Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of computational fluid dynamics in the design of dynamic contrast enhanced imaging phantoms

Phantoms for dynamic contrast enhanced (DCE) imaging modalities such as DCE computed tomography (DCE-CT) and DCE magnetic resonance imaging (DCE-MRI) are valuable tools for evaluating and comparing imaging systems. It is important for the contrast-agent distribution within the phantom to possess a time dependence that replicates a curve observed clinically, known as the ‘tumor-enhancement curve’. It is also important for the concentration field within the lesion to be as uniform as possible. This study demonstrates how computational fluid dynamics (CFD) can be applied to achieve these goals within design constraints. The distribution of the contrast agent within the simulated phantoms was investigated in relation to the influence of three factors of the phantom design. First, the interaction between the inlets and the uniformity of the contrast agent within the phantom was modeled. Second, pumps were programmed using a variety of schemes and the resultant dynamic uptake curves were compared to tumor-enhancement curves obtained from clinical data. Third, the effectiveness of pulsing the inlet flow rate to produce faster equilibration of the contrast-agent distribution was quantified. The models employed a spherical lesion and design constraints (lesion diameter, inlet-tube size and orientation, contrast-agent flow rates and fluid properties) taken from a recently published DCE-MRI phantom study. For DCE-MRI in breast cancer detection, where the target tumor-enhancement curve varies on the scale of hundreds of seconds, optimizing the number of inlet tubes and their orientation was found to be adequate for attaining concentration uniformity and reproducing the target tumor-enhancement curve. For DCE-CT in liver tumor detection, where the tumor-enhancement curve varies on a scale of tens of seconds, the use of an iterated inlet condition (programmed into the pump) enabled the phantom to reproduce the target tumor-enhancement curve within a few per cent beyond about 6 s of wash-in. This time was cut in half by the final CFD-derived strategy of flow pulsing. Driving the pump with a 25% duty cycle pulsatile waveform produced a nearly uniform concentration in the phantom in just a few seconds under typical conditions. Comparisons with published x-ray measurements using tumor-enhancement curves for both benign and malignant breast lesions showed a difference of approximately 4% between the CFD predictions and measurements of the contrast-agent concentration averaged over the lesion volume. The techniques derived using CFD optimization can be used in future phantom designs, including as starting points for future CFD phantom studies employing new lesion geometries and tumor-enhancement curves.
Preferences for chemotherapy in patients with advanced non-small cell lung cancer: descriptive study based on scripted interviews

Abstract Objective:To determine how patients with lung cancer value the trade off between the survival benefit of chemotherapy and its toxicities. Design:Scripted interviews that included three hypothetical scenarios. Each scenario described the same patient with metastatic non-small cell lung cancer with an expected survival of 4 months without treatment. Subjects were asked to indicate the minimum survival benefit required to accept the side effects of chemotherapy in the first two scenarios (mild toxicity and severe toxicity). In the third scenario, subjects were asked to choose between chemotherapy and supportive care when the benefit of chemotherapy was either to prolong life by 3 months or to palliate symptoms. Subjects:81 patients previously treated with cis-platinum based chemotherapy for advanced non-small cell lung cancer. Main outcome measure:Survival threshold for accepting chemotherapy. Results:The minimum survival threshold for accepting the toxicity of chemotherapy varied widely in patients. Several patients would accept chemotherapy for a survival benefit of 1 week, while others would not choose chemotherapy even for a survival benefit of 24 months. The median survival threshold for accepting chemotherapy was 4.5 months for mild toxicity and 9 months for severe toxicity. When given the choice between supportive care and chemotherapy only 18 (22%) patients chose chemotherapy for a survival benefit of 3 months; 55 (68%) patients chose chemotherapy if it substantially reduced symptoms without prolonging life. Conclusions:Patients' willingness to accept chemotherapy for the treatment of metastatic lung cancer varies widely. Many would not choose chemotherapy for its likely survival benefit of 3 months but would if it improved quality of life. The conflict between these patients' preferences and the care they previously received has several explanations, one being that some patients had not received the treatment they would have chosen had they been fully informed.
Brief report: effect of ambrisentan treatment on exercise-induced pulmonary hypertension in systemic sclerosis: a prospective single-center, open-label pilot study.

