cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5124358.v1
title: Supplementary Material for: Cross-Talk between Available Guidelines for the Management of Patients with Beta-Thalassemia Major

description: Efforts to optimize the management of patients with β-thalassemia major (TM) continue to expand. Evidence from biomedical research evaluating safe and careful processing measures of blood products, the efficacy and safety of oral iron chelators, and noninvasive techniques for the assessment of iron overload are translated into better patient outcomes. The construction of TM management guidelines facilitated the incorporation of such evidence into practice. However, as several aspects of the management of TM remain controversial or governed by resource availability, a concern regarding potential variations in recommendations made by the different guidelines becomes rational, especially for physicians treating TM patients outside countries where the guidelines were constructed. In this work, we overview currently available guidelines for the management of TM and explore apparent similarities and differences between them. The evaluated guidelines included the Thalassaemia International Federation, US, Canadian, UK, Italian and Australian guidelines. We noted a general consensus for most aspects of management, although some guidelines provided more comprehensive and contemporary recommendations than others. We did not identify differences warranting concern, although minor differences in iron overload assessment strategy and more notable variations in the recommendations for iron chelation therapy were observed.
DOI: 10.6084/m9.figshare.5124349
title: Supplementary Material for: MiR-17-3p Inhibits Angiogenesis by Downregulating Flk-1 in the Cell Growth Signal Pathway

description: MicroRNAs (miRs) are endogenously expressed small noncoding RNAs that regulate gene expression at the posttranscriptional level. Previous works indicated that the miR-17-92 cluster could regulate endothelial cell (EC) functions involved in angiogenesis. miR-17-3p, a component of the miR-17-92 cluster, could control the angiogenic activity of human umbilical vein ECs in a cell-autonomous manner in vitro. A 21-bp fragment from the Flk-1 3′-untranslated region containing miR-17-3p targeting sites was required for the rapid downregulation of Flk-1 expression by in silico and experimental analysis. Subsequently, the downstream cell growth pathway was inhibited by forced upregulation of miR-17-3p. Based on these data, we conclude that miR-17-3p is a negative regulator of the angiogenic phenotype of ECs through its ability to modulate the expression of Flk-1, which is implicated in the pleiotropic effects of miR-17-92 in angiogenesis.
DOI: 10.6084/m9.figshare.5124364.v1
title: Supplementary Material for: Prediction, Microarray and Northern Blot Analyses Identify New Intergenic Small RNAs in <b><i>Aliivibrio salmonicida</i></b>

description: Bacterial small RNAs (sRNAs) are <i>trans</i>-encoded regulatory RNAs that typically bind mRNAs by short-sequence complementarities and change the expression of the corresponding proteins. Some of the well-characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS), and carbon metabolism (Spot 42). However, many sRNAs remain to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae, the function is known for only 9. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrionaceae, i.e. the <i>Aliivibrio salmonicida</i>, which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6-Mb genome identified a total of 252 potential ncRNAs (including 233 putative sRNAs). Depending on the set threshold value for fluorescence signal in our microarray approach, we identified 50–80 putative ncRNAs, 12 of which were verified by Northern blot analysis. In total, we identified 9 new sRNAs.
DOI: 10.6084/m9.figshare.5124343
title: Supplementary Material for: Allgemeine Wirkfaktoren bei der Behandlung chronisch depressiver Patienten – Vergleich zweier Psychotherapieansätze

