Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of cepstrum-based methods for radial blind deconvolution of ultrasound images

This paper compares the performance of seven different cepstrum-based methods for radial blind deconvolution of medical ultrasound images. The first is the generalized cepstrum method. The second is the spectral root cepstrum method. These methods have received little attention so far. The last five methods are all based on the complex cepstrum, but different computational techniques in the spatial and frequency domain are employed. Using in vivo radio frequency data from a clinical scanner, the generalized cepstrum method gave the best images closely followed by the complex cepstrum using phase unwrapping or polynomial rooting. The complex cepstrum method using higher-order statistics was ranked as low as number five. These results are an important guideline for selecting a specific cepstrum-based radial deconvolution method for implementation in ultrasound scanners.
Effect of trifloxystrobin on hatching, survival, and gene expression of endocrine biomarkers in early life stages of medaka (Oryzias latipes)

Trifloxystrobin is a systemic broad‐spectrum foliar strobilurin fungicides that enters the aquatic environment during agricultural application. It is highly toxic and poses a potential risk to aquatic organisms, whereas the effect on the development of early life stages of fish are unclear. In this study, hatchability, time to hatching, and larval mortality were measured. Additionally, the expression of biomarker genes, including those involved in sex hormone pathways (er, vtg, cyp17, and cyp19a), thyroid hormone pathways (trα and dio2), and aryl hydrocarbon receptor pathways (ahr and cyp1a), was determined after embryos of medaka (Oryzias latipes) were exposed to different levels of trifloxystrobin (0, 0.1, 1, 10, and 100 μg/L) for 28 days. The results showed that there were significant differences between controls and the 100 μg/L treatment group in both hatchability and time to hatching of fertilized eggs (p < 0.05). Larval mortality was significantly increased in the 0.1, 1, and 10 μg/L treatment groups (p < 0.05). These results indicate that embryonic and larval development may be affected by trifloxystrobin exposure. Moreover, the mRNA levels of the er gene were significantly up‐regulated at levels of trifloxystrobin above 1 μg/L treatment groups. Up‐regulation of vtg, cyp17, and cyp19a mRNA levels was observed in the larvae at the lower concentration treatment groups. The mRNA levels of cyp1a genes were significantly up‐regulated at all of the treatment groups. These results suggest that trifloxystrobin is a potential endocrine disruptor through effects on the sex hormone pathway and xenobiotic metabolism. The changes in cyp1a expression can be used as a highly sensitive biomarker to assess trifloxystrobin contamination in the early life stages of fish. © 2013 Wiley Periodicals, Inc. Environ Toxicol 30: 648–655, 2015.
Microflora of Patients with Stool Abnormality

patients, with the exception of patients with infectious diarrhea. Alterations of the intestinal microflora probably reflect the physiological state of the patient, and fermentative reactions due to microorganisms present in the gut may possibly induce diarrhea. Since 1970, bacteriological techniques for cultivating strictly obligate anaerobes have been vigorously developed and many studies on the intestinal microflora of patients with clinical problems have been reported in
Augmenting knowledge-based medical systems with tacit healthcare expertise: towards an intelligent tacit knowledge acquisition info-structure

The knowledge-rich nature of the healthcare domain has made it an ideal environment for the application of knowledge-based techniques. However, the abstract nature of tacit healthcare knowledge has resulted in the under-utilization of such a vital component of the overall healthcare delivery system. Therefore, we present a six-step approach to procure tacit healthcare knowledge using healthcare scenarios. This process is supported by a healthcare scenario composer, which is a key component of a wider framework called the Tacit Knowledge Acquisition Info-Structure (TKAI). This information structure aims to combine the effectiveness of healthcare scenarios, ontologies and artificial intelligence techniques to facilitate the efficient acquisition, representation, refinement and dissemination of expert-quality tacit healthcare knowledge from/to healthcare experts.
Past Methylphenidate Exposure and Stress Fractures in Combat Soldiers: A Case-Control Study