OBJECTIVE Exercise-induced pulmonary hypertension (ePH) may represent an early, clinically relevant phase in the spectrum of pulmonary vascular disease. The purpose of this pilot study was to describe the changes in hemodynamics and exercise capacity in patients with systemic sclerosis (SSc) spectrum-associated ePH treated with open-label daily ambrisentan. METHODS Patients were treated with ambrisentan, 5 mg or 10 mg once daily, for 24 weeks. At baseline and 24 weeks, patients with SSc spectrum disorders exercised in a supine position, on a lower extremity cycle ergometer. All patients had normal hemodynamics at rest. We defined baseline ePH as a mean pulmonary artery pressure of >30 mm Hg with maximum exercise and a transpulmonary gradient (TPG) of >15 mm Hg. The primary end point was change in pulmonary vascular resistance (PVR) with exercise. Secondary end points included an improvement from baseline in 6-minute walking distance, health-related quality of life assessments, and cardiopulmonary hemodynamics. RESULTS Of the 12 enrolled patients, 11 completed the study. At 24 weeks there were improvements in mean exercise PVR (85.8 dynes × second/cm(5) ; P = 0.003) and mean distance covered during 6-minute walk (44.5 meters; P = 0.0007). Improvements were also observed in mean exercise cardiac output (1.4 liters/minute; P = 0.006), mean pulmonary artery pressure (-4.1 mm Hg; P = 0.02), and total pulmonary resistance (-93.0 dynes × seconds/cm(5) ; P = 0.0008). Three patients developed resting pulmonary arterial hypertension during the 24 weeks. CONCLUSION Exercise hemodynamics and exercise capacity in patients with SSc spectrum-associated ePH improved over 24 weeks with exposure to ambrisentan. Placebo-controlled studies are needed to confirm whether this is a drug-related effect and to determine optimal therapeutic regimens for patients with ePH.
Bone augmentation as an adjunct to dental implant rehabilitation in patients with diabetes mellitus: A review of literature

The aim of the present article is to review the success of bone augmentation performed as an adjunct to dental implant rehabilitation in patients with diabetes mellitus. A literature review was conducted in PubMed on this topic, which yielded a total of 102 publications. For inclusion, publications had to be human studies, written in English language and should report on the success of bone augmentation as an adjunct to dental implant rehabilitation in diabetic patients. After screening the titles and abstracts, 11 full texts publications were obtained, of which seven were included in the review. These studies provided data on various bone augmentation techniques such as sinus floor elevation (SFE), guided bone regeneration (GBR), and onlay bone grafting. Even though the current review revealed that there are not many studies reporting data relevant to the analyzed topic, the data obtained suggests that; (1) staged GBR technique should be considered more feasible and predictable for bone augmentation, (2) clinicians must take meticulous care when planning and conducting SFE, and (3) block bone augmentation technique should be avoided.
Bimodal pattern of killing of DNA-repair-defective or anoxically grown Escherichia coli by hydrogen peroxide

Two modes of killing of Escherichia coli K-12 by hydrogen peroxide can be distinguished. Mode-one killing was maximal with hydrogen peroxide at a concentration of 1 to 2 mM. At higher concentrations the killing rate was approximately half maximal and was independent of H2O2 concentration but first order with respect to exposure time. Mode-one killing required active metabolism during the H2O2 challenge, and it resulted in sfiA-independent filamentation of both cells which survived and those which were killed by the challenge. This mode of killing was enhanced in xth, polA, recA, and recB strains and was accelerated in all strains by an unidentified, anoxia-induced cell function. A strain carrying both xth and recA mutations appeared to undergo spontaneous mode-one killing only under aerobic conditions. Mode-one killing appeared to result from DNA damage which normally occurs at a low, nonlethal level during aerobic growth. Mode-two killing occurred at higher doses of H2O2 and exhibited a multihit dependence on both H2O2 concentration and exposure time. Mode-two killing did not require active metabolism, and killed cells did not filament, although survivors demonstrated a dose-dependent growth lag. Strains with DNA-repair defects were not especially susceptible to mode-two killing.
Effects of Hyperglycemia and Effects of Ketosis on Cerebral Perfusion, Cerebral Water Distribution, and Cerebral Metabolism