description: <b><i>Hintergrund:</i></b> Das Ausmaß, in dem allgemeine Wirkfaktoren die Wirksamkeit von Psychotherapie bei chronischer Depression beeinflussen, ist bisher wenig untersucht: Welche allgemeinen Wirkfaktoren unterscheiden erfolgreiche und weniger erfolgreiche Psychotherapien bei chronisch depressiven Patienten? <b><i>Patienten und Methoden:</i></b> Mit Hilfe des Berner Patienten- und Therapeutenstundenbogens (TSTB/PSTB) wurden bei 29 chronisch depressiven Patienten während einer 16-wöchigen Behandlung mit dem Cognitive Behavioral Analysis System of Psychotherapy (CBASP) oder der Interpersonellen Psychotherapie (IPT) wöchentlich die Wirkfaktoren erhoben und mittels Varianzanalyse verglichen. Als primäres Erfolgsmaß diente die 24-Item Hamilton Depressionsskala (HRSD-24). Ergebnisse: Aus Patientensicht zeigten sich signifikante Unterschiede zwischen erfolgreichen (Response-Kriterium definiert als mindestens 50%-Verbesserung im HRSD-24) und weniger erfolgreichen Therapien im Ausmaß «Motivationaler Klärung» (p = 0,02) und «Problembewältigung» (p = 0,01). Es konnten keine bedeutsamen Unterschiede bezüglich allgemeiner Wirkfaktoren von CBASP- versus IPT-Therapien nachgewiesen werden. <b><i>Diskussion:</i></b> Unabhängig von der spezifischen Therapiemethode bestätigt sich aus Patientensicht die Bedeutung intensiver Motivationaler Klärung sowie bewältigender Strategien für eine erfolgreiche Behandlung chronischer Depressionen.
DOI: 10.6084/m9.figshare.5124346
title: Supplementary Material for: A Novel Aberrant Splice Site Mutation in <b><i>RAB23</i></b> Leads to an Eight Nucleotide Deletion in the mRNA and Is Responsible for Carpenter Syndrome in a Consanguineous Emirati Family

description: Carpenter syndrome is caused by mutations in the <i>RAB23</i> gene that encodes a small GTPase of the Rab subfamily of proteins. Rab proteins are known to be involved in the regulation of cellular trafficking and signal transduction. Currently, only few mutations in <i>RAB23 </i>have been reported in patients with Carpenter syndrome. In this paper, we report the clinical features, molecular and functional analysis of 2 children from an Emirati consanguineous family with this syndrome. The affected children exhibit the typical features including craniosynostosis, typical facial appearance, polysyndactyly, and obesity. Molecular analysis of the <i>RAB23</i> gene revealed a homozygous mutation affecting the first nucleotide of the acceptor splice site of exon 5 (c.482-1G&gt;A). This mutation affects the authentic mRNA splicing and activates a cryptic acceptor site within exon 5. Thus, the erroneous splicing results in an eight nucleotide deletion, followed by a frameshift and premature termination codon at position 161 (p.V161fsX3). Due to the loss of the C-terminally prenylatable cysteine residue, the truncated protein will probably fail to associate with the target cellular membranes due to the absence of the necessary lipid modification. The p.V161fsX3 extends the spectrum of <i>RAB23</i> mutations and points to the crucial role of prenylation in the pathogenesis of Carpenter syndrome within this family.
DOI: 10.6084/m9.figshare.5124352.v1
title: Supplementary Material for: Spatiotemporal Dynamics of Complement C5a Production within Bacterial Extracellular Polymeric Substance

description: Opsonization and anaphylatoxin production are early events in the innate response to bacterial pathogens. Opsonization alone is frequently not lethal and production of anaphy-latoxins, especially C5a, allows for recruitment of cellular defenses. Complement biochemistry is extensively studied and computational models have been reported previously. However, a critical feature of complement-mediated attack is its spatial dependence: diffusion of mediators into and away from a bacterium is central to understanding C5a generation. Spatial dependence is especially important in biofilms, where diffusion limitation is crucial to bacterial counterdefense. Here we develop a model of opsonization and C5a production in the presence of a common blood-borne pathogen, <i>Staphylococcus epidermidis</i>. Our results indicate that when complement attacks a single cell, diffusion into the extracellular polymeric substance (EPS) is complete within 10 ms and that production of C5a peaks over the next 15 min. When longer diffusion lengths (as in an EPS-rich biofilm) are incorporated, diffusion limitation appears such that the intensity and duration of C5a production is increased. However, the amount of C5a produced under several likely clinical scenarios where single cells or sparse biofilms are present is below the k<sub>D</sub> of the C5a receptor suggesting that complement activation by a single bacterium may be difficult to detect when diffusion is taken into account.
DOI: 10.6084/m9.figshare.5124340
title: Supplementary Material for: Head-Shaking Aids in the Diagnosis of Acute Audiovestibular Loss due to Anterior Inferior Cerebellar Artery Infarction

