005 and June 2010 were analyzed at our institution. <b><i>Results: </i></b>The histological types were: adenocarcinoma (79%), squamous cell carcinoma (13%), and others. Patients received a median number of 3 prior lines of treatment before inclusion. 1 complete response (CR), 11 (16%) partial responses (PRs), and 29 (41%) stable diseases (SDs) were observed (according to Response Evaluation Criteria in Solid Tumors (RECIST)). The median overall survival (OS) time was 18 months and the median progression-free survival (PFS) time was 4.1 months. The median PFS of these patients within their prior therapy line before phase I inclusion was 4.3 months. A performance status score of 0 and the number of prior lines of treatment were significant for OS and PFS in multivariate analysis, respectively. Grade 3/4 toxicities were observed in 20 (27%) patients, and there was 1 treatment-related death. <b><i>Conclusion: </i></b>Patients in good general condition and with limited pretreatment derived an improved benefit, suggesting that phase I studies may be a valid option for pretreated NSCLC patients.
DOI: 10.6084/m9.figshare.5125135.v1
title: Supplementary Material for: Which Social Network or Support Factors are Associated with Cognitive Abilities in Old Age?

description: <b><i>Background:</i></b> Social networks and support have been proposed as cognitively protective in old age. As studies often consider these social factors in isolation the question of which characteristics of the social environment are beneficial remains. <b><i>Objective:</i></b> The current study examined associations between measures of social networks (including contact with friends/family, marital status and living arrangement), feelings of loneliness and social support, and a range of cognitive outcomes. <b><i>Methods:</i></b> Social network, loneliness and support data were available in the Lothian Birth Cohort 1936 (LBC1936, n = 1,091) at age 70. Participants completed a battery of cognitive tests, and factor scores were available for general cognitive ability, and the cognitive domains of processing speed and memory. Childhood cognitive ability data from age 11 were also available. <b><i>Results:</i></b> When examined in separate ANCOVAs, lower loneliness and more social support were significantly associated with better cognitive abilities at age 70, though not memory (independently of age, sex, childhood cognitive ability and social class), accounting for about 0.5-1.5% of the variance. When the social factors were considered simultaneously, higher loneliness remained associated with lower general cognitive ability (η<sub>p</sub><sup>2</sup> = 0.005, p = 0.046), and those living alone (η<sub>p</sub><sup>2</sup> = 0.007, p = 0.014) or with less social support (η<sub>p</sub><sup>2</sup> = 0.007, p = 0.016) had slower processing speed. When these final models were repeated including a depression symptoms score as a covariate, the associations between loneliness and general cognitive ability, and social support and processing speed, were no longer significant. However, the association between living alone and processing speed remained (η<sub>p</sub><sup>2</sup> = 0.006, p = 0.031). <b><i>Conclusions:</i></b> Of the social factors considered, loneliness, social support and living arrangement were most consistently associated with aspects of cognitive ability in older people, and these associations appeared to be partly, though not wholly, accounted for by symptoms of depression. Although longitudinal follow-up is required to examine the causal direction of the effects more definitively, it may be beneficial to promote the development of interventions to reduce loneliness and social isolation, and to increase social support.
DOI: 10.6084/m9.figshare.5125096
title: LGK and TEM-1.1 Enzyme Solubility Datasets

description: Solubility datasets for LGK and TEM-1 from:<br>Klesmith, J. R., Bacik, J.-P., Wrenbeck, E. E., Michalczyk, R., and Whitehead, T. A. (2017) Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning, Proceedings of the National Academy of Sciences 114, 2265-2270.
DOI: 10.6084/m9.figshare.5125126
title: Supplementary Material for: MicroRNA Profiling in Chemoresistant and Chemosensitive Acute Myeloid Leukemia

description: MicroRNA (miRNA) deregulation is associated with progression and treatment outcome in various types of cancers. To identify miRNAs related to therapeutic response, we applied an miRNA microarray followed by PCR verification of 33 available diagnostic bone marrow core biopsies from 33 acute myeloid leukemia patients including 15 chemoresistant and 18 chemosensitive patients. We found 3 significantly upregulated miRNAs, miR-363, miR-532-5p and miR-342-3p, related to therapeutic response (q &lt; 0.05). Further validation of miR-532-5p and miR-363 expression by quantitative RT-PCR confirmed microarray analysis results. Genes targeted by miR-363 include <i>RGS17</i> and <i>HIPK3,</i> both reported to be associated with drug response<i>.</i>
DOI: 10.6084/m9.figshare.5125132.v1
title: Supplementary Material for: Clinical Benefit for Patients with Non-Small Cell Lung Cancer Enrolled in Phase I Trials

