Miracle-dz/UniFAR-FTUs huggingface dataset:
Alteration of the anatomical covariance network after corpus callosotomy in pediatric intractable epilepsy

Purpose This study aimed to use graph theoretical analysis of anatomical covariance derived from structural MRI to reveal how the gray matter connectivity pattern is altered after corpus callosotomy (CC). Materials and methods We recruited 21 patients with epilepsy who had undergone CC. Enrollment criteria were applied: (1) no lesion identified on brain MRI; (2) no history of other brain surgery; and (3) age not younger than 3 years and not older than 18 years at preoperative MRI evaluation. The most common epilepsy syndrome was Lennox-Gastaut syndrome (11 patients). For voxel-based morphometry, the normalized gray matter images of pre-CC and post-CC patients were analyzed with SPM12 (voxel-level threshold of p<0.05 [familywise error-corrected]). Secondly, the images of both groups were subjected to graph theoretical analysis using the Graph Analysis Toolbox with SPM8. Each group was also compared with 32 age- and sex-matched control patients without brain diseases. Results Comparisons between the pre- and post-CC groups revealed a significant reduction in seizure frequency with no change in mean intelligence quotient/developmental quotient levels. There was no relationship among the three groups in global network metrics or in targeted attack. A regional comparison of betweenness centrality revealed decreased connectivity to and from the right middle cingulate gyri and medial side of the right superior frontal gyrus and a partial shift in the distribution of betweenness centrality hubs to the normal location. Significantly lower resilience to random failure was found after versus before CC and versus controls (p = 0.0450 and p = 0.0200, respectively). Conclusion Graph theoretical analysis of anatomical covariance derived from structural imaging revealed two neural network effects of resection associated with seizure reduction: the reappearance of a structural network comparable to that in healthy children and reduced connectivity along the median line, including the middle cingulate gyrus.
Limits in reliability of leg-spring and joint stiffness measures during single-leg hopping within a sled-based system

Research examining the reliability of stiffness measures during hopping has shown strong consistency in leg-spring stiffness (kleg), but high variability in joint stiffness (kjoint) measures. Sled-based systems (SBS) reduce movement degrees-of-freedom and are used to examine stretch-shortening cycle (SSC) function under controlled conditions. The aim of this study was to examine the reliability of kleg and kjoint during single-leg hopping within an SBSKinematic and kinetic data were collected on four occasions (Day_1, Day_2, Day_3 and Day_3Offset). Participants completed two trials of single-leg hopping at different frequencies (1.5, 2.2 and 3.0 Hz) while attached to an inclined-SBS. Stiffness was determined using models of leg-spring (kleg) and torsional (kjoint) stiffness. Statistical analysis identified absolute and relative measures of reliability. Results showed moderate reliability for kleg at 1.5 Hz between inter-day testing bouts, and weak consistency at 2.2 and 3.0 Hz. Examination of intra-day comparisons showed weak agreement for repeated measures of kleg at 1.5 and 2.2 Hz, but moderate agreement at 3.0 Hz. Limits in kleg reliability were accompanied by weak-to-moderate agreement in kjoint measures across inter- and intra-day testing bouts. Results showed limits in the reliability of stiffness measures relative to previous reports on overground hopping. Lack of consistency in kleg and kjoint may be due to the novelty of hopping within the current inclined-SBS. Constraints imposed on the hopping task resulting from SBS design (e.g. additional chair mass, restricting upper body movement) may have also influenced limits in kleg and kjoint reliability. Researchers should consider these findings when employing inclined-SBS of a similar design to examine SSC function.
Rational engineering of 2-deoxyribose-5-phosphate aldolases for the biosynthesis of (R)-1,3-butanediol

