Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating local scaling properties for the classification of interstitial lung disease patterns

Local scaling properties of texture regions were compared in their ability to classify morphological patterns known as 'honeycombing' that are considered indicative for the presence of fibrotic interstitial lung diseases in high-resolution computed tomography (HRCT) images. For 14 patients with known occurrence of honeycombing, a stack of 70 axial, lung kernel reconstructed images were acquired from HRCT chest exams. 241 regions of interest of both healthy and pathological (89) lung tissue were identified by an experienced radiologist. Texture features were extracted using six properties calculated from gray-level co-occurrence matrices (GLCM), Minkowski Dimensions (MDs), and the estimation of local scaling properties with Scaling Index Method (SIM). A k-nearest-neighbor (k-NN) classifier and a Multilayer Radial Basis Functions Network (RBFN) were optimized in a 10-fold cross-validation for each texture vector, and the classification accuracy was calculated on independent test sets as a quantitative measure of automated tissue characterization. A Wilcoxon signed-rank test was used to compare two accuracy distributions including the Bonferroni correction. The best classification results were obtained by the set of SIM features, which performed significantly better than all the standard GLCM and MD features (p < 0.005) for both classifiers with the highest accuracy (94.1%, 93.7%; for the k-NN and RBFN classifier, respectively). The best standard texture features were the GLCM features 'homogeneity' (91.8%, 87.2%) and 'absolute value' (90.2%, 88.5%). The results indicate that advanced texture features using local scaling properties can provide superior classification performance in computer-assisted diagnosis of interstitial lung diseases when compared to standard texture analysis methods.
Hardware-in-the-loop simulation of PUMA 560 via internet

This study introduces a remotely accessible hardware-in-the-loop simulator (HILS), which is used for the development of the PUMA 560 dynamics and control. The HILS setup aims to give on-site and remote students/researchers the capability to experiment with any robotic configuration and control algorithm of their choice, without the need for the physical existence of the equipment in the laboratory. To increase the flexibility offered by the system, the HILS setup is made a part of the UAF RemoteLab facility, with the developed client/server communication, which gives remote access to all Matlab/Simulink based applications. As an implementation example, in this study, the HILS setup is used to develop dynamics and PD+ control of PUMA 560 as a graduate project. Experimental results and animations are also presented
Offspring‐driven local dispersal in female sand lizards (Lacerta agilis)

We report on a field study in which determinants of female breeding dispersal (i.e. the shift in the mean home range coordinates between successive breeding events) was investigated. Offspring were released in full sib groups (or half sib ones if there was within‐clutch multiple paternity) at a separation distance from the females that varied between ‘families’. This allowed for analysis of ‘offspring nearness’ effects on maternal dispersal. When a female's offspring were released more closely to her, she responded with greater dispersal. Furthermore, when the data set was truncated at 100 m maternal–offspring separation distance at offspring release (because perception at longer distances is likely to be unrealistic), maternal dispersal resulted in greater separation distance between female and offspring in the following year. A corresponding analysis for juveniles revealed no effect of maternal nearness on offspring dispersal but identified a significant effect of clutch size, to our surprise with dispersal declining with increasing clutch size. We discuss this result in a context of the ‘public information hypothesis’ (reinterpreted for juveniles in a nonsocial foraging species), suggesting that conspecific abundance perhaps acts as an indicator of local habitat quality. Thus, our analysis suggests a microgeographic structuring of the adult female population driven by genetic factors, either through inbreeding avoidance, or from simply avoiding individuals with a similar genotype regardless of their pedigree relatedness, while a nongenetic factor seems more important in their offspring.
Basel III Leverage and Capital Ratio over the Economic Cycle in the Czech Republic and its Comparison with the CEE Region

This paper investigates the implications and effectiveness of Basel III leverage requirements for the banking sector in the Czech Republic and its comparison with the Central and Eastern European (CEE) region. We discuss the relationships between the leverage and capital ratios and analyse their constraining effects and cyclical qualities. The empirical analysis consists of examination of the correlation patterns between the leverage and capital ratio in relation to the changes in the business cycles. We propose an empirical model that allows testing how the leverage ratios and their variables respond to the changes in the economic cycles of the CEE region. The analysis of correlation patterns among the variables suggests that the total assets or exposure in contrast to the Tier 1 capital are the main contributors to the cyclical movements. The regression analysis shows that the leverage ratio in normal times is strongly pro-cyclical to the capital ratio and counter-cyclical in the crisis period. The empirical evidence indicating the active balance sheet management in response to the cyclical changes advocates in favour of constraining regulations on the leverage.
An evaluation of the transdiagnostic cognitive-behavioural model of eating disorders.

