cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127448
title: Supplementary Material for: Treating Treatment-Resistant Patients with Panic Disorder and Agoraphobia Using Psychotherapy: A Randomized Controlled Switching Trial

description: <b><i>Background:</i></b> Nonresponsiveness to therapy is generally acknowledged, but only a few studies have tested switching to psychotherapy. This study is one of the first to examine the malleability of treatment-resistant patients using acceptance and commitment therapy (ACT). <b><i>Methods:</i></b> This was a randomized controlled trial that included 43 patients diagnosed with primary panic disorder and/or agoraphobia (PD/A) with prior unsuccessful state-of-the-art treatment (mean number of previous sessions = 42.2). Patients were treated with an ACT manual administered by novice therapists and followed up for 6 months. They were randomized to immediate treatment (n = 33) or a 4-week waiting list (n = 10) with delayed treatment (n = 8). Treatment consisted of eight sessions, implemented twice weekly over 4 weeks. Primary outcomes were measured with the Panic and Agoraphobia Scale (PAS), the Clinical Global Impression (CGI), and the Mobility Inventory (MI). <b><i>Results:</i></b> At post-treatment, patients who received ACT reported significantly more improvements on the PAS and CGI (d = 0.72 and 0.89, respectively) than those who were on the waiting list, while improvement on the MI (d = 0.50) was nearly significant. Secondary outcomes were consistent with ACT theory. Follow-up assessments indicated a stable and continued improvement after treatment. The dropout rate was low (9%). <b><i>Conclusions:</i></b> Despite a clinically challenging sample and brief treatment administered by novice therapists, patients who received ACT reported significantly greater changes in functioning and symptomatology than those on the waiting list, with medium-to-large effect sizes that were maintained for at least 6 months. These proof-of-principle data suggest that ACT is a viable treatment option for treatment-resistant PD/A patients. Further work on switching to psychotherapy for nonresponders is clearly needed.
DOI: 10.6084/m9.figshare.5127451
title: Supplementary Material for: High Expression of Major Histocompatibility Complex Class I in Clear Cell Renal Cell Carcinoma Is Associated with Improved Prognosis

description: <b><i>Introduction:</i></b> In this study we analyzed major histocompatibility complex class I (MHCI) expression as a potential prognostic immune marker for patients with clear cell renal cell carcinoma (ccRCC). <b><i>Patients and Methods:</i></b> 34 patients with localized ccRCC (pT1-pT3) who had undergone nephrectomy and had at least 4 years of clinical follow-up data were included in the study. Immunohistochemical staining for MHCI was performed on tumor sections. An automated image analysis algorithm was applied to representative tumor areas to quantitate the proportion of stained pixels (positivity score = positive pixels/total pixels) on scanned digital slides. <b><i>Results:</i></b> At the end of the study, the patients who were alive had increased MHCI expression (mean positivity score 0.80) compared to those who died of the disease (mean positivity score 0.53; p &lt; 0.0001, t test). Patients who were alive with recurrence had increased MHCI expression (positivity score 0.81) compared to those who succumbed to their disease recurrence (positivity score 0.53; p &lt; 0.0001, t test). Survival was higher among patients with high MHCI expression compared to patients with low MHCI expression (p &lt; 0.0001, Mantel-Cox). <b><i>Conclusions:</i></b> With an automated high-throughput image analysis technique, this study shows that higher tumor cell MHCI expression promotes increased survival and reduced incidence of recurrence compared to patients with lower tumor cell MHCI expression.
DOI: 10.6084/m9.figshare.5127454.v1
title: Supplementary Material for: Clinical and Molecular Heterogeneity in Brazilian Patients with Sotos Syndrome