Carbon–carbon bond formation is one of the most important reactions in biocatalysis and organic chemistry. In nature, aldolases catalyze the reversible stereoselective aldol addition between two carbonyl compounds, making them attractive catalysts for the synthesis of various chemicals. In this work, we identified several 2-deoxyribose-5-phosphate aldolases (DERAs) having acetaldehyde condensation activity, which can be used for the biosynthesis of (R)-1,3-butanediol (1,3BDO) in combination with aldo-keto reductases (AKRs). Enzymatic screening of 20 purified DERAs revealed the presence of significant acetaldehyde condensation activity in 12 of the enzymes, with the highest activities in BH1352 from Bacillus halodurans, TM1559 from Thermotoga maritima, and DeoC from Escherichia coli. The crystal structures of BH1352 and TM1559 at 1.40–2.50 Å resolution are the first full-length DERA structures revealing the presence of the C-terminal Tyr (Tyr224 in BH1352). The results from structure-based site-directed mutagenesis of BH1352 indicated a key role for the catalytic Lys155 and other active-site residues in the 2-deoxyribose-5-phosphate cleavage and acetaldehyde condensation reactions. These experiments also revealed a 2.5-fold increase in acetaldehyde transformation to 1,3BDO (in combination with AKR) in the BH1352 F160Y and F160Y/M173I variants. The replacement of the WT BH1352 by the F160Y or F160Y/M173I variants in E. coli cells expressing the DERA + AKR pathway increased the production of 1,3BDO from glucose five and six times, respectively. Thus, our work provides detailed insights into the molecular mechanisms of substrate selectivity and activity of DERAs and identifies two DERA variants with enhanced activity for in vitro and in vivo 1,3BDO biosynthesis.
Cooperative blockade of PKCα and JAK2 drives apoptosis in glioblastoma.

The mechanistic target of rapamycin (mTOR) signaling is dysregulated prominently in human cancers including glioblastoma, suggesting mTOR as a robust target for therapy. Inhibitors of mTOR have had limited success clinically however, in part because their mechanism of action is cytostatic rather than cytotoxic. Here, we tested three distinct mTOR kinase inhibitors (TORKis) PP242, KU-0063794, and sapanisertib against glioblastoma cells. All agents similarly decreased proliferation of glioblastoma cells, whereas PP242 uniquely induced apoptosis. Apoptosis induced by PP242 resulted from off-target cooperative inhibition of Janus kinase 2 (JAK2) and protein kinase C alpha (PKCα). Induction of apoptosis was also decreased by additional on-target inhibition of mTOR, due to induction of autophagy. As EGFR inhibitors can block PKCα, EGFR inhibitors erlotinib and osimertinib were tested separately in combination with the JAK2 inhibitor AZD1480. Combination therapy induced apoptosis of glioblastoma tumors in both flank and in patient-derived orthotopic xenograft models, providing a preclinical rationale to test analogous combinations in patients.
Impact of negative lymph nodes on colon cancer survival and exploring relevant transcriptomics differences through real-world data analyses.

Background The prognostic role and underlying heterogeneity of negative lymph nodes (NLNs) on colon cancer is not well understood. The purpose of this study was to construct NLN-based prognostic models and reveal relevant mechanisms affecting NLNs by analyzing omic data. Methods This inception cohort study included 314,398 colon cancer patients from the US Surveillance, Epidemiology, and End Results (SEER) database. Receiver operating characteristic (ROC) curve was used to determine the cut-off of NLNs. Nomograms were constructed and validated using SEER data and the Cancer Genome Atlas (TCGA) data, respectively. The differentially expressed genes (DEGs) were analyzed using edgeR. Enrichment analyses were performed by Metascape. Results Multivariate analysis confirmed the high NLN had improved cancer-specific survival (CSS) and overall survival (OS) compared to low NLN [hazard ratio (HR) =0.610, 95% confidence interval (CI), 0.601-0.620] for CSS and (HR =0. 682, 95% CI, 0.674-0.690) for OS. Nomograms were established for CSS and OS with the c-statistic 0.790 (95% CI, 0.788-0.792) for CSS and 0.734 (95% CI, 0.732-0.736) for OS. High NLN was associated with less B cell (P=0.002) and macrophage infiltration (P<0.0001), high microsatellite instability (MSI) (OR =4.325, P=0.001), and hypermutation (OR =4.285, P=0.001; high vs. low). Transcriptomics analysis demonstrated histone modifiers were the most significant different biological processes between the high and low NLN group. Conclusions The NLN-based models can aid in personalized risk stratification for colon cancer. This study postulates that high NLN may represent a biological subtype with less macrophage infiltration, high MSI status, hypermutation, and histone modifier gene enriched expression, and thus warrants further investigation.
Evaluation of the accuracy of deformable image registration on MRI with a physical phantom