OBJECTIVE To determine if the relationships between additional maintaining factors and core eating disorder maintaining mechanisms outlined in the cognitive-behavioural model of eating disorders are transdiagnostic. METHOD Patients (n = 1451) diagnosed with anorexia nervosa, bulimia nervosa (BN) or eating disorder not otherwise specified completed the Eating Disorder Examination Questionnaire, Eating Disorder Inventory-2 and Personality Assessment Inventory prior to entering treatment. RESULTS Multi-group structural equation modelling results suggested that low self-esteem, overevaluation of weight and shape, and mood intolerance processes were transdiagnostic. However, some differences between diagnostic groups were observed. Dietary restraint was only positively associated with binge eating in BN, interpersonal difficulties were only associated with dietary restraint in eating disorder not otherwise specified and perfectionism was not associated with core eating disorder maintaining mechanisms in BN. DISCUSSION A mixture of transdiagnostic and disorder-specific processes was implicated in the maintenance of eating disorders, although longitudinal research is needed to validate results.
Mitochondrial DNA‐like sequences in the nucleus (NUMTs): Insights into our African origins and the mechanism of foreign DNA integration

Nuclear mitochondrial DNA sequences (NUMTs) are common in eukaryotes. However, the mechanism by which they integrate into the nuclear genome remains a riddle. We analyzed 247 NUMTs in the human nuclear DNA (nDNA), along with their flanking regions. This analysis revealed that some NUMTs have accumulated many changes, and thus have resided in the nucleus a long time, while others are >94% similar to the reference human mitochondrial DNA (mtDNA), and thus must be recent. Among the latter, two NUMTs, encompassing the COI gene, carry a set of transitions characteristic of the extant African‐specific L macrohaplogroup mtDNAs and are more homologous to human mtDNA than to chimp. Screening for one of these NUMTs revealed its presence in all human samples tested, confirming that the African macrohaplogroup L mtDNAs were present in the earliest modern humans and thus were the first human mtDNAs. An analysis of flanking sequences of the NUMTs revealed that 59% were within 150 bp of repetitive elements, with 26% being within 15 bp of and 33% being within 15–150 bp of repetitive elements. Only 14% were integrated into a repetitive element. This association of NUMTs with repetitive elements is highly nonrandom (p<0.001). These data suggest that the vicinity of transposable elements influences the ongoing integration of mtDNA sequences and their subsequent duplication within the nDNA. Finally, NUMTs appear to preferentially integrate into DNA with different GC content than the surrounding chromosomal band. Our results suggest that chromosomal structure might influence integration of NUMTs. Hum Mutat 23:125–133, 2004. © 2003 Wiley‐Liss, Inc.
Comparison of neuroendoscopic surgery and craniotomy for supratentorial hypertensive intracerebral hemorrhage

