Miracle-dz/UniFAR-FTUs huggingface dataset:
The presence and role of interstitial cells of Cajal in the proximal intestine of shorthorn sculpin (Myoxocephalus scorpius)

ABSTRACT Rhythmic contractions of the mammalian gastrointestinal tract can occur in the absence of neuronal or hormonal stimulation owing to the generation of spontaneous electrical activity by interstitial cells of Cajal (ICC) that are electrically coupled to smooth muscle cells. The myogenically driven component of gastrointestinal motility patterns in fish probably also involves ICC; however, little is known of their presence, distribution and function in any fish species. In the present study, we combined immunohistochemistry and in vivo recordings of intestinal motility to investigate the involvement of ICC in the motility of the proximal intestine in adult shorthorn sculpin (Myoxocephalus scorpius). Antibodies against anoctamin 1 (Ano1, a Ca2+-activated Cl− channel), revealed a dense network of multipolar, repeatedly branching cells in the myenteric region of the proximal intestine, similar in many regards to the mammalian ICC-MY network. The addition of benzbromarone, a potent blocker of Ano1, altered the motility patterns seen in vivo after neural blockade with TTX. The results indicate that ICC are integral for the generation and propagation of the majority of rhythmic contractile patterns in fish, although their frequency and amplitude can be modulated via neural activity. Summary: Gastrointestinal motility patterns in shorthorn sculpin are primarily generated by the interstitial cells of Cajal (ICC).
Impaired delayed hypersensitivity in juvenile rheumatoid arthritis.

Juvenile rheumatoid arthritis (JRA) is thought by many to be a different disease from rheumatoid arthritis in adults (RA), partly because of the infrequency of pathological serological phenomena (Calabro, 1966). Recent investigations have, however, shown that antigammaglobulin and antinuclear antibodies are often found in sera from patients with JRA (KAss and Munthe, 1969; Torrigiani, Ansell, Chown, and Roitt, 1969; Zutshi, Ansell, Bywaters, Epstein, Holborow, and Reading, 1969; Bianco, Panush, Stillman, and Schur, 1971). It is unknown whether these autoantibodies result from an abnormal antigen stimulation in a normal immunological apparatus or from a normal antigen stimulation in an abnormal immunological apparatus. Scant information is available regarding the possible alteration of cellular immune reactions in patients with JRA (Panush, Bianco, Schur, Rocklin, David, and Stillman, 1972). The purpose of this investigation was to study the immunological apparatus in patients with JRA. The present report describes the results of testing of delayed hypersensitivity in a group of patients, compared with the results obtained in ageand sexmatched controls.
COMPARISON OF METHODS FOR THE PREDICTION OF THE METABOLIC SITES FOR CYP3A4-MEDIATED METABOLIC REACTIONS

Predictions of the metabolic sites for new chemical entities, synthesized or only virtual, are important in the early phase of drug discovery to guide chemistry efforts in the synthesis of new compounds with reduced metabolic liability. This information can now be obtained from in silico predictions, and therefore, a thorough and unbiased evaluation of the computational techniques available is needed. Several computational methods to predict the metabolic hot spots are emerging. In this study, metabolite identification using MetaSite and a docking methodology, GLUE, were compared. Moreover, the published CYP3A4 crystal structure and computed CYP3A4 homology models were compared for their usefulness in predicting metabolic sites. A total of 227 known CYP3A4 substrates reported to have one or more metabolites adding up to 325 metabolic pathways were analyzed. Distance-based fingerprints and four-point pharmacophore derived from GRID molecular interaction fields were used to characterize the substrate and protein in MetaSite and the docking methodology, respectively. The CYP3A4 crystal structure and homology model with the reactivity factor enabled achieved a similar prediction success (78%) using the MetaSite method. The docking method had a relatively lower prediction success (∼57% for the homology model), although it still may provide useful insights for interactions between ligand and protein, especially for uncommon reactions. The MetaSite methodology is automated, rapid, and has relatively accurate predictions compared with the docking methodology used in this study.
Molecular Genetics of the Usher Syndrome in Lebanon: Identification of 11 Novel Protein Truncating Mutations by Whole Exome Sequencing