description: <b><i>Objective:</i></b> To determine the patterns and diagnostic value of head-shaking nystagmus (HSN) in patients with acute audiovestibular loss. <b><i>Method:</i></b> Eighteen patients underwent evaluation of spontaneous nystagmus, gaze-evoked nystagmus, HSN, head impulse test, ocular tilt reaction, subjective visual vertical, bithermal caloric tests, and pure-tone audiogram. The findings were compared with those of 21 patients with labyrinthitis.<b><i> Results:</i></b> Fifteen patients (83%) exhibited HSN, and the horizontal HSN usually beat contralesionally (10/14, 71%). However, 9 (50%) patients also showed patterns of central HSN that included perverted HSN (n = 7), HSN in the opposite direction of spontaneous nystagmus (n = 4), and HSN beating towards unilateral canal paresis or abnormal head impulse testing (n = 3). Overall, central HSN, gaze-evoked nystagmus, and normal head impulse testing were specific for anterior inferior cerebellar artery (AICA) infarction. Moreover, central HSN was the only sign that indicated stroke in 1 of our patients with isolated audiovestibular syndrome. Lesion subtraction analyses revealed that damage to the flocculus was relatively frequent in patients with perverted HSN. <b><i>Conclusions:</i></b> In AICA infarction, HSN was common with both peripheral and central patterns. Careful evaluation of HSN may provide clues for AICA infarction in patients with acute audiovestibular loss.
DOI: 10.6084/m9.figshare.5124340.v1
title: Supplementary Material for: Head-Shaking Aids in the Diagnosis of Acute Audiovestibular Loss due to Anterior Inferior Cerebellar Artery Infarction

description: <b><i>Objective:</i></b> To determine the patterns and diagnostic value of head-shaking nystagmus (HSN) in patients with acute audiovestibular loss. <b><i>Method:</i></b> Eighteen patients underwent evaluation of spontaneous nystagmus, gaze-evoked nystagmus, HSN, head impulse test, ocular tilt reaction, subjective visual vertical, bithermal caloric tests, and pure-tone audiogram. The findings were compared with those of 21 patients with labyrinthitis.<b><i> Results:</i></b> Fifteen patients (83%) exhibited HSN, and the horizontal HSN usually beat contralesionally (10/14, 71%). However, 9 (50%) patients also showed patterns of central HSN that included perverted HSN (n = 7), HSN in the opposite direction of spontaneous nystagmus (n = 4), and HSN beating towards unilateral canal paresis or abnormal head impulse testing (n = 3). Overall, central HSN, gaze-evoked nystagmus, and normal head impulse testing were specific for anterior inferior cerebellar artery (AICA) infarction. Moreover, central HSN was the only sign that indicated stroke in 1 of our patients with isolated audiovestibular syndrome. Lesion subtraction analyses revealed that damage to the flocculus was relatively frequent in patients with perverted HSN. <b><i>Conclusions:</i></b> In AICA infarction, HSN was common with both peripheral and central patterns. Careful evaluation of HSN may provide clues for AICA infarction in patients with acute audiovestibular loss.
DOI: 10.6084/m9.figshare.5124346.v1
title: Supplementary Material for: A Novel Aberrant Splice Site Mutation in <b><i>RAB23</i></b> Leads to an Eight Nucleotide Deletion in the mRNA and Is Responsible for Carpenter Syndrome in a Consanguineous Emirati Family

description: Carpenter syndrome is caused by mutations in the <i>RAB23</i> gene that encodes a small GTPase of the Rab subfamily of proteins. Rab proteins are known to be involved in the regulation of cellular trafficking and signal transduction. Currently, only few mutations in <i>RAB23 </i>have been reported in patients with Carpenter syndrome. In this paper, we report the clinical features, molecular and functional analysis of 2 children from an Emirati consanguineous family with this syndrome. The affected children exhibit the typical features including craniosynostosis, typical facial appearance, polysyndactyly, and obesity. Molecular analysis of the <i>RAB23</i> gene revealed a homozygous mutation affecting the first nucleotide of the acceptor splice site of exon 5 (c.482-1G&gt;A). This mutation affects the authentic mRNA splicing and activates a cryptic acceptor site within exon 5. Thus, the erroneous splicing results in an eight nucleotide deletion, followed by a frameshift and premature termination codon at position 161 (p.V161fsX3). Due to the loss of the C-terminally prenylatable cysteine residue, the truncated protein will probably fail to associate with the target cellular membranes due to the absence of the necessary lipid modification. The p.V161fsX3 extends the spectrum of <i>RAB23</i> mutations and points to the crucial role of prenylation in the pathogenesis of Carpenter syndrome within this family.
DOI: 10.6084/m9.figshare.5124325
title: Supplementary Material for: How Do We Apply Video-Assisted Retroperitoneal Necrosectomy with Minimal Access?

