Miracle-dz/UniFAR-FTUs huggingface dataset:
Glomerular capillary wall permeability to albumin and horseradish peroxidase

Summary: Tritium labelled albumin present in urine fractions from in vivo rat filtration studies and isolated perfused rat kidneys (IPK) has been shown by gel chromatographic analysis to be severely degraded (approximately 90%) to small peptides. the in vivo degradation of rat serum albumin and bovine serum albumin has been shown to be similar. the degradation has a marked influence on the fractional clearance analysis. the fractional clearance for albumin in the isolated perfused kidney as determined by Lowry assay was 0.00180 ± 0.0007, 0.0060 ± 0.0033 by Biuret assay and 0.0075 ± 0.0039 as measured by total radioactivity in the urine. Specific analysis of intact albumin by gel chromatography gave a fractional clearance of 0.00039 ± 0.00016, which is comparable to in vivo values. Degradation of albumin in the urine from IPK experiments was inhibited by 42% by including 150 mmol/L lysine, an inhibitor of tubular cell uptake, in the perfusate. Inhibition of degradation of anionic horseradish peroxidase was also observed. These studies demonstrate that albumin is degraded during renal passage probably by tubular cells. In a series of isolated perfused kidney systems using different inhibitors of protein tubular uptake, namely lysine, ammonium chloride, chloroquine and cytochalasin B, we estimate the glomerular sieving coefficient of albumin to be approximately 0.074 as determined using [3H]‐albumin. This glomerular sieving coefficient is considerably higher than originally thought, yet it is in accord with the size selectivity characteristics of the glomerular capillary wall as determined by transport probes calibrated for hydrodynamic size by gel exclusion chromatography. the tubular inhibitors also destroyed charge selectivity of the anionic and neutral forms of albumin and horseradish peroxidase. the tubular inhibitors were characterized in terms of their effect on tubular lysozyme uptake and glomerular size selectivity as determined using polydisperse dextran fractions. By accounting for the destination of all the tritium labelled albumin in the urine, perfusate, whole kidney and isolated glomeruli we conclude that a major rapid transtubular cell pathway must exist that directs albumin from the tubular lumen to either the renal lymphatics or peritubular capillaries or both. This pathway appears to be an overload pathway because since the albumin concentration in the perfusate was lowered from 50 mg/mL to 2.0 mg/mL it was not active. the pathway is also inactive for other proteins, such as horseradish peroxidase, that are at relatively low concentration.
The Regulation of Oxytocin Receptor Gene Expression during Adipogenesis

Although it has been reported that oxytocin stimulates lipolysis in adipocytes, changes in the expression of oxytocin receptor (OTR) mRNA in adipogenesis are still unknown. The present study aimed to investigate the expression of OTR mRNA during adipocyte differentiation and fat accumulation in adipocytes. OTR mRNA was highly expressed in adipocytes prepared from mouse adipose tissues compared to stromal‐vascular cells. OTR mRNA expression was increased during the adipocyte differentiation of 3T3‐L1 cells. OTR expression levels were higher in subcutaneous and epididymal adipose tissues of 14‐week‐old male mice compared to 7‐week‐old male mice. Levels of OTR mRNA expression were higher in adipose tissues at four different sites of mice fed a high‐fat diet than in those of mice fed a normal diet. The OTR expression level was also increased by refeeding for 4 h after fasting for 16 h. Oxytocin significantly induced lipolysis in 3T3‐L1 adipocytes. In conclusion, a new regulatory mechanism is demonstrated for oxytocin to control the differentiation and fat accumulation in adipocytes via activation of OTR as a part of the hypothalamic‐pituitary‐adipose axis.
Does oligomenorrhoea/amenorrhoea and underweight imply athlete triad syndrome in young female dancers?

Abstract The aim of this study was to compare the bone mineral density (BMD) of young dancers suspected of suffering from the female athlete triad syndrome and eumenorrhoeic/normal weight dancers with eumenorrhoeic non-exercising controls. Full-time dance students from a collegiate academy of performing arts were recruited. The female athlete triad syndrome was suspected when oligo/amenorrhoea was present together with underweight (body mass index below 18.5 kg · m−2). The non-exercising group consisted of eumenorrhoeic age-matched patients presenting to an adolescent gynaecology clinic. All participants had a full hormonal profile, pelvic ultrasound, bio-impedance estimation of body fat, together with dual energy X-ray absorptiometry (DXA) and quantitative peripheral computed tomography scans (pQCT) to determine bone mineral density. A total of 47 dancers aged 17–20 years were recruited, of whom 14 (29.7%) fell within the criteria for suspected female athlete triad syndrome. Comparing the dancers with suspected female athlete triad with 36 non-exercising controls showed no significant differences in BMD at most sites between the two groups. Comparing the normal dancers (n=33) with the same control group showed the dancers had significantly higher BMD at the hip sites (P<0.005), as well as higher core tibial volumetric BMD (P=0.04) than the controls. Young dancers with oligo/amenorrhoea and apparent under-nutrition that fitted the clinical diagnosis of female athlete triad syndrome did not have lower BMD than non-exercising eumenorrhoeic controls, while eumenorrhoeic dancers actually had higher BMD. In addition, no significant differences were seen between eumenorrhoeic dancers and those with suspected female athlete triad. The risk of osteoporosis was apparently offset by the benefits of regular intensive weight-bearing exercises in those participants with suspected female athlete triad.
Association of Rectal and Urethral Colonization With Urinary Tract Infection in Patients With Indwelling Catheters