Background Usher syndrome (USH) is a genetically heterogeneous condition with ten disease-causing genes. The spectrum of genes and mutations causing USH in the Lebanese and Middle Eastern populations has not been described. Consequently, diagnostic approaches designed to screen for previously reported mutations were unlikely to identify the mutations in 11 unrelated families, eight of Lebanese and three of Middle Eastern origins. In addition, six of the ten USH genes consist of more than 20 exons, each, which made mutational analysis by Sanger sequencing of PCR-amplified exons from genomic DNA tedious and costly. The study was aimed at the identification of USH causing genes and mutations in 11 unrelated families with USH type I or II. Methods Whole exome sequencing followed by expanded familial validation by Sanger sequencing. Results We identified disease-causing mutations in all the analyzed patients in four USH genes, MYO7A, USH2A, GPR98 and CDH23. Eleven of the mutations were novel and protein truncating, including a complex rearrangement in GPR98. Conclusion Our data highlight the genetic diversity of Usher syndrome in the Lebanese population and the time and cost-effectiveness of whole exome sequencing approach for mutation analysis of genetically heterogeneous conditions caused by large genes.
SPECTRAL COMPOSITION OF EATING SOUNDS GENERATED BY CRISPY, CRUNCHY AND CRACKLY FOODS

Separate air and bone conducted food sounds generated by six subjects biting into eight foods were recorded and analysed by a fast Fourier transform (FFT) signal analyser. A panel of 60 subjects classified the 8 foods according to their texture: crispy, crunchy and crackly and these textural characteristics were described by spectral characteristics of biting sounds. Crispy foods (such as extruded flat breads) were found to generate high pitched sounds that show a high level of frequencies higher than 5 kHz, especially for air conduction. Crunchy foods (such as raw carrot) generate low pitched sounds with a characteristic peak on frequency range 1.25 to 2 kHz for air conduction. And crackly foods (such as dry biscuits) generate low pitched sounds with a high level of bone conduction. We hypothesize that discrimination between crunchy and crackly foods could be due to vibrations propagated by bone conduction that also generated vibrotactile sensations.
Existence of hyperbolic calorons

Recent work of Harland shows that the SO(3)-symmetric, dimensionally reduced, charge-N self-dual Yang–Mills calorons on the hyperbolic space H3×S1 may be obtained through constructing N-vortex solutions of an Abelian Higgs model as in the study of Witten on multiple instantons. In this paper, we establish the existence of such minimal action charge-N calorons by constructing arbitrarily prescribed N-vortex solutions of the Witten type equations.
The utility of radioiodine scans prior to iodine 131 ablation in patients with well-differentiated thyroid cancer.

BACKGROUND The utility of radioiodine (RAI) scans prior to (131)I ablation is controversial. The objective of this study was to evaluate the utility of RAI scans prior to (131)I ablation in patient with well-differentiated thyroid cancer. METHOD All RAI scans performed prior to (131)I ablation from July 2000 to November 2006 at Washington Hospital Center were reviewed retrospectively. Patients were excluded who were suspected of having 1) loco-regional disease, 2) distant metastases, and/or 3) physiological uptake that might alter management prior to the pre-ablation RAI scans. RAI scans were performed either 24 hours after dosing with 37-148 MBq of (123)I or 48 hours after dosing with 37-148 MBq of (131)I with imaging of the whole body, the thyroid bed/neck with a pinhole collimator, and the neck and chest with a parallel-hole collimator. One reviewer blindly evaluated each set of scans using six criteria, and for the purpose of this study, the thresholds for each criterion for which the patient's management may have been altered prior to (131)I ablation are noted in parentheses: 1) the number of foci of RAI uptake in thyroid bed/neck (0 or > or =6), 2) the location(s) of these foci in the thyroid bed/neck (outside the thyroid bed), 3) the size of the largest foci in thyroid bed/neck (> or =1 lobe), 4) the percent uptake in the thyroid bed/neck (> or =15%), 5) uptake suggestive of distant metastases, and 6) significant altered biodistribution (e.g., any breast, marked salivary gland, or marked gastrointestinal uptake). RESULTS Of 355 sets of scans reviewed, 53% of patients had findings on the RAI scans that might have altered the patient's management prior to their (131)I ablation. The data grouped by the criteria noted above were 1) 12% with six or more foci suggesting local metastases and 6% (22) with no focal uptake, 2) 14% with suggestion of lymph node metastases, 3) 1.1% with at least one focus > or =1 lobe, 4) 8% with > or =15% uptake, 5) 4% with distant metastases, 6) 16% demonstrating altered distribution with 6% breast, 3% salivary, 10% GI, and 0.3% urinary bladder. CONCLUSION Pre-ablation RAI scans demonstrate a significant number of findings that may alter the management of patients with well-differentiated thyroid cancer prior to (131)I ablation.
Design of a micro-cartridge system for the robotic assembly of exchangeable AFM-probe tips