description: Sotos syndrome (SoS) is a multiple anomaly, congenital disorder characterized by overgrowth, macrocephaly, distinctive facial features and variable degree of intellectual disability. Haploinsufficiency of the <i>NSD1</i> gene at 5q35.3, arising from 5q35 microdeletions, point mutations, and partial gene deletions, accounts for a majority of patients with SoS. Recently, mutations and possible pathogenetic rare CNVs, both affecting a few candidate genes for overgrowth, have been reported in patients with Sotos-like overgrowth features. To estimate the frequency of <i>NSD1</i> defects in the Brazilian SoS population and possibly reveal other genes implicated in the etiopathogenesis of this syndrome, we collected a cohort of 21 Brazilian patients, who fulfilled the diagnostic criteria for SoS, and analyzed the <i>NSD1</i> and <i>PTEN</i> genes by means of multiplex ligation-dependent probe amplification and mutational screening analyses. We identified a classical <i>NSD1</i> microdeletion, a novel missense mutation (p.C1593W), and 2 previously reported truncating mutations: p.R1984X and p.V1760Gfs*2. In addition, we identified a novel de novo <i>PTEN</i> gene mutation (p.D312Rfs*2) in a patient with a less severe presentation of SoS phenotype, which did not include pre- and postnatal overgrowth. For the first time, our study implies <i>PTEN</i> in the pathogenesis of SoS and further emphasizes the existence of ethno-geographical differences in <i>NSD1</i> molecular alterations between patients with SoS from Europe/North America (70-93%) and those from South America (10-19%).
DOI: 10.6084/m9.figshare.5127460.v1
title: Supplementary Material for: Development and Mapping of CL-Repeat Display Markers on the Maize B Chromosome

description: The CL-repeat is a repetitive sequence that is unique to the maize B chromosome, where it resides in the centromeric knob and the first 3 distal heterochromatic regions of the long arm. Given this organization, it would be desirable to identify molecular markers that are specifically distributed in the B chromosome. In this report, the CL-repeat has been used to develop a class of molecular markers for the maize B chromosome. To this end, a modified transposon display procedure designated as CL-repeat display was used to generate and display 26 genomic fragments that are specific to the B chromosome, all of which were cloned and sequenced. The sequences of 19 fragments were highly homologous to the 5′ or 3′ terminus of the CL-repeat. Five of these fragments also contained sequences that were homologous to sequences of the B chromosome centromere. Four of the other 7 fragments shared homology with B chromosome centromere sequences, and the remaining 3 were of unidentified sequences. Using 13 B-10L translocations with various breakpoints along the B chromosome long arm, the 26 CL-repeat display markers were mapped to definite regions of the B chromosome. This strategy should be feasible for the development of molecular markers for the B chromosome in maize and in other species where B chromosome-specific repeats have been identified.
DOI: 10.6084/m9.figshare.5127445
title: Supplementary Material for: A Modified Nerve-Sparing Panhysterectomy for Benign Uterine Diseases: Techniques and Evaluation of Postoperative Pelvic Dysfunctions

description: <b><i>Objective:</i></b> To describe a modified nerve-sparing panhysterectomy and to investigate the feasibility and impact of this nerve-sparing technique in improving postoperative pelvic visceral dysfunctions of benign uterine disease patients. <b><i>Methods:</i></b> From January 2008 to January 2010, a total of 300 patients diagnosed with benign uterine diseases at the Second Affiliated Hospital of Nantong University were enrolled. Of those, 150 randomly selected patients underwent modified panhysterectomy (research group), while the other 150 patients underwent conventional panhysterectomy (control group). The surgery-related parameters, including operation time, intraoperative blood loss, length of hospital stay, postoperative indwelling catheter time, and first voiding and defecation time were compared between the two groups. The extent of nerve damage in both groups was examined using the nerve-specific marker S-100 via immunohistochemistry. Besides, postoperative assessments of bladder and bowel functions were conducted within 1 year after the operation. <b><i>Results:</i></b> The surgery-related parameters in the two groups showed no significant difference (p &gt; 0.05). Immunohistochemistry results showed significantly reduced damage of the nerves in the research group. We also found a better bladder and bowel function in the research group (p &lt; 0.05) and in younger patients (p &lt; 0.05) compared with that in the control group. Recovery trends of the bladder and bowel function were found in both groups (χ<sup>2</sup> = 7.512, p = 0.006 in the research group; χ<sup>2</sup> = 7.299, p = 0.007 in the control group). <b><i>Conclusion:</i></b> Modified panhysterectomy for benign uterine diseases seems feasible and safe, with the main advantage of improving postoperative urocystic and rectal dysfunctions through the preservation of the pelvic autonomic nerves.
DOI: 10.6084/m9.figshare.5127457.v1
title: Supplementary Material for: Genome-Wide Analysis of the WRKY Transcription Factors in <b><i>Aegilops tauschii</i></b>