Diabetic ketoacidosis (DKA) may cause brain injuries in children. The mechanisms responsible are difficult to elucidate because DKA involves multiple metabolic derangements. We aimed to determine the independent effects of hyperglycemia and ketosis on cerebral metabolism, blood flow, and water distribution. We used magnetic resonance spectroscopy to measure ratios of cerebral metabolites (ATP to inorganic phosphate [Pi], phosphocreatine [PCr] to Pi, N-acetyl aspartate [NAA] to creatine [Cr], and lactate to Cr) and diffusion-weighted imaging and perfusion-weighted imaging to assess cerebral water distribution (apparent diffusion coefficient [ADC] values) and cerebral blood flow (CBF) in three groups of juvenile rats (hyperglycemic, ketotic, and normal control). ATP-to-Pi ratio was reduced in both hyperglycemic and ketotic rats in comparison with controls. PCr-to-Pi ratio was reduced in the ketotic group, and there was a trend toward reduction in the hyperglycemic group. No significant differences were observed in NAA-to-Cr or lactate-to-Cr ratio. Cortical ADC was reduced in both groups (indicating brain cell swelling). Cortical CBF was also reduced in both groups. We conclude that both hyperglycemia and ketosis independently cause reductions in cerebral high-energy phosphates, CBF, and cortical ADC values. These effects may play a role in the pathophysiology of DKA-related brain injury.
An Unbiased Detector of Curvilinear Structures

The extraction of curvilinear structures is an important low-level operation in computer vision that has many applications. Most existing operators use a simple model for the line that is to be extracted, i.e., they do not take into account the surroundings of a line. This leads to the undesired consequence that the line will be extracted in the wrong position whenever a line with different lateral contrast is extracted. In contrast, the algorithm proposed in this paper uses an explicit model for lines and their surroundings. By analyzing the scale-space behavior of a model line profile, it is shown how the bias that is induced by asymmetrical lines can be removed. Furthermore, the algorithm not only returns the precise subpixel line position, but also the width of the line for each line point, also with subpixel accuracy.
Development and Validation of Extracurricular Instructional Package (EIP) in Social Studies

The purpose of this study is to develop extracurricular activities for social studies instruction and to compare learning outcomes in the extracurricular activities and the conventional groups. To achieve these objectives two research questions and three hypotheses were formulated. Four instruments were developed. The validated extracurricular instructional package((EIP) was presented to the experimental group while the control group was taught the same social studies topics using the conventional approach. the major findings were that (1) JS 1 Students taught with extracurricular instructional packages relationship develop more cooperative attitude to work (2) exhibited cordial relationship with others (3) developed positive attitude to work. Recommendations were made: Teachers work load should be restructured to accommodate their involvement in extracurricular programs (2) More flexible time-release from teaching or in structuring the allow time for activities during school day etc.
Breeding Biology and Status of the California Least Tern Sterna antillarum browni at Alameda Point, San Francisco Bay, California

Abstract The largest breeding colony of the endangered California Least Tern (Sterna antillarum browni) north of San Luis Obispo County occurs at Alameda Point, San Francisco Bay, California. Data on population size, reproductive success, and food habits were collected since the colony’s inception in 1976, while more specific data on breeding chronology (dates of active nesting and nest initiation dates), clutch size, hatching success, and size of prey dropped at the breeding site were collected from 2000-2004. The number of breeding pairs increased by 10.4% per year, making this colony the largest colony in San Francisco Bay and representing 6% of the state population. Breeding success varied but is generally superior to the state’s combined productivity numbers. Of the 32 Least Tern sites monitored in 2004, only five other colonies had higher breeding success than Alameda Point in that year. Despite the colony’s success, both hatching and breeding success have declined since the mid-1990s. Terns at this urban location forage in central and south San Francisco Bay, characterized by both marine and estuarine water. Dropped prey collected since 1981 indicate that silversides (family Atherinopsidae) were the most abundant prey in all years. Breeding success was positively correlated with the proportion of Northern Anchovy (Engraulis mordax, family Engraulididae), the second most common prey collected, suggesting that this high-energy fish may be beneficial to these terns. Potential factors limiting growth of this crucial northern Least Tern colony include predation and human disturbance, an inadequate protected nesting area, and environmental variability and its effects on prey abundance.
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding small-subunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.
Input and Output Gain Modulation by the Lateral Interhemispheric Network in Early Visual Cortex