Modern processes of micro- and nanofabrication imply several metrology steps on critical dimensions in order to assure and assess device perfomences. Particularly, manufacturing processes of novel disruptive photonic devices and nanoelectronic circuit architectures require improved three dimensional acquisition and visualization techniques for their metrology. Amongst others line width and sidewall roughness are the most important parameters for nanooptical components but the determination of these parameters becomes increasingly demanding, since the continuous shrinkage of these devices demand an even higher lateral resolution of the measurements. The atomic force microscope (AFM) is a common tool for this characterization and a standard instrument for all kinds of research and development disciplines. However, the characterization of three dimensional high-aspect ratio and sidewall structures remains a hardly accomplishable task. Novel exchangeable and customizable scanning probe tips, so-called NanoBits, can be attached to standard AFM cantilevers offering unprecedented freedom in adapting the shape and size of the tips to the surface topology of the specific application. The ultimate goal is the realization of an in-situ exchange of NanoBits within the regular AFM environment. For this, NanoBits have to be provided in a freestanding way, making them accessible for the AFM cantilever. The direct fabrication of such structures is still challenging, hence the robotic preassembly of NanoBits cartridges is proposed, where every cartridge can carry several different NanoBits. Within this paper all components required for the realization of this concept are presented.
Male courtship song frequency as an indicator of male genetic quality in an insect species, Drosophila montana

Most theoretical models on evolution of male secondary sexual characters and female preferences for these characters suggest that the male characters evolve in response to female preferences that may themselves evolve in response to direct or indirect benefits of choice. InDrosophila montana (a species of theD. virilis group), females use male song in their mate choice, preferring males that produce songs with short sound pulses and a high carrier frequency. We demonstrate here that the females get indirect benefits from their choice: in our data the frequency of the male song correlated with the survival rate of the male's progeny from egg to adulthood (indirect benefit for the female), but not with the fecundity of his mating partner (no direct benefit for the female). Male wing centroid asymmetry did not correlate with male wing song characters, nor with female egg production nor the fitness of her progeny, suggesting that fluctuating asymmetry in male wings does not play a major role in sexual signalling. The fact that the male song gives the female information on the male's condition/genetic quality inD. montana suggests that in this species the evolution of female preferences for male song characters could have evolved through condition–dependent viability selection presented in some ‘good genes’ models.
Evolving concepts on adjusting human resting energy expenditure measurements for body size

Establishing if an adult's resting energy expenditure (REE) is high or low for their body size is a pervasive question in nutrition research. Early workers applied body mass and height as size measures and formulated the Surface Law and Kleiber's Law, although each has limitations when adjusting REE. Body composition methods introduced during the mid‐20th century provided a new opportunity to identify metabolically homogeneous ‘active’ compartments. These compartments all show improved correlations with REE estimates over body mass–height approaches, but collectively share a common limitation: REE‐body composition ratios are not ‘constant’ but vary across men and women and with race, age and body size. The now‐accepted alternative to ratio‐based norms is to adjust for predictors by applying regression models to calculate ‘residuals’ that establish if an REE is relatively high or low. The distinguishing feature of statistical REE‐body composition models is a ‘non‐zero’ intercept of unknown origin. The recent introduction of imaging methods has allowed development of physiological tissue–organ‐based REE prediction models. Herein, we apply these imaging methods to provide a mechanistic explanation, supported by experimental data, for the non‐zero intercept phenomenon and, in that context, propose future research directions for establishing between‐subject differences in relative energy metabolism.
Performance of mutation pathogenicity prediction methods on missense variants