Background: In recent years, neuroendoscopy has been used as a method for treating intracerebral hemorrhages (ICHs). However, the efficacy and safety of neuroendoscopic surgery is still controversial compared with that of craniotomy. Our aim was to compare the outcomes of neuroendoscopic surgery and craniotomy in patients with supratentorial hypertensive ICH using a meta-analysis. Methods: We searched on PubMed, EMBASE, and Cochrane Central Register of Controlled Trials to identify relevant studies in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Quality of eligible studies was evaluated and the related data were extracted by 2 reviewers independently. This study assessed clinical outcomes, evacuation rates, complications, operation time, and hospital stay for patients who underwent neuroendoscopic surgery (NE group) or craniotomy (craniotomy group). Results: Meta-analysis included 1327 subjects from verified studies of acceptable quality. There was no significant heterogeneity between the included studies based on clinical outcomes. Compared with craniotomy, neuroendoscopic surgery significantly improved clinical outcomes in both randomized controlled studies (RCTs) group (relative risk: 0.62; 95% confidence interval [CI], 0.47–0.81, P < .001) and non-RCTs group (relative risk: 0.84; 95% CI: 0.75–0.95, P = .005); decreased the rate of death (relative risk: 0.53; 95% CI, 0.37–0.76, P < .001) in non-RCTs group but not in RCTs group (relative risk: 0.58; 95% CI, 0.26–1.29, P = .18); increased evacuation rates in non-RCTs group (standard mean differences: 0.75; 95% CI, 0.24–1.26, P = .004) and had a tendency of higher evacuation rates in RCTs group (standard mean differences: 1.34; 95% CI, 0.01–2.68, P = .05); reduced the total risk of complications in non-RCTs group (relative risk: 0.45; 95% CI, 0.25–0.83, P = .01) and RCTs group (relative risk: 0.37; 95% CI, 0.28–0.49, P < .001); reduced the operation time in non-RCTs group (standard mean differences: 3.26; 95% CI: 1.20–5.33, P < .001) and RCTs group (standard mean differences: 4.37; 95% CI: 3.32–5.41, P < .001). Conclusions: Our results suggested that the NE group showed better clinical outcomes than the craniotomy group for patients with supratentorial hypertensive ICH. Moreover, the patients who underwent neuroendoscopy had a higher evacuation rate, lower risk of complications, and shorter operation time compared with those that underwent a craniotomy.
Technical devices in jejunal pouch reconstruction following total gastrectomy, including postoperative results.

BACKGROUND/AIMS Either straight Roux-en-Y anastomosis or jejunal interposition used to be adopted following total gastrectomy. However, dissatisfaction with regard to postoperative quality of life has prompted the development of new techniques. The purpose of this study is to describe and assess the authors' technical devices in jejunal pouch (J-pouch) reconstruction following total gastrectomy and the results of these operations. PATIENTS AND METHODS A prospective study of 17 patients with malignant gastric disease (nine with J-pouch interposition, eight with J-pouch Roux-en-Y reconstruction) was performed. To facilitate the side-to-side anastomosis of the jejunal loop, the authors used an autosuture instrument. The anastomosis was then checked for hemostasis using a vaginoscope. RESULTS An Endo GIA with a 60-mm long white cartridge (closed height of staples, 1.0 mm) is the instrument of choice to create the J-pouch. This autosuture instrument fires triple staggered staple lines, which minimizes bleeding from the anastomosed site and reduces operative time. No anastomotic leaks were associated with the autosuture instrument. The vaginoscope facilitates a direct observation of the staple lines internally and if necessary, enables secure hemostasis with sutures. Bowel motility was satisfactory for both surgical procedures, as measured by the percentage of radiopaque markers which were expelled from the pouch. There were no serious complications, and all patients have currently survived, a maximum of 5 years and 6 months after surgery, except for one patient who died from recurrent disease. CONCLUSION The authors' procedures for J-pouch reconstruction are advantageous due to a favorable postoperative quality of life, with low complication rates.
Embedding low cost optimal watermark during high level synthesis for reusable IP core protection

Intellectual property (IP) cores have emerged as a promising solution to the challenges of future design as well as mounting time to market pressure. However, due to increasing globalization of design supply chain, possibility of intervention and typical attacks is on the rise, which therefore mandates protection of IP cores from piracy/counterfeiting even at behavioral level. This paper presents a technique for generating low cost watermarking solution during high level synthesis (HLS) based on multi-variable signature encoding for security of reusable IP cores. The watermark generated by the proposed approach satisfies the following properties: (a) low embedding cost (b) robustness (c) low watermark creation time (d) strong proof of authorship (e) lower hardware overhead. Comparison with similar technique revealed that proposed approach obtains watermarked solution with lower embedding cost with less storage overhead and creation time.
PRKAA1/AMPKα1 is required for autophagy-dependent mitochondrial clearance during erythrocyte maturation