description: <b><i>Aim: </i></b>To analyze the clinical features and outcomes of advanced non-small cell lung cancer (NSCLC) patients treated in phase I trials. <b><i>Patients and Methods: </i></b>The clinical characteristics, efficacy and toxicity data of 70 pretreated NSCLC patients enrolled in 17 phase I trials between January 2005 and June 2010 were analyzed at our institution. <b><i>Results: </i></b>The histological types were: adenocarcinoma (79%), squamous cell carcinoma (13%), and others. Patients received a median number of 3 prior lines of treatment before inclusion. 1 complete response (CR), 11 (16%) partial responses (PRs), and 29 (41%) stable diseases (SDs) were observed (according to Response Evaluation Criteria in Solid Tumors (RECIST)). The median overall survival (OS) time was 18 months and the median progression-free survival (PFS) time was 4.1 months. The median PFS of these patients within their prior therapy line before phase I inclusion was 4.3 months. A performance status score of 0 and the number of prior lines of treatment were significant for OS and PFS in multivariate analysis, respectively. Grade 3/4 toxicities were observed in 20 (27%) patients, and there was 1 treatment-related death. <b><i>Conclusion: </i></b>Patients in good general condition and with limited pretreatment derived an improved benefit, suggesting that phase I studies may be a valid option for pretreated NSCLC patients.
DOI: 10.6084/m9.figshare.5125138.v1
title: Supplementary Material for: Comparative Organization and Gene Expression Profiles of the Porcine Pseudoautosomal Region

description: The pseudoautosomal region (PAR) has important biological functions in spermatogenesis, male fertility and early development. Even though pig (<i>Sus scrofa</i>, SSC) is an agriculturally and biomedically important species, and its genome is sequenced, current knowledge about the porcine PAR is sparse. Here we defined the PAR in SSCXp/Yp by demarcating the sequence of the pseudoautosomal boundary at X:6,743,567 bp in intron 3-4 of <i>SHROOM2</i> and showed that <i>SHROOM2</i> is truncated in SSCY. Cytogenetic mapping of 20 BAC clones containing 15 PAR and X-specific genes revealed that the pig PAR is largely collinear with other mammalian PARs or Xp terminal regions. The results improved the current SSCX sequence assembly and facilitated distinction between the PAR and X-specific genes to study their expression in adult and embryonic tissues. A pilot analysis showed that the PAR genes are expressed at higher levels than X-specific genes during early development, whereas the expression of PAR genes was higher at day 60 compared to day 26, and higher in embryonic tissues compared to placenta. The findings advance the knowledge about the comparative organization of the PAR in mammals and suggest that the region might have important functions in early development in pigs.
DOI: 10.6084/m9.figshare.5125093
title: Butaite_etal_Nat.Commun.2017_Siderophore_cheating_in_natural_pseudomonads_Data.xlsx

description: Data used for statistical analyses and to generate graphs for the paper. More detailed description is provided in the file.<br>
DOI: 10.6084/m9.figshare.5125126.v1
title: Supplementary Material for: MicroRNA Profiling in Chemoresistant and Chemosensitive Acute Myeloid Leukemia

description: MicroRNA (miRNA) deregulation is associated with progression and treatment outcome in various types of cancers. To identify miRNAs related to therapeutic response, we applied an miRNA microarray followed by PCR verification of 33 available diagnostic bone marrow core biopsies from 33 acute myeloid leukemia patients including 15 chemoresistant and 18 chemosensitive patients. We found 3 significantly upregulated miRNAs, miR-363, miR-532-5p and miR-342-3p, related to therapeutic response (q &lt; 0.05). Further validation of miR-532-5p and miR-363 expression by quantitative RT-PCR confirmed microarray analysis results. Genes targeted by miR-363 include <i>RGS17</i> and <i>HIPK3,</i> both reported to be associated with drug response<i>.</i>