Background: Previous research has revealed decreased bone mineral density (BMD) among children and adolescents who receive methylphenidate (MP) treatment for attention deficit hyperactivity disorder (ADHD). These findings have major clinical implications given that the prevalence of medication-treated ADHD is on the rise worldwide. We decided to investigate the clinical effect of MP exposure on the incidence of stress fractures, for which a low BMD is a risk factor. Hypothesis: Exposure to MP is a risk factor for stress fractures. Study Design: Case-control study; Level of evidence, 3. Methods: This is a case-control study of combat soldiers who served in the military for 3 years between 2005 and 2015. The case group included 2400 soldiers with at least 1 stress fracture diagnosed by a bone scan. The control group comprised 6187 combat soldiers without a diagnosis of a stress fracture. The use of MP was determined by an automated text search of medical records and manual sorting of the results. Other study variables included age; sex; weight; height; body mass index (BMI); place of birth; and characterization of fractures by location, side, and grade. Odds ratios of stress fractures, the attributable proportion among the exposed, and the population attributable fraction were calculated using standard contingency tables. Logistic regression was fitted after adjusting for covariates. Results: The previous use of MP was associated with a higher risk of stress fractures (odds ratio, 1.15 [95% CI, 1.07-1.24]). The attributable proportion was 13.2%, and the population attributable fraction was 0.3%. Logistic regression demonstrated an increased risk of stress fractures associated with past MP use, preserved after adjusting for BMI, sex, and place of birth (P = .005). Female sex, BMI ≤20 kg/m2, and 20 < BMI ≤25 kg/m2 were independent positive predictors of a stress fracture, while African origin was a negative predictor. Most participants who used MP had only 1 fracture (77.8%), while the majority of participants who did not use MP in the past had ≥2 coincident fractures (53.5%) (P = .003). Conclusion: This study supports the hypothesis that an MP-associated reduction in BMD has a clinical effect in the form of an increased incidence of stress fractures. The high percentage of fractures attributed to MP use may serve as a basis for risk stratification, that is, the referral of patients with a history of MP use to BMD measurements.
Carcinogenic potential of metal nanoparticles in BALB/3T3 cell transformation assay

Metal‐based nanoparticles (NPs), are currently used in many application fields including consumer products, pharmaceuticals, and biomedical treatments. In spite to their wide applications, an in‐depth study of their potential toxic effects is still lacking. The aim of the present research was to investigate the potential initiator or promoter‐like activity of different metallic NPs such as gold, iron, cobalt, and cerium using the Balb/3T3 two‐stage transformation assay. The results indicated that all the selected metallic NPs, except for cobalt, when used as initiators did not induce any transformation in Balb/3T3 cell line. Moreover, Au and Fe3O4 NPs, when used in place of the tumor promoter treatment TPA, increased significantly the number of Foci/dish as compared to the MCA treatment alone. The number of Foci/dish was 2.6 for Au NPs and 2.13 for Fe3O4 ones, similar to those obtained by the positive control treatment (MCA + TPA), whereas 1.27 for MCA treatment alone. On the contrary, CeO2 NPs did not show any difference in the number of Foci/dish, as compared to MCA alone, but it decreased the number of foci by 65% in comparison to the positive control (MCA + TPA). As expected, cobalt NPs showed an increased cytotoxicity and only a few surviving cells were found at the time of analysis showing a number of Foci/dish of 0.13. For the first time, our data clearly showed that Au and Fe3O4 NPs act as promoters in the two stage transformational assay, suggesting the importance to fully investigate the NPs carcinogenic potential with different models. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 509–519, 2016.
A double-blind, placebo-controlled trial of beclomethasone dipropionate 600 μg/day in the treatment of non-atopic rhinitis