AMP-activated protein kinase α1 knockout (prkaa1−/−) mice manifest splenomegaly and anemia. The underlying molecular mechanisms, however, remain to be established. In this study, we tested the hypothesis that defective autophagy-dependent mitochondrial clearance in prkaa1−/− mice exacerbates oxidative stress, thereby enhancing erythrocyte destruction. The levels of ULK1 phosphorylation, autophagical flux, mitochondrial contents, and reactive oxygen species (ROS) were examined in human erythroleukemia cell line, K562 cells, as well as prkaa1−/− mouse embryonic fibroblasts and erythrocytes. Deletion of Prkaa1 resulted in the inhibition of ULK1 phosphorylation at Ser555, prevented the formation of ULK1 and BECN1- PtdIns3K complexes, and reduced autophagy capacity. The suppression of autophagy was associated with enhanced damaged mitochondrial accumulation and ROS production. Compared with wild-type (WT) mice, prkaa1−/− mice exhibited a shortened erythrocyte life span, hemolytic destruction of erythrocytes, splenomegaly, and anemia, all of which were alleviated by the administration of either rapamycin to activate autophagy or Mito-tempol, a mitochondria-targeted antioxidant, to scavenge mitochondrial ROS. Furthermore, transplantation of WT bone marrow into prkaa1−/− mice restored mitochondrial removal, reduced intracellular ROS levels, and normalized hematologic parameters and spleen size. Conversely, transplantation of prkaa1 −/− bone marrow into WT mice recapitulated the prkaa1−/− mouse phenotypes. We conclude that PRKAA1-dependent autophagy-mediated clearance of damaged mitochondria is required for erythrocyte maturation and homeostasis.
Interaction of bioactive glasses with peritoneal macrophages and monocytes in vitro.

Macrophage activation was analyzed following exposure to pure, crystalline alpha-quartz powders, two bioactive gel-glass powders of different compositions, and a melt-derived glass, 45S5 Bioglass. The release of reactive oxygen metabolites (chemiluminescence test), modifications of cell morphology, the amount of tumor necrosis factor alpha (TNFalpha) secreted, and the amount of TNFalpha mRNA expression were evaluated. The 45S5 Bioglass powders elicited the highest chemiluminescence response while the two solgel glasses had a lower response with less of an oxidative burst difference between them. Particulate bioactive glasses are actively ingested by mouse peritoneal macrophages, and only the 58S solgel glass had a moderate toxic effect on the macrophages. Macrophage cell morphology showed increased size and cell spreading, consistent with the high level of cytokine secretion induced by 45S5 Bioglass. The 45S5 Bioglass powders led to an increased release of TNFalpha and expression of TNFalpha mRNA relative to unstimulated and control treated monocytes. Bioactive glasses (and particularly 45S5 Bioglass) that in vivo induce rapid bone growth appear to activate an autocrine-like process in which the response evoked by the material (for example monocyte and macrophage activation with cytokine production) enhances subsequent interactions with cells in contact with the material.
Social network moderators of naltrexone and behavioral treatment effects on heavy drinking in the COMBINE study.

BACKGROUND Oral naltrexone is an efficacious medication for treatment of alcohol dependence, but small effect sizes and variability in outcomes suggest the presence of person-level moderators of naltrexone response. Identification of contextual or psychosocial moderators may assist in guiding clinical recommendations. Given the established importance of social networks in drinking outcomes, as well as the potential effects of naltrexone in reducing cue reactivity which may be especially important among those with more heavy drinkers and more alcohol cues in their networks, we examined pretreatment social network variables as potential moderators of naltrexone treatment effects in the COMBINE study. METHODS The sample included all COMBINE study participants in medication conditions with full data on the Important People Inventory (IPI) and covariates at intake (N = 1,197). The intake IPI assessed whether participants had any frequent drinkers in their network and the average frequency of contact with these drinkers. The effects of treatment condition, pretreatment network variables, and their interactions on percent heavy drinking days were tested in hierarchical linear models, controlling for demographics and baseline clinical covariates. RESULTS In treatment conditions involving medical management and combined behavioral intervention (CBI), the effects of active naltrexone on heavy drinking were significantly greater for individuals with frequent drinkers in their network (z = -2.66, p < 0.01) and greater frequency of contact with those drinkers (z = -3.19, p < 0.01). These network variables did not moderate the effects of active naltrexone without CBI. CONCLUSIONS When delivered in conjunction with behavioral interventions, naltrexone can be more potent for alcohol-dependent adults who have greater contact with frequent drinkers prior to treatment, which may indicate patterns of environmental exposure to alcohol. Contextual, social risk factors are a potential avenue to guide personalized treatment of alcohol dependence.
Human LDL receptor gene: HincII polymorphism detected by gene amplification.