description: The WRKY transcription factors (TFs) play important roles in responding to abiotic and biotic stress in plants. However, due to its unfinished genome sequencing, relatively few WRKY TFs with full-length coding sequences (CDSs) have been identified in wheat. Instead, the <i>Aegilops tauschii</i> genome, which is the D-genome progenitor of the hexaploid wheat genome, provides important resources for the discovery of new genes. In this study, we performed a bioinformatics analysis to identify WRKY TFs with full-length CDSs from the <i>A. tauschii</i> genome. A detailed evolutionary analysis for all these TFs was conducted, and quantitative real-time PCR was carried out to investigate the expression patterns of the abiotic stress-related WRKY TFs under different abiotic stress conditions in <i>A. tauschii</i> seedlings. A total of 93 WRKY TFs were identified from <i>A. tauschii</i>, and 79 of them were found to be newly discovered genes compared with wheat. Gene phylogeny, gene structure and chromosome location of the 93 WRKY TFs were fully analyzed. These studies provide a global view of the WRKY TFs from <i>A. tauschii</i> and a firm foundation for further investigations in both <i>A. tauschii</i> and wheat.
DOI: 10.6084/m9.figshare.5127436
title: Supplementary Material for: Evaluation of a Possible Role of <b><i>Stigmatella aurantiaca</i></b> ACE in Aβ Peptide Degradation: A Molecular Modeling Approach

description: Amyloid-β (Aβ)-degrading enzymes are known to degrade Aβ peptides, a causative agent of Alzheimer's disease. These enzymes are responsible for maintaining Aβ concentration. However, loss of such enzymes or their Aβ-degrading activity because of certain genetic as well as nongenetic reasons initiates the accumulation of Aβ peptides in the human brain. Considering the limitations of the human enzymes in clearing Aβ peptide, the search for microbial enzymes that could cleave Aβ is necessary. Hence, we built a three-dimensional model of angiotensin-converting enzyme (ACE) from <i>Stigmatella aurantiaca</i> using homology modeling technique. Molecular docking and molecular dynamics simulation techniques were used to outline the possible cleavage mechanism of Aβ peptide. These findings suggest that catalytic residue Glu 434 of the model could play a crucial role to degrade Aβ peptide between Asp 7 and Ser 8. Thus, ACE from <i>S. aurantiaca</i> might cleave Aβ peptides similar to human ACE and could be used to design new therapeutic strategies against Alzheimer's disease.
DOI: 10.6084/m9.figshare.5127439
title: Supplementary Material for: Synthesis and Physicochemical Characterization of D-Tagatose-1-Phosphate: The Substrate of the Tagatose-1-Phosphate Kinase in the Phosphotransferase System-Mediated D-Tagatose Catabolic Pathway of <b><i>Bacillus licheniformis</i></b>

description: We report the first enzymatic synthesis of D-tagatose-1-phosphate (Tag-1P) by the multicomponent phosphoenolpyruvate:sugar phosphotransferase system (PEP-PTS) present in tagatose-grown cells of <i>Klebsiella pneumoniae</i>. Physicochemical characterization by <sup>31</sup>P and <sup>1</sup>H nuclear magnetic resonance spectroscopy reveals that, in solution, this derivative is primarily in the pyranose form. Tag-1P was used to characterize the putative tagatose-1-phosphate kinase (TagK) of the <i>Bacillus licheniformis</i> PTS-mediated D-tagatose catabolic pathway (<i>Bli</i>-TagP). For this purpose, a soluble protein fusion was obtained with the 6 His-tagged trigger factor (TF<sup>His6</sup>) of <i>Escherichia coli</i>. The active fusion enzyme was named TagK-TF<sup>His6</sup>. Tag-1P and D-fructose-1-phosphate are substrates for the TagK-TF<sup>His6</sup> enzyme, whereas the isomeric derivatives D-tagatose-6-phosphate and D-fructose-6-phosphate are inhibitors. Studies of catalytic efficiency (k<sub>cat</sub>/K<sub>m</sub>) reveal that the enzyme specificity is markedly in favor of Tag-1P as the substrate. Importantly, we show in vivo that the transfer of the phosphate moiety from PEP to the <i>B. licheniformis</i> tagatose-specific Enzyme II in <i>E. coli</i> is inefficient. The capability of the PTS general cytoplasmic components of <i>B. subtilis</i>, HPr and Enzyme I to restore the phosphate transfer is demonstrated.
DOI: 10.6084/m9.figshare.5127442
title: Supplementary Material for: Early Decline in Six-Minute Walk Distance from the Time of Diagnosis Predicts Clinical Worsening in Pulmonary Arterial Hypertension