To assess the role of antecedent rectal and urethral colonization in the pathogenesis of catheter-associated urinary tract infections, we prospectively studied 64 patients, obtaining urine, rectal, and urethral cultures on study entry, two days later, and every four days thereafter. Of 55 patients who remained catheterized for at least three days, urethral colonization with the same microorganism present in bladder urine was observed in the sampling period preceding the onset of bacteriuria in 12 of 18 infections in women and five of 17 in men. Rectal colonization with the infecting strain preceded bacteriuria in 14 of 18 infections in women and five of 17 in men. The identity of the urinary, urethral, and rectal isolates was confirmed by speciation, serotyping, antibiograms, and biotyping. We conclude that rectal and periurethral colonization often precedes catheter-associated bacteriuria, especially in women, and that effective preventive measures aimed at transurethral infection should be developed. ( JAMA 1984;252:2028-2030)
Acoustic-based proton range verification in heterogeneous tissue: simulation studies

Acoustic-based proton range verification (protoacoustics) is a potential in vivo technique for determining the Bragg peak position. Previous measurements and simulations have been restricted to homogeneous water tanks. Here, a CT-based simulation method is proposed and applied to a liver and prostate case to model the effects of tissue heterogeneity on the protoacoustic amplitude and time-of-flight range verification accuracy. For the liver case, posterior irradiation with a single proton pencil beam was simulated for detectors placed on the skin. In the prostate case, a transrectal probe measured the protoacoustic pressure generated by irradiation with five separate anterior proton beams. After calculating the proton beam dose deposition, each CT voxel’s material properties were mapped based on Hounsfield Unit values, and thermoacoustically-generated acoustic wave propagation was simulated with the k-Wave MATLAB toolbox. By comparing the simulation results for the original liver CT to homogenized variants, the effects of heterogeneity were assessed. For the liver case, 1.4 cGy of dose at the Bragg peak generated 50 mPa of pressure (13 cm distal), a 2× lower amplitude than simulated in a homogeneous water tank. Protoacoustic triangulation of the Bragg peak based on multiple detector measurements resulted in 0.4 mm accuracy for a δ-function proton pulse irradiation of the liver. For the prostate case, higher amplitudes are simulated (92–1004 mPa) for closer detectors (<8 cm). For four of the prostate beams, the protoacoustic range triangulation was accurate to ⩽1.6 mm (δ-function proton pulse). Based on the results, application of protoacoustic range verification to heterogeneous tissue will result in decreased signal amplitudes relative to homogeneous water tank measurements, but accurate range verification is still expected to be possible.
PET attenuation correction for flexible MRI surface coils in hybrid PET/MRI using a 3D depth camera

PET attenuation correction for flexible MRI radio frequency surface coils in hybrid PET/MRI is still a challenging task, as position and shape of these coils conform to large inter-patient variabilities. The purpose of this feasibility study is to develop a novel method for the incorporation of attenuation information about flexible surface coils in PET reconstruction using the Microsoft Kinect V2 depth camera. The depth information is used to determine a dense point cloud of the coil’s surface representing the shape of the coil. From a CT template—acquired once in advance—surface information of the coil is extracted likewise and converted into a point cloud. The two point clouds are then registered using a combination of an iterative-closest-point (ICP) method and a partially rigid registration step. Using the transformation derived through the point clouds, the CT template is warped and thereby adapted to the PET/MRI scan setup. The transformed CT template is converted into an attenuation map from Hounsfield units into linear attenuation coefficients. The resulting fitted attenuation map is then integrated into the MRI-based patient-specific DIXON-based attenuation map of the actual PET/MRI scan. A reconstruction of phantom PET data acquired with the coil present in the field-of-view (FoV), but without the corresponding coil attenuation map, shows large artifacts in regions close to the coil. The overall count loss is determined to be around 13% compared to a PET scan without the coil present in the FoV. A reconstruction using the new μ-map resulted in strongly reduced artifacts as well as increased overall PET intensities with a remaining relative difference of about 1% to a PET scan without the coil in the FoV.
Computer-aided assessment of breast density: comparison of supervised deep learning and feature-based statistical learning