Introduction The role of inhaled steroids in the management of atopic rhinitis is well established (Cockroft et al., 1976; Incaudo etal., 1980; Mygind, 1973) with a positive response rate of 80-90 per cent (Cockroft etal, 1976; Morrison Smith et al., 1975; Tarlo et al., 1977). In contrast, their role in non-atopic rhinitis is under-researched: only a handful of trials have identified patients with this condition as a sub-group in a larger rhinitis trial (Gibson et al., 1974; Knight and Kolin, 1983; Kohan etal., 1989; Tarlo etal, 1977) and only three trials have been aimed exclusively at patients with non-atopic rhinitis (Bende and Rundcrantz, 1985; Jones and Kenyon, 1988; Pipkorn and Berge, 1983). In a double-blind, cross-over study of 25 patients with perennial rhinitis, Gibson etal. (1974) isolated a subgroup of nine patients with non-atopic rhinitis and found that six of them (66 per cent) preferred beclomethasone dipropionate (BDP) 200 (xg daily to placebo. In a similar trial, Tarlo et al. (1977) found that the response rate of nine patients with non-atopic rhinitis to BDP 400 [xg daily rose from 54 per cent at three weeks to 73 per cent at six months. They suggested that some patients may require a longer period of treatment and others may need a higher dose of BDP to elicit a positive response. Jones and Kenyon (1988), in the only controlled trial designed to look solely at non-atopic rhinitis, matched 22 patients with non-atopic rhinitis after six weeks of BDP 400 \ig against 22 untreated controls with non-atopic rhinitis and 22 'normal' patients. Measured by rhinomanometry and symptom scoring they found a response rate of only 23 per cent in the treated group and suggested that a longer course of BDP might have improved upon this result. This argument is given weight by the results of Knight and Kolin (1983) who found a greater response in patients with non-atopic rhinitis when treatment was prolonged to 48 weeks.
Better Research Needed on the Impact of Charter Schools

Randomized trials, although a promising approach, reflect impacts of only a limited subset of highly sought-after schools. Charter schools have been promoted as a solution to what many view as the public school malaise in the United States. Charter schools, although publicly funded, can operate fairly independently of large district bureaucracies and teacher unions, for instance, by setting their own curriculum and teaching methods and by avoiding the system that grants the most senior teachers first choice of job openings, regardless of their classroom effectiveness. Proponents hope that the semi-independent governance structure of charters will encourage these schools to generate fresh ideas. President Obama has followed Presidents Bush and Clinton in identifying charter schools as a key element of school reform.
Signal Perception in Frogs and Bats and the Evolution of Mating Signals

Receiver perception limits the evolution of increasingly elaborate calls in túngara frogs. Psychophysics measures the relationship between a stimulus’s physical magnitude and its perceived magnitude. Because decisions are based on perception of stimuli, this relationship is critical to understanding decision-making. We tested whether psychophysical laws explain how female túngara frogs (Physalaemus pustulosus) and frog-eating bats (Trachops cirrhosus) compare male frog calls, and how this imposes selection on call evolution. Although both frogs and bats prefer more elaborate calls, they are less selective as call elaboration increases, because preference is based on stimulus ratios. Thus, as call elaboration increases, both relative attractiveness and relative predation risk decrease because of how receivers perceive and compare stimuli. Our data show that female cognition can limit the evolution of sexual signal elaboration.
A Key Enzyme in the Biogenesis of Lysosomes Is a Protease That Regulates Cholesterol Metabolism

Defects in a sterol regulatory pathway also cause defects in lysosome assembly leading to mucolipidosis and disease. Mucolipidosis II is a severe lysosomal storage disorder caused by defects in the α and β subunits of the hexameric N-acetylglucosamine-1-phosphotransferase complex essential for the formation of the mannose 6-phosphate targeting signal on lysosomal enzymes. Cleavage of the membrane-bound α/β-subunit precursor by an unknown protease is required for catalytic activity. Here we found that the α/β-subunit precursor is cleaved by the site-1 protease (S1P) that activates sterol regulatory element–binding proteins in response to cholesterol deprivation. S1P-deficient cells failed to activate the α/β-subunit precursor and exhibited a mucolipidosis II–like phenotype. Thus, S1P functions in the biogenesis of lysosomes, and lipid-independent phenotypes of S1P deficiency may be caused by lysosomal dysfunction.
Architecture of behavior-based mobile robot in dynamic environment