description: <b><i>Background:</i></b> The six-minute walk distance (6MWD) is commonly used to assess pulmonary arterial hypertension (PAH). However, the role of 6MWD in predicting outcomes in PAH is controversial. Clinical worsening is being increasingly considered as a clinically meaningful end point in PAH. <b><i>Objectives:</i></b> We aimed to investigate whether early longitudinal changes in 6MWD (Δ6MWD) in meters and percent predicted (%pred) from the time of diagnosis predict clinical worsening of PAH. <b><i>Methods:</i></b> One hundred patients with group I PAH were retrospectively assessed. 6MWD was calculated using American (%pred US) or Canadian (%pred CAN) reference equations. Δ6MWD at 6 months were recorded. Clinical worsening was defined as either: development of right heart failure, hospital admission for PAH, referral for lung transplantation or initiation of prostanoids after oral therapy failed. Optimal 6-month differences in 6MWD to detect worsening were defined with receiver operating characteristics (ROC) analysis. <b><i>Results:</i></b> Progressors, i.e. patients with clinical worsening, and nonprogressors showed significant differences in Δ6MWD. The most clinically significant declines in 6MWD at 6 months were ≥35 m, ≥8%pred US and ≥6%pred CAN. ROC and Cox proportional hazard analyses showed equivalent results for 6MWD %pred and meters. Six-month declines in 6MWD predicted worsening with a high specificity (94%) but a low sensitivity (33%). <b><i>Conclusions:</i></b> Early declines in 6MWD (within the first 6 months) predict future clinical worsening of PAH with high specificity. Δ6MWD may still be part of a comprehensive assessment of a patient's clinical status. However, given the poor sensitivity, a decline in 6MWD should be used with other clinical tools to make an appropriate assessment of the progression of PAH.
DOI: 10.6084/m9.figshare.5127445.v1
title: Supplementary Material for: A Modified Nerve-Sparing Panhysterectomy for Benign Uterine Diseases: Techniques and Evaluation of Postoperative Pelvic Dysfunctions

description: <b><i>Objective:</i></b> To describe a modified nerve-sparing panhysterectomy and to investigate the feasibility and impact of this nerve-sparing technique in improving postoperative pelvic visceral dysfunctions of benign uterine disease patients. <b><i>Methods:</i></b> From January 2008 to January 2010, a total of 300 patients diagnosed with benign uterine diseases at the Second Affiliated Hospital of Nantong University were enrolled. Of those, 150 randomly selected patients underwent modified panhysterectomy (research group), while the other 150 patients underwent conventional panhysterectomy (control group). The surgery-related parameters, including operation time, intraoperative blood loss, length of hospital stay, postoperative indwelling catheter time, and first voiding and defecation time were compared between the two groups. The extent of nerve damage in both groups was examined using the nerve-specific marker S-100 via immunohistochemistry. Besides, postoperative assessments of bladder and bowel functions were conducted within 1 year after the operation. <b><i>Results:</i></b> The surgery-related parameters in the two groups showed no significant difference (p &gt; 0.05). Immunohistochemistry results showed significantly reduced damage of the nerves in the research group. We also found a better bladder and bowel function in the research group (p &lt; 0.05) and in younger patients (p &lt; 0.05) compared with that in the control group. Recovery trends of the bladder and bowel function were found in both groups (χ<sup>2</sup> = 7.512, p = 0.006 in the research group; χ<sup>2</sup> = 7.299, p = 0.007 in the control group). <b><i>Conclusion:</i></b> Modified panhysterectomy for benign uterine diseases seems feasible and safe, with the main advantage of improving postoperative urocystic and rectal dysfunctions through the preservation of the pelvic autonomic nerves.
DOI: 10.6084/m9.figshare.5127433
title: Supplementary Material for: Autophagy Controls Acquisition of Aging Features in Macrophages