description: <b><i>Background:</i></b> The conservative treatment of acute necrotizing pancreatitis has greatly improved due to broad antibiotic treatment and improved organ support in intensive care units. Nevertheless, infected necrosis or persistent multi-organ dysfunction are predictors of poor outcome. In these patients, there is still a need to perform necrosectomy. Open surgery results in extensive operative trauma and is associated with high morbidity and mortality. Therefore, several minimally invasive techniques have been developed recently. Retroperitoneal necrosectomy has been shown to be safe and to reduce morbidity and mortality compared to the open procedure. <b><i>Methods and Results:</i></b> In an instructive video, we show the technique of video-assisted retroperitoneal necrosectomy with minimal access, including the preoperative percutaneous drainage and several accesses to the necrosis. We discuss the indication for retroperitoneal necrosectomy as well as the optimal time point of the intervention. <b><i>Conclusion:</i></b> In the management of acute necrotizing pancreatitis, the multidisciplinary approach is crucial. The initial treatment by the intensive care units should be extended to intervention or surgery in case of infected necrosis or persistent multi-organ dysfunction. We show here a minimal access solution with the placement of a percutaneous drain followed by video-assisted retroperitoneal necrosectomy.
DOI: 10.6084/m9.figshare.5124313
title: Supplementary Material for: Neuronal and Behavioral Correlates of Health Anxiety: Results of an Illness-Related Emotional Stroop Task

description: <b><i>Background:</i></b> Health anxiety (HA) is defined as the objectively unfounded fear or conviction of suffering from a severe illness. Predominant attention allocation to illness-related information is regarded as a central process in the development and maintenance of HA, yet little is known about the neuronal correlates of this attentional bias. <b><i>Methods:</i></b> An emotional Stroop task with body symptom, illness, and neutral words was employed to elicit emotional interference in healthy participants with high (HA+, n = 12) and low (HA–, n = 12) HA during functional magnetic resonance imaging. <b><i>Results:</i></b> Prolonged reaction times for indicating the color of symptom words and a decrease in rostral anterior cingulate cortex (rACC) activation were seen in HA+ participants. Emotional interference effects on the behavioral level were negatively related to rACC activity over the whole group. Groups did not differ during the processing of threatening illness words. <b><i>Conclusion:</i></b> The results indicate stronger attention allocation toward body symptom words already in subclinical HA. This attentional bias appears to be linked to hypoactivity of the rACC which impedes effective emotional interference reduction, leading instead to a ruminative processing of the stimulus content.
DOI: 10.6084/m9.figshare.5124316
title: Supplementary Material for: Bayesian Modeling of Pretransplant Variables Accurately Predicts Kidney Graft Survival

description: <b><i>Introduction:</i></b> Machine learning can enable the development of predictive models that incorporate multiple variables for a systems approach to organ allocation. We explored the principle of Bayesian Belief Network (BBN) to determine whether a predictive model of graft survival can be derived using pretransplant variables. Our hypothesis was that pretransplant donor and recipient variables, when considered together as a network, add incremental value to the classification of graft survival. <b><i>Methods:</i></b> We performed a retrospective analysis of 5,144 randomly selected patients (age ≥18, deceased donor kidney only, first-time recipients) from the United States Renal Data System database between 2000 and 2001. Using this dataset, we developed a machine-learned BBN that functions as a pretransplant organ-matching tool. <b><i>Results:</i></b> A network of 48 clinical variables was constructed and externally validated using an additional 2,204 patients of matching demographic characteristics. This model was able to predict graft failure within the first year or within 3 years (sensitivity 40%; specificity 80%; area under the curve, AUC, 0.63). Recipient BMI, gender, race, and donor age were amongst the pretransplant variables with strongest association to outcome. A 10-fold internal cross-validation showed similar results for 1-year (sensitivity 24%; specificity 80%; AUC 0.59) and 3-year (sensitivity 31%; specificity 80%; AUC 0.60) graft failure. <b><i>Conclusion:</i></b> We found recipient BMI, gender, race, and donor age to be influential predictors of outcome, while wait time and human leukocyte antigen matching were much less associated with outcome. BBN enabled us to examine variables from a large database to develop a robust predictive model.
DOI: 10.6084/m9.figshare.5124319
title: Supplementary Material for: Talar Maturity Determined by Epiphyseal Closure of the Calcaneus