Abstract Background and purpose Magnetic resonance imaging (MRI) has gained popularity in radiation therapy simulation because it provides superior soft tissue contrast, which facilitates more accurate target delineation compared with computed tomography (CT) and does not expose the patient to ionizing radiation. However, image registration errors in commercial software have not been widely reported. Here we evaluated the accuracy of deformable image registration (DIR) by using a physical phantom for MRI. Methods and materials We used the “Wuphantom” for end‐to‐end testing of DIR accuracy for MRI. This acrylic phantom is filled with water and includes several fillable inserts to simulate various tissue shapes and properties. Deformations and changes in anatomic locations are simulated by changing the rotations of the phantom and inserts. We used Varian Velocity DIR software (v4.0) and CT (head and neck protocol) and MR (T1‐ and T2‐weighted head protocol) images to test DIR accuracy between image modalities (MRI vs CT) and within the same image modality (MRI vs MRI) in 11 rotation deformation scenarios. Large inserts filled with Mobil DTE oil were used to simulate fatty tissue, and small inserts filled with agarose gel were used to simulate tissues slightly denser than water (e.g., prostate). Contours of all inserts were generated before DIR to provide a baseline for contour size and shape. DIR was done with the MR Correctable Deformable DIR method, and all deformed contours were compared with the original contours. The Dice similarity coefficient (DSC) and mean distance to agreement (MDA) were used to quantitatively validate DIR accuracy. We also used large and small regions of interest (ROIs) during between‐modality DIR tests to simulate validation of DIR accuracy for organs at risk (OARs) and propagation of individual clinical target volume (CTV) contours. Results No significant differences in DIR accuracy were found for T1:T1 and T2:T2 comparisons (P > 0.05). DIR was less accurate for between‐modality comparisons than for same‐modality comparisons, and was less accurate for T1 vs CT than for T2 vs CT (P < 0.001). For between‐modality comparisons, use of a small ROI improved DIR accuracy for both T1 and T2 images. Conclusion The simple design of the Wuphantom allows seamless testing of DIR; here we validated the accuracy of MRI DIR in end‐to‐end testing. T2 images had superior DIR accuracy compared with T1 images. Use of small ROIs improves DIR accuracy for target contour propagation.
Quantification of speech and synchrony in the conversation of adults with autism spectrum disorder

Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder characterized by impairments in social reciprocity and communication together with restricted interest and stereotyped behaviors. The Autism Diagnostic Observation Schedule (ADOS) is considered a ‘gold standard’ instrument for diagnosis of ASD and mainly depends on subjective assessments made by trained clinicians. To develop a quantitative and objective surrogate marker for ASD symptoms, we investigated speech features including F0, speech rate, speaking time, and turn-taking gaps, extracted from footage recorded during a semi-structured socially interactive situation from ADOS. We calculated not only the statistic values in a whole session of the ADOS activity but also conducted a block analysis, computing the statistical values of the prosodic features in each 8s sliding window. The block analysis identified whether participants changed volume or pitch according to the flow of the conversation. We also measured the synchrony between the participant and the ADOS administrator. Participants with high-functioning ASD showed significantly longer turn-taking gaps and a greater proportion of pause time, less variability and less synchronous changes in blockwise mean of intensity compared with those with typical development (TD) (p<0.05 corrected). In addition, the ASD group had significantly wider distribution than the TD group in the within-participant variability of blockwise mean of log F0 (p<0.05 corrected). The clinical diagnosis could be discriminated using the speech features with 89% accuracy. The features of turn-taking and pausing were significantly correlated with deficits of ASD in reciprocity (p<0.05 corrected). Additionally, regression analysis provided 1.35 of mean absolute error in the prediction of deficits in reciprocity, to which the synchrony of intensity especially contributed. The findings suggest that considering variance of speech features, interaction and synchrony with conversation partner are critical to characterize atypical features in the conversation of people with ASD.
Effects of Additional Kinesiotaping Over the Conventional Physiotherapy Exercise on Pain, Quadriceps Strength and Knee Functional Disability in Knee Osteoarthritis Participants: A Randomized Controlled Study. -