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans. The number of SNPs identified in the human genome is growing rapidly, but attaining experimental knowledge about the possible disease association of variants is laborious and time‐consuming. Several computational methods have been developed for the classification of SNPs according to their predicted pathogenicity. In this study, we have evaluated the performance of nine widely used pathogenicity prediction methods available on the Internet. The evaluated methods were MutPred, nsSNPAnalyzer, Panther, PhD‐SNP, PolyPhen, PolyPhen2, SIFT, SNAP, and SNPs&GO. The methods were tested with a set of over 40,000 pathogenic and neutral variants. We also assessed whether the type of original or substituting amino acid residue, the structural class of the protein, or the structural environment of the amino acid substitution, had an effect on the prediction performance. The performances of the programs ranged from poor (MCC 0.19) to reasonably good (MCC 0.65), and the results from the programs correlated poorly. The overall best performing methods in this study were SNPs&GO and MutPred, with accuracies reaching 0.82 and 0.81, respectively. Hum Mutat 32:1–11, 2011. © 2011 Wiley‐Liss, Inc.
Validation of a quantitative assay of arbutin using gas chromatography in Origanum majorana and Arctostaphylos uva-ursi extracts.

INTRODUCTION Arbutin is a skin-whitening agent that occurs naturally in the bark and leaves of various plants. It is commonly quantified in plant extracts and skin-whitening products by HPLC. OBJECTIVE To develop an alternative gas chromatographic method for the separation and quantification of arbutin in Origanum majorana and Arctostaphylos uva-ursi extracts. METHODOLOGY N,O-Bis(trimethylsilyl)acetamide and trimethylchlorosilane were used as silylation reagents, and the gas chromatographic separation of silylated extracts and standards was performed using a DB-5 narrow bore column. GC-MS was used for the compound identification, and the quantification was carried out by GC-FID. The quantitative results were compared with those of HPLC analysis. RESULTS The developed method gave a good sensitivity with linearity in the range 0.33-500 mg/mL and recovery >98%, allowing the quantification of arbutin in O. majorana and A. uva-ursi extracts. The relative standard deviations (RSD) relating to intra-day and inter-day precision were <0.002% and <4.8%, respectively. The GC results correlated well with those obtained by HPLC analysis. CONCLUSION The analysis of marjoram and bearberry samples showed that the established GC method was rapid, selective, and demonstrated that arbutin could be screened alternatively by gas chromatography.
CLIMATE CHANGE IMPACTS ON THE HYDROLOGY AND PRODUCTIVITY OF A PINE PLANTATION 1

ABSTRACT: There are increasing concerns in the forestry community about global climate change and variability associated with elevated atmospheric CO2. Changes in precipitation and increases in air temperature could impose additional stress on forests during the next century. For a study site in Carteret County, North Carolina, the General Circulation Model, HADCM2, predicts that by the year 2099, maximum air temperature will increase 1.6 to 1.9°C, minimum temperature will increase 2.5 to 2.8°C, and precipitation will increase 0 to 10 percent compared to the mid‐1990s. These changes vary from season to season. We utilized a forest ecosystem process model, PnET‐II, for studying the potential effects of climate change on drainage outflow, evapotranspiration, leaf area index (LAI) and forest Net Primary Productivity (NPP). This model was first validated with long term drainage and LAI data collected at a 25‐ha mature loblolly pine (Pinus taeda L.) experimental watershed located in the North Carolina lower coastal plain. The site is flat with poorly drained soils and high groundwater table. Therefore, a high field capacity of 20 cm was used in the simulation to account for the topographic effects. This modeling study suggested that future climate change would cause a significant increase of drainage (6 percent) and forest productivity (2.5 percent). Future studies should consider the biological feedback (i.e., stomata conductance and water use efficiency) to air temperature change.
ECMO in ARDS: a long‐term follow‐up study regarding pulmonary morphology and function and health‐related quality of life