description: The talus is used in many kinds of studies on primates including fossil species, and most of the individuals studied are adults. One of the most important indicators of adult individuals is epiphyseal closure; however, because the talus has no epiphysis, it is difficult to determine the maturity of the talus. The calcaneus has one epiphysis, and it has been used along with the talus in some analyses. The objective of this study was to quantify the maturation trajectory of the talus using epiphyseal closure of the calcaneus as a benchmark. We used 71 skeletons of free-ranging <i>Macaca fuscata fuscata</i> males of known day-age. We did not identify any size increase with age in talar dimensions among specimens with complete calcaneal epiphyseal closure. Thus, in male <i>M. fuscata</i><i>fuscata</i>, the maturation trajectory of the talus can be quantified using epiphyseal closure of the calcaneus as a benchmark.
DOI: 10.6084/m9.figshare.5124322
title: Supplementary Material for: Gender Differences in the Long-Chain Polyunsaturated Fatty Acid Status: Systematic Review of 51 Publications

description: <b><i>Background/Aims:</i></b> Sex hormones may influence the activity of enzymes which are involved in the synthesis of long-chain polyunsaturated fatty acids. The objective of this review was to assess the role of gender in determining the fatty acid composition of human samples, like plasma and erythrocyte membrane lipids, and adipose tissue. <b><i>Methods:</i></b> The method included a structured search strategy on MEDLINE, Scopus and the Cochrane databases, with formal inclusion/exclusion criteria, data extraction procedure and meta-analysis. <b><i>Results:</i></b> We evaluated 51 publications, dated from 1975 to 2011. Meta-analysis showed significantly lower values of both arachidonic acid (AA) and docosahexaenoic acid (DHA) in total plasma lipids (32 and 33 studies) and in plasma phospholipids (PL; 21 and 23 studies) in men than in women. Primary analysis of the phospholipid fraction showed the mean difference in AA to be 0.42% weight/weight (95% CI: 0.18–0.65, n = 7,769) and in DHA 0.37% weight/weight (95% CI: 0.24–0.51, n = 8,541), while there was no gender difference in the values of linoleic acid and α-linolenic acid. <b><i>Conclusions:</i></b> This systematic review based on 51 publications showed significantly lower contribution of AA and DHA to plasma total lipids and plasma PL in men than in women. Gender distribution should be regarded as a significant potential confounding factor in every study assessing data on fatty acid composition.
DOI: 10.6084/m9.figshare.5124325.v1
title: Supplementary Material for: How Do We Apply Video-Assisted Retroperitoneal Necrosectomy with Minimal Access?

description: <b><i>Background:</i></b> The conservative treatment of acute necrotizing pancreatitis has greatly improved due to broad antibiotic treatment and improved organ support in intensive care units. Nevertheless, infected necrosis or persistent multi-organ dysfunction are predictors of poor outcome. In these patients, there is still a need to perform necrosectomy. Open surgery results in extensive operative trauma and is associated with high morbidity and mortality. Therefore, several minimally invasive techniques have been developed recently. Retroperitoneal necrosectomy has been shown to be safe and to reduce morbidity and mortality compared to the open procedure. <b><i>Methods and Results:</i></b> In an instructive video, we show the technique of video-assisted retroperitoneal necrosectomy with minimal access, including the preoperative percutaneous drainage and several accesses to the necrosis. We discuss the indication for retroperitoneal necrosectomy as well as the optimal time point of the intervention. <b><i>Conclusion:</i></b> In the management of acute necrotizing pancreatitis, the multidisciplinary approach is crucial. The initial treatment by the intensive care units should be extended to intervention or surgery in case of infected necrosis or persistent multi-organ dysfunction. We show here a minimal access solution with the placement of a percutaneous drain followed by video-assisted retroperitoneal necrosectomy.