description: Macrophages provide a bridge linking innate and adaptive immunity. An increased frequency of macrophages and other myeloid cells paired with excessive cytokine production is commonly seen in the aging immune system, known as ‘inflamm-aging'. It is presently unclear how healthy macrophages are maintained throughout life and what connects inflammation with myeloid dysfunction during aging. Autophagy, an intracellular degradation mechanism, has known links with aging and lifespan extension. Here, we show for the first time that autophagy regulates the acquisition of major aging features in macrophages. In the absence of the essential autophagy gene Atg7, macrophage populations are increased and key functions such as phagocytosis and nitrite burst are reduced, while the inflammatory cytokine response is significantly increased - a phenotype also observed in aged macrophages. Furthermore, reduced autophagy decreases surface antigen expression and skews macrophage metabolism toward glycolysis. We show that macrophages from aged mice exhibit significantly reduced autophagic flux compared to young mice. These data demonstrate that autophagy plays a critical role in the maintenance of macrophage homeostasis and function, regulating inflammation and metabolism and thereby preventing immunosenescence. Thus, autophagy modulation may prevent excess inflammation and preserve macrophage function during aging, improving immune responses and reducing the morbidity and mortality associated with inflamm-aging.
DOI: 10.6084/m9.figshare.5127427
title: Supplementary Material for: Neuroanatomical and Morphological Trait Clusters in the Ant Genus <b><i>Pheidole:</i></b> Evidence for Modularity and Integration in Brain Structure

description: A central question in brain evolution concerns how selection has structured neuromorphological variation to generate adaptive behavior. In social insects, brain structures differ between reproductive and sterile castes, and worker behavioral specializations related to morphology, age, and ecology are associated with intra- and interspecific variation in investment in functionally different brain compartments. Workers in the hyperdiverse ant genus <i>Pheidole </i>are morphologically and behaviorally differentiated into minor and major subcastes that exhibit distinct species-typical patterns of brain compartment size variation. We examined integration and modularity in brain organization and its developmental patterning in three ecotypical <i>Pheidole</i> species by analyzing intra- and interspecific morphological and neuroanatomical covariation. Our results identified two trait clusters, the first involving olfaction and social information processing and the second composed of brain regions regulating nonolfactory sensorimotor functions. Patterns of size covariation between brain compartments within subcastes were consistent with levels of behavioral differentiation between minor and major workers. Globally, brains of mature workers were more heterogeneous than brains of newly eclosed workers, suggesting diversified developmental trajectories underscore species- and subcaste-typical brain organization. Variation in brain structure associated with the striking worker polyphenism in our sample of <i>Pheidole</i> appears to originate from initially differentiated brain templates that further diverge through species- and subcaste-specific processes of maturation and behavioral development.
DOI: 10.6084/m9.figshare.5127430
title: Supplementary Material for: Correlation of EEG Slowing with Cognitive Domains in Nondemented Patients with Parkinson's Disease

description: <b><i>Background:</i></b> Cognitive deficits in Parkinson's disease (PD) are heterogeneous and can be classified into cognitive domains. Quantitative EEG is related to and predictive of cognitive status in PD. In this cross-sectional study, the relationship of cognitive domains and EEG slowing in PD patients without dementia is investigated. <b><i>Methods:</i></b> A total of 48 patients with idiopathic PD were neuropsychologically tested. Cognitive domain scores were calculated combining Z-scores of test variables. Slowing of EEG was measured with median EEG frequency. Linear regression was used for correlational analyses and to control for confounding factors. <b><i>Results:</i></b> EEG median frequency was significantly correlated to cognitive performance in most domains (episodic long-term memory, rho = 0.54; overall cognitive score, rho = 0.47; fluency, rho = 0.39; attention, rho = 0.37; executive function, rho = 0.34), but not to visuospatial functions and working memory. <b><i>Conclusion:</i></b> Global EEG slowing is a marker for overall cognitive impairment in PD and correlates with impairment in the domains attention, executive function, verbal fluency, and episodic long-term memory, but not with working memory and visuospatial functions. These disparate effects warrant further investigations.