Background: A high survival rate can be achieved in patients with severe acute respiratory distress syndrome (ARDS) using extracorporeal membrane oxygenation (ECMO). The technique and the costs are, however, debated and follow‐up studies in survivors are few. The aim of this study was to evaluate long‐term pulmonary health after ECMO and severe ARDS.
Knowledge and Attitude Regarding Organ Donation among Relatives of Patients Referred to the Emergency Department

Introduction: Organ donation is one of the surviving procedures, which can increase the life expectancy of end-stage patients. Inappropriate beliefs and attitude of individuals to organ donation, their poor knowledge, and the socio-economic level are one of the most important barriers for organ donation. Therefore, here knowledge and attitude levels among relatives of trauma patients regarding organ donation were evaluated. Methods: This cross-sectional study was done on relatives of trauma patients referred to the emergency department of Sina Hospital, Tabriz, Iran, through 2013 to 2014. The questionnaire included parts of demographic data and socio-economic situations as well as status of knowledge and attitude regarding organ donation. A score between 0-7 was belonged to each person based on his/her level of knowledge. Attitude level had a score between 0-12. Chi- square, Fisher, and Mann–Whitney U test were performed to assess the relation between demographic variables and the level of knowledge and attitude. P<0.05 was considered as a significant level. Results: 79 persons (57.1% male) with the mean age of 31.3±11.3 years were evaluated. 57 (73.1%) of subjects agreed with organ transplant. The main causes of disagreement among relatives regarding organ donation were dissatisfaction of the donor's relatives (25%) and religious issues (15%). 49 (62.02%) studied people had inappropriate attitude and 27 (34.2%) ones had good knowledge. male gender (OR=5.87; 95%CI: 3.32-8.42; p=0.001) and self-employed job (OR=7.78; 95%CI: 4.64-10.92; p=0.001) are independent factors associated with poor knowledge about organ donation. Self-employed job (OR=3.86; 95%CI: 1.41-6.11; p=0.009) and poor knowledge (OR=15.3; 95%CI: 9.03-21.57; p<0.001) were related to inappropriate attitude toward organ donation. Conclusion: The present study showed that 73.1% of participants agreed with organ donation. The major causes of disagreements were dissatisfaction of other relatives and religious beliefs. 62.0% of the studied people had positive view regarding organ donation and 34.2% of them well informed about. The most important causative factors for poor knowledge in this context were male gender and self-employed occupation. In addition, poor knowledge and self-employed job were two factors associated with inappropriate attitude toward organ donation.
Structures of D5d-C80 and Ih-Er3N@C80 Fullerenes and Their Rotation Inside Carbon Nanotubes Demonstrated by Aberration-Corrected Electron Microscopy

Time-dependent orientational changes of D5d-C80 and Ih-Er3N@C80 fullerenes inside single-walled carbon nanotubes (SWNTs) were demonstrated by aberration-corrected transmission electron microscopy (TEM) at real atomic-level resolution. Detailed structure of the ellipsoidal D5d-C80 fullerene, e.g., the pyrene-like tetracyclic component in its cylindrical body, was unambiguously identified by the TEM images. The Er−Er distances in Ih-Er3N@C80 were estimated to be 0.35 ± 0.03 nm, and the C3 symmetry axis of the Er3N cluster was suggested to agree with one of the S6 axes of the spherical Ih-C80 cage. Our results indicate that atomic-resolution TEM enables the investigation of the orientations of individual molecules inside SWNTs in relation to the interactions of the molecules with the outer graphene walls.
Photochromic sensors: a versatile approach for recognition and discrimination

Photochromic sensors are widely used in detecting and monitoring analytes. Due to the photoswitchable properties, photochromic sensors show advantages in providing more recognition states and sensing information, and thus better sensitivity to external stimulations. Via reasonable design of photochromic sensors with various ionophores, dyes, platforms and metallic complexations, it is promising to achieve visual, sensitive and high-throughput detection. In this review, we summarized the applications of photochromic sensors in the areas of specific recognition and multi-analyte discrimination, based on their isomerization to light, as well as pH, temperature, solvent, etc. Specially, the multi-analyte determination was introduced, which has aroused extensive interest in recent years.