Source/Description: Synthetic Oligonucleotides SP76 ('5-TCTCCTTATCCACTTGTGT GTCTAG-3') and SP77 ('5-CTTCGATCTCGTACGTAAGCCACAC-3') were prepared on a DNA synthesizer (Applied Biosystems). These oligonucleotides flank exon 12 of the LDL receptor gene (see figure). Polymorphism: There is a HincII polymorphic site located within exon 12 of the human LDL receptor gene. DNA sequence analysis revealed that the polymorphism is caused by a single base substitution (T to C). The polymorphism is detected by digesting amplified genomic DNA with HincII (New England Biolabs). Protocol: Human genomic DNA is subjected to gene amplification (1) using SP76 and 32P end-labeled SP77 (2). The amplified DNA is then size fractionated on a 6% polyacrylamide nondenaturing gel and subjected to autoradiography. The 190 bp DNA fragment encompassing EXON 12 and the sequence corresponding to the two flanking oligonucleotides is excised from the gel and purified (see right lane of figure). The purified DNA is then digested with HincII and fractionated by gel electrophoresis on a 6% acrylamide gel. Autoradiography reveals 98 bp or 133 bp bands corresponding to the presence or absence of the polymorphic site (see figure). The difference between the sizes of these two fragments (35bp) requires the use of gene amplification. Frequency: In 10 unrelated American caucasian individuals: 98 bp 0.45, 133 bp 0.55. Chromosomal localisation: 19pl3.1-13.3 Mendelian inheritance: Co-dominant segregation is shown in one family. References: 1. Saiki, R. K. , T. L. Bugawan, G.T. Horn, K. B. Mullis, and H. A. Erlich (1986) Nature 324: 163-166. 2. Maniatis, T. , E.F. Fritsch, and J. Sambrook (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory. P. 122. 3. Lindgren, V. , K.L. Luskey, D.W. Russell, and V. Franke (1985) Proc. Natl. Acad. Sci. 83: 8567-8571.
Mechanism of Action of Neisseria gonorrhoeae O-Acetylpeptidoglycan Esterase, an SGNH Serine Esterase*

Background: O-Acetylpeptidoglycan esterase functions to release O-acetyl groups from peptidoglycan, thereby permitting the continued metabolism of this essential cell wall component. Results: Gly-236 and Asn-268 were identified as participating at the oxyanion hole to stabilize the tetrahedral species in the reaction mechanism. Conclusion: Ape1a functions as a classical serine esterase. Significance: Ape represents a novel target for the development of new antibiotics. O-Acetylpeptidoglycan esterase from Neisseria gonorrhoeae functions to release O-acetyl groups from the C-6 position of muramoyl residues in O-acetylated peptidoglycan, thereby permitting the continued metabolism of this essential cell wall heteropolymer. It has been demonstrated to be a serine esterase with sequence similarity to the family CE-3 carbohydrate esterases of the CAZy classification system. In the absence of a three-dimensional structure for any Ape, further knowledge of its structure and function relationship is dependent on modeling and kinetic studies. In this study, we predicted Neisseria gonorrhoeae Ape1a to be an SGNH hydrolase with an adopted α/β-hydrolase fold containing a central twisted four-stranded parallel β-sheet flanked by six α-helices with the putative catalytic triad, Asp-366, His-369, and Ser-80 appropriately aligned within a pocket. The role of eight invariant and highly conserved residues localized to the active site was investigated by site-directed replacements coupled with kinetic characterization and binding studies of the resultant engineered enzymes. Based on these data and theoretical considerations, Gly-236 and Asn-268 were identified as participating at the oxyanion hole to stabilize the tetrahedral species in the reaction mechanism, whereas Gly-78, Asp-79, His-81, Asn-235, Thr-267, and Val-368 are proposed to position appropriately the catalytic residues and participate in substrate binding.