Background: Osteoarthritis (OA) is a major public health problem. Prevalence of knee OA is 3445%in Indian population with clinical symptoms of pain, reduced muscle strength and knee function. Objective: This study to determine the effectiveness of additional kinesiotaping (KT) over the conventional physiotherapy on pain, quadriceps strength and functional disability in knee osteoarthritis participants. Methods: A randomized controlled study.30 knee osteoarthritis individuals were recruited and randomly allocated in to two groups (conventional PT & kinesiotaping plus conventional PT; N=15 in each group). Both groups received the same conventional PT program of muscle stretching and strengthening exercises for 3 weeks and the KT group additionally received kinesiotaping at thrice per week for three weeks. All the groups underwent 3 weeks of supervised intervention program. NPRS, HHD and modified WOMAC for knee pain, quadriceps strength and knee functional disability were recorded at baseline and after three weeks of interventions. Results: Comparing pretreatment and 3rd week values, significant improvements were found in pain, quadriceps strength and functional performance of both groups (p<0.05). The KT group had significantly better than the control group at the end of three weeks (p<0.05). Conclusion: The addition of kinesiotaping to the CPT was capable of reducing pain, improving quadriceps strength and knee functional ability in knee OA participants.
Analysis of transient ST segment changes during ambulatory monitoring using the Karhunen-Loeave transform

The authors present an algorithm based on the Karhunen-Loeave transform (KLT) for robust automated detection of ischemic ST segment episodes and measurement of the duration of ischemia in two-channel ambulatory electrocardiographic data. The algorithm operates as a postprocessor to an existing arrhythmia detector. The episode detector incorporates a single-scan trajectory recognition technique in the KLT feature space. The algorithm differentiates between true ischemic ST segment changes and non-ischemic ST deviations caused by axis shifts. In evaluations using the European Society of Cardiology ST-T database, the algorithm achieved a gross ST episode sensitivity of 85.2%, with a positive predictivity of 86.2%. The gross ischemic ST duration sensitivity was 75.8%, with a positive predictivity of 78.0%. <<ETX>>
Diversity of a cytokinin dehydrogenase gene in wild and cultivated barley

The cytokinin dehydrogenase gene HvCKX2.1 is the regulatory target for the most abundant heterochromatic small RNAs in drought-stressed barley caryopses. We investigated the diversity of HvCKX2.1 in 228 barley landraces and 216 wild accessions and identified 14 haplotypes, five of these with ten or more members, coding for four different protein variants. The third largest haplotype was abundant in wild accessions (51 members), but absent from the landrace collection. Protein structure predictions indicated that the amino acid substitution specific to haplotype 3 could result in a change in the functional properties of the HvCKX2.1 protein. Haplotypes 1–3 have overlapping geographical distributions in the wild population, but the average rainfall amounts at the collection sites for haplotype 3 plants are significantly higher during November to February compared to the equivalent data for plants of haplotypes 1 and 2. We argue that the likelihood that haplotype 3 plants were excluded from landraces by sampling bias that occurred when the first wild barley plants were taken into cultivation is low, and that it is reasonable to suggest that plants with haplotype 3 are absent from the crop because these plants were less suited to the artificial conditions associated with cultivation. Although the cytokinin signalling pathway influences many aspects of plant development, the identified role of HvCKX2.1 in the drought response raises the possibility that the particular aspect of cultivation that mitigated against haplotype 3 relates in some way to water utilization. Our results therefore highlight the possibility that water utilization properties should be looked on as a possible component of the suite of physiological adaptations accompanying the domestication and subsequent evolution of cultivated barley.
Biophysical Characterization of (Silica-coated) Cobalt Ferrite Nanoparticles for Hyperthermia Treatment