The authors are developing a compact cart-type robot system which moves around an office. They propose a behavior-based architecture with three clustered (reflexive, purposive, and adaptive) agents that realizes efficiency in attaining the mission of the robot, and robustness against the various kinds of failures that may occur in a dynamic environment. The reflexive-level group consists of agents with contact, infrared, and ultrasonic sensors which maintain minimal safety of the robot. The role of the purposive-level group is to achieve the global mission of the robot, such as 'if the robot detects a small fire in the office, find and reach a fire extinguisher as soon as possible'. The adaptive-level group stands by to recover from failure in the purposive-level group or in a deadlock situation. Experimental results showed the effectiveness of the method. <<ETX>>
Inclusion of Small Indigenous Fish Improves Nutritional Quality During the First 1000 Days

Background: Within food-based approaches to improve nutrition during the first 1000 days of life, improved formulations of food products and the use of animal source foods, such as fish, are 2 widely cited strategies; however, there are few examples where the 2 strategies are combined. Furthermore, although small indigenous fish are highly nutritious and available to the poor in many regions of the world, their importance is often overlooked. Objective: To document the development of 2 nutritious fish-based food products in Bangladesh: a chutney for pregnant and lactating women (PLW) and a complementary food (CF) for infants and young children (6-23 months), including potential contributions to recommended or desirable nutrient intakes in the first 1000 days, processing methods, and nutrient composition. Methods: Local nutrient-rich ingredients and simple processing methods based on traditional knowledge (for the chutney), and a literature review (for the CF), were selected and trial batches produced. Products were analyzed for nutrient composition using standard analytical procedures and results compared with recommended or desirable nutrient intakes for women and children. Results: Both products could contribute significantly to micronutrient intakes of PLW (24% of iron and 35% of calcium recommended intakes) and macro- and micronutrient intake of infants and young children (≥65% of vitamin A, ≥61% of zinc, and 41% of iron desirable intakes) when consumed in the proposed serving size. Conclusion: Inclusion of small indigenous fish as an underutilized animal source food in combination with other local nutrient-rich ingredients in food products represents a promising food-based strategy to improve nutrition, with many additional potential benefits for communities involved in production, and therefore warrants further investigation.
Long Unfolded Linkers Facilitate Membrane Protein Import Through the Nuclear Pore Complex

Natively unfolded linkers facilitate nuclear membrane protein import. Active nuclear import of soluble cargo involves transport factors that shuttle cargo through the nuclear pore complex (NPC) by binding to phenylalanine-glycine (FG) domains. How nuclear membrane proteins cross through the NPC to reach the inner membrane is presently unclear. We found that at least a 120-residue-long intrinsically disordered linker was required for the import of membrane proteins carrying a nuclear localization signal for the transport factor karyopherin-α. We propose an import mechanism for membrane proteins in which an unfolded linker slices through the NPC scaffold to enable binding between the transport factor and the FG domains in the center of the NPC.
Trace Metals as Biomarkers for Eumelanin Pigment in the Fossil Record

X-ray maps of fossil feather pigments reveal color patterning in extinct bird species. Well-preserved fossils of pivotal early bird and nonavian theropod species have provided unequivocal evidence for feathers and/or downlike integuments. Recent studies have reconstructed color on the basis of melanosome structure; however, the chemistry of these proposed melanosomes has remained unknown. We applied synchrotron x-ray techniques to several fossil and extant organisms, including Confuciusornis sanctus, in order to map and characterize possible chemical residues of melanin pigments. Results show that trace metals, such as copper, are present in fossils as organometallic compounds most likely derived from original eumelanin. The distribution of these compounds provides a long-lived biomarker of melanin presence and density within a range of fossilized organisms. Metal zoning patterns may be preserved long after melanosome structures have been destroyed.
Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway

The ID complex reveals how phosphorylation and ubiquitination could influence its stability and DNA-binding functions. Fanconi anemia is a cancer predisposition syndrome caused by defects in the repair of DNA interstrand cross-links (ICLs). Central to this pathway is the Fanconi anemia I–Fanconi anemia D2 (FANCI-FANCD2) (ID) complex, which is activated by DNA damage–induced phosphorylation and monoubiquitination. The 3.4 angstrom crystal structure of the ~300 kilodalton ID complex reveals that monoubiquitination and regulatory phosphorylation sites map to the I-D interface, suggesting that they occur on monomeric proteins or an opened-up complex and that they may serve to stabilize I-D heterodimerization. The 7.8 angstrom electron-density map of FANCI-DNA crystals and in vitro data show that each protein has binding sites for both single- and double-stranded DNA, suggesting that the ID complex recognizes DNA structures that result from the encounter of replication forks with an ICL.
Predictors of Treatment Resistance and Relapse in Chinese Patients with Antineutrophil Cytoplasmic Antibody-associated Disease