Neurons in the cerebral cortex are constantly integrating different types of inputs. Dependent on their origin, these inputs can be modulatory in many ways and, for example, change the neuron's responsiveness, sensitivity, or selectivity. To investigate the modulatory role of lateral input from the same level of cortical hierarchy, we recorded in the primary visual cortex of cats while controlling synaptic input from the corresponding contralateral hemisphere by reversible deactivation. Most neurons showed a pronounced decrease in their response to a visual stimulus of different contrasts and orientations. This indicates that the lateral network acts via an unspecific gain-setting mechanism, scaling the output of a neuron. However, the interhemispheric input also changed the contrast sensitivity of many neurons, thereby acting on the input. Such a contrast gain mechanism has important implications because it extends the role of the lateral network from pure response amplification to the modulation of a specific feature. Interestingly, for many neurons, we found a mixture of input and output gain modulation. Based on these findings and the known physiology of callosal connections in the visual system, we developed a simple model of lateral interhemispheric interactions. We conclude that the lateral network can act directly on its target, leading to a sensitivity change of a specific feature, while at the same time it also can act indirectly, leading to an unspecific gain setting. The relative contribution of these direct and indirect network effects determines the outcome for a particular neuron.
Clonal analysis reveals common lineage relationships between head muscles and second heart field derivatives in the mouse embryo

Head muscle progenitors in pharyngeal mesoderm are present in close proximity to cells of the second heart field and show overlapping patterns of gene expression. However, it is not clear whether a single progenitor cell gives rise to both heart and head muscles. We now show that this is the case, using a retrospective clonal analysis in which an nlaacZ sequence, converted to functional nlacZ after a rare intragenic recombination event, is targeted to the αc-actin gene, expressed in all developing skeletal and cardiac muscle. We distinguish two branchiomeric head muscle lineages, which segregate early, both of which also contribute to myocardium. The first gives rise to the temporalis and masseter muscles, which derive from the first branchial arch, and also to the extraocular muscles, thus demonstrating a contribution from paraxial as well as prechordal mesoderm to this anterior muscle group. Unexpectedly, this first lineage also contributes to myocardium of the right ventricle. The second lineage gives rise to muscles of facial expression, which derive from mesoderm of the second branchial arch. It also contributes to outflow tract myocardium at the base of the arteries. Further sublineages distinguish myocardium at the base of the aorta or pulmonary trunk, with a clonal relationship to right or left head muscles, respectively. We thus establish a lineage tree, which we correlate with genetic regulation, and demonstrate a clonal relationship linking groups of head muscles to different parts of the heart, reflecting the posterior movement of the arterial pole during pharyngeal morphogenesis.
Ensemble of support vector machines for land cover classification

This letter presents the results of two different ensemble approaches to increase the accuracy of land cover classification using support vector machines. Finite ensemble approaches, based on boosting and bagging and infinite ensemble created by embedding the infinite hypothesis in the kernel of support vector machines, are discussed. Results suggest that the infinite ensemble approach provides a significant increase in the classification accuracy in comparison to the radial basis function kernel‐based support vector machines. While using finite ensemble approaches, bagging works well and provides a comparable performance to the infinite ensemble approach, whereas boosting decreases the performance of support vector machines. Comparison in terms of computational cost suggests that finite ensemble approaches require a large processing time in comparison to the infinite ensemble approach.
Quantitative histological analysis of the mouse testis after the long-term administration of nickel in feed

In this study, the effects of nickel chloride (NiCl2) applied per os on testis histopathology and morphometry of mice were investigated. The metal was applied in pellets at a dose of 10 mg NiCl2/kg bw to male mice 4 weeks of age. After 3, 6, 9 and 12 weeks of nickel administration, the relative volume of whole seminiferous tubule, germinal epithelium, tubule lumen, interstitium and blood vessels as well as the diameter of seminiferous tubules were determined in the experimental and corresponding control groups. Microscopic examination of testis showed significant changes in all nickel-exposed groups. The degeneration of germinal epithelium, with released germ cells into the lumen of the tubules, and occurrence of empty spaces in the seminiferous epithelium were found in all experimental groups. The changes in the testes were time-dependent. The relative volume of empty spaces in the seminiferous epithelium significantly increased (P < 0.001) in all experimental groups when compared with the corresponding control. A significant decrease in the relative volume of seminiferous epithelium was observed after 6 and 12 weeks of Ni-exposure. The increased luminization of the tubules was found after 6 (P < 0.001), 9 (P < 0.01) and 12 (P < 0.001) weeks. Interstitial tissue significantly decreased after 6 and 9 weeks of Ni exposure and increased after 12 weeks of Ni intake. The seminiferous tubule diameter significantly (P < 0.001) decreased after 12 weeks. Results of this study report a serious, time-dependent changes in the testes, mainly in the germinal epithelium, after a peroral intake of nickel.