Magnetic hyperthermia is a technique that describes the heating of material through an external magnetic field. Classic hyperthermia is a medical condition where the human body overheats, being usually triggered by a heat stroke, which can lead to severe damage to organs and tissue due to the denaturation of cells. In modern medicine, hyperthermia can be deliberately induced to specified parts of the body to destroy malignant cells. Magnetic hyperthermia describes the way that this overheating is induced and it has the inherent advantage of being a minimal invasive method when compared to traditional surgery methods. This work presents a particle system that offers huge potential for hyperthermia treatments, given its good loss value, i.e., the particles dissipate a lot of heat to their surroundings when treated with an ac magnetic field. The measurements were performed in a low-cost custom hyperthermia setup. Additional toxicity assessments on Jurkat cells show a very low short-term toxicity on the particles and a moderate low toxicity after two days due to the prevalent health concerns towards nanoparticles in organisms.
PRELIMINARY STUDY ON STRONG MOTION DATA OF THE 2016 CENTRAL ITALY SEISMIC SEQUENCE V 6

1. What’s New 2. Introduction 3. Geographic Information 4. Strong Motion Data 5. SHAKEMAPS 6. Comparison with GMPE 7. Elastic and Inelastic Response Spectra from 24/08/2016 event 8. Elastic response spectra for different events recorded at the same sites 9. The Italian seismic code and recorded spectra 10. Pulse-like near-source ground motions 11. Illustration (example) of damage accumulation during the sequence on a single degree of freedom system Data and resources References Appendix 1
Draft Genome Sequences of Two Textile Azo Dye-Degrading Shewanella sp. Strains Isolated from a Textile Effluent in Peru

Here, we report the annotated genome sequences of two Shewanella sp. strains isolated from textile industry wastewater effluent in Peru. Potential genes for encoding enzymes that enable the strain to decolorize and degrade textile azo dyes were detected in both genomes. ABSTRACT Here, we report the annotated genome sequences of two Shewanella sp. strains isolated from textile industry wastewater effluent in Peru. Potential genes for encoding enzymes that enable the strain to decolorize and degrade textile azo dyes were detected in both genomes.
Do Women Principals Really Face With Barriers in Schools? Critics of Glass Ceiling Syndrome in Turkey*

Article History: Received 10.10. 2011 Received in revised form 05.05. 2012 Accepted 08.05. 2012 Available online 10.08. 2012 Administration of schools and achieving the goals in democratic and transparent society requires gender neutral settings. Together with the researches that aimed to unveil the gendered stereotypical behavior in organizational settings, some other related topics have also been investigated such as women’s barriers for principals, democratic and liberal discourse of gendered identity, cross-cultural perspective for gendered stereotypes. Although cultures are context specific and unique for each society depending on religious, historical, societal and geographical backgrounds; classification, stereotypes and cultural metaphors have more or less resembled each other, or the studies in different context seem as if they have reiterated one another. Women’s traditional roles of domestic responsibility have begun to change since equality movements together with some legislation have put in force in different settings. Most of the researches that were conducted in different societal and cultural settings had resulted in conclusion that women face with unequal conditions in administration. The purpose of the paper is to present the clear insights of women principals. Qualitative research design was used to figure out unique perspectives of 8 women principals in school administration. The study reveals that women principals in this context have not exposed certain barriers or stereotypes on the process of selection, promotion and in practice; rather, they have been supported by superiors. © 2012 IOJES. All rights reserved