Objective. The prevalence and significance of treatment resistance and relapse in patients from China with antineutrophil cytoplasmic antibody-associated (ANCA) disease are poorly understood. Methods. A total of 98 patients with ANCA vasculitis, diagnosed between January 2003 and December 2009 in the China-Japan Friendship Hospital, were enrolled in this retrospective study. Results. Fifteen patients (15.3%) were categorized as having cytoplasmic and/or proteinase 3 (PR3) ANCA and 83 patients (84.7%) had perinuclear and/or myeloperoxidase (MPO) ANCA. After the induction phase treatment, the disease was resistant to therapy in 24 (25%) of the patients. A response to initial treatment occurred in 74 patients (75%). Of these 74 patients, remission was achieved and sustained with or without maintenance therapy in 41 patients (55%). Multivariable logistic regression models revealed that female sex was a statistically significant predictor of treatment resistance (OR 2.85; 95% CI: 1.06–2.86; p = 0.036). Additionally, elevated serum creatinine level, with each increment of 150 μmol/l, predicted resistance (p = 0.002). Among the 74 patients where remission was achieved, Cox proportional hazards models detected that those with PR3 ANCA were 1.31 times more likely to experience a relapse than were patients with MPO ANCA (95% CI: 1.01–5.35; p = 0.0001). Lung involvement was associated with an increased risk of relapse (HR 1.87; 95% CI: 1.12–4.35; p = 0.014). Although not significant, advanced age tended to be associated with relapse (p = 0.08). Conclusion. Our findings highlight the important effect of female sex and severity of renal disease at presentation as predictors of treatment resistance, and PR3 ANCA and lung involvement as predictors of relapse.
Comparison of squash smears and frozen sections versus paraffin sections in the intra-operative diagnosis of central nervous system lesions

Background: Utility of squash cytology is well established in the intra-operative diagnosis of brain tumors, thereby guiding the neurosurgeon in the surgical management. A comparative study between squash smears, frozen sections and paraffin sections was done with an aim to study the diagnostic accuracy as well as limitations of these techniques. The present study was also undertaken to evaluate the discordant cases in intraoperative consultation of central nervous system (CNS) lesions. Methods: A total of 221 neurosurgical specimens were received in the Department of Pathology over three years duration, of which intra-operative consultation was requested in 110 cases. Both frozen and squash preparation was performed on all cases and stained with hematoxylin and eosin. An intra-operative diagnosis was made after examination of the squash smears and frozen section slides. The diagnosis given on squash smears and frozen section were then compared with final diagnosis given on paraffin-embedded sections. Immunohistochemistry was performed in a few diagnostically challenging cases. Results: This study compares the diagnostic accuracy of squash smears and frozen sections from 110 surgical specimens. The 110 cases included thirty six astrocytomas (32.7%), twenty four meningiomas (21.8%), twelve schwannomas (10.9%), two hematolymphoid tumors (1.8%), eight medulloblastomas (7.3%), three oligodendrogliomas (2.7%), four pituitary adenomas (3.6%), four ependymomas (3.6%), four metastatic tumors (3.6%), one paraganglioma (0.9%), two pineal parenchymal tumors (1.8%) and ten infections (9.1%). The accuracy of squash smears was 93.6%, and when combined with frozen sections the accuracy increased to 97.3%. Conclusion: Squash smears are simple, rapid, economical and very effective tool in the diagnosis of brain tumors. However, in few matrix rich/fibrous tumors like meningiomas and schwannomas, frozen sections are more useful. Hence, overall the combined use of squash smear and frozen section study increases the intra-operative diagnostic accuracy of CNS lesions.