Breast density is one of the most significant factors that is associated with cancer risk. In this study, our purpose was to develop a supervised deep learning approach for automated estimation of percentage density (PD) on digital mammograms (DMs). The input ‘for processing’ DMs was first log-transformed, enhanced by a multi-resolution preprocessing scheme, and subsampled to a pixel size of 800 µm × 800 µm from 100 µm × 100 µm. A deep convolutional neural network (DCNN) was trained to estimate a probability map of breast density (PMD) by using a domain adaptation resampling method. The PD was estimated as the ratio of the dense area to the breast area based on the PMD. The DCNN approach was compared to a feature-based statistical learning approach. Gray level, texture and morphological features were extracted and a least absolute shrinkage and selection operator was used to combine the features into a feature-based PMD. With approval of the Institutional Review Board, we retrospectively collected a training set of 478 DMs and an independent test set of 183 DMs from patient files in our institution. Two experienced mammography quality standards act radiologists interactively segmented PD as the reference standard. Ten-fold cross-validation was used for model selection and evaluation with the training set. With cross-validation, DCNN obtained a Dice’s coefficient (DC) of 0.79 ± 0.13 and Pearson’s correlation (r) of 0.97, whereas feature-based learning obtained DC = 0.72 ± 0.18 and r = 0.85. For the independent test set, DCNN achieved DC = 0.76 ± 0.09 and r = 0.94, while feature-based learning achieved DC = 0.62 ± 0.21 and r = 0.75. Our DCNN approach was significantly better and more robust than the feature-based learning approach for automated PD estimation on DMs, demonstrating its potential use for automated density reporting as well as for model-based risk prediction.
AFM imaging of extracellular polymer release by marine diatom Cylindrotheca closterium (Ehrenberg) Reiman & J.C. Lewin

Extracellular polysaccharide production by marine diatoms is a significant route by which photosynthetically produced organic carbon enters the trophic web and may influence the physical environment in the sea. This study highlights the capacity of atomic force microscopy (AFM) for investigating diatom extracellular polysaccharides with a subnanometer resolution. Here we address a ubiquitous marine diatom Cylindrotheca closterium, isolated from the northern Adriatic Sea, and its extracellular polymeric substance (EPS) at a single cell level. We applied a simple procedure for AFM imaging of diatom cells on mica under ambient conditions (in air) to achieve visualization of their EPS with molecular resolution. The EPS represents a web of polysaccharide fibrils with two types of cross‐linking: fibrils association forming junction zones and fibril–globule interconnections with globules connecting two or more fibrils. The fibril heights were 0.4–2.6 nm while globules height was in the range of 3–12 nm. Polymer networks of native gel samples from the Northern Adriatic and the network formed by polysaccharides extracted from the C. closterium culture share the same features regarding the fibril heights, pore openings and the mode of fibril association, proving that the macroscopic gel phase in the Northern Adriatic can be formed directly by the self‐assembly of diatom released polysaccharide fibrils. Copyright © 2011 John Wiley & Sons, Ltd.
Ex vivo validation of a stoichiometric dual energy CT proton stopping power ratio calibration

A major source of uncertainty in proton therapy is the conversion of Hounsfield unit (HU) to proton stopping power ratio relative to water (SPR). In this study, we measured and quantified the accuracy of a stoichiometric dual energy CT (DECT) SPR calibration. We applied a stoichiometric DECT calibration method to derive the SPR using CT images acquired sequentially at 80kVp and 140kVp. The dual energy index was derived based on the HUs of the paired spectral images and used to calculate the effective atomic number (Zeff), relative electron density (ρe), and SPRs of phantom and biological materials. Two methods were used to verify the derived SPRs. The first method measured the sample’s water equivalent thicknesses to deduce the SPRs using a multi-layer ion chamber (MLIC) device. The second method utilized Gafchromic EBT3 film to directly compare relative ranges between sample and water after proton pencil beam irradiation. Ex vivo validation was performed using five different types of frozen animal tissues with the MLIC and three types of fresh animal tissues using film. In addition, the residual ranges recorded on the film were used to compare with those from the treatment planning system using both DECT and SECT derived SPRs. Bland–Altman analysis indicates that the differences between DECT and SPR measurement of tissue surrogates, frozen and fresh animal tissues has a mean of 0.07% and standard deviation of 0.58% compared to 0.55% and 1.94% respectively for single energy CT (SECT) and SPR measurement. Our ex vivo study indicates that the stoichiometric DECT SPR calibration method has the potential to be more accurate than SECT calibration under ideal conditions although beam hardening effects and other image artifacts may increase this uncertainty.
Modelling the interaction between the p53 DNA‐binding domain and the p28 peptide fragment of Azurin

Recent experimental data reveal that the peptide fragment of Azurin called p28, constituted by the amino acid residues from 50 to 77 of the whole protein, retains both the Azurin cellular penetration ability and antiproliferative activity. p28 is hypothesized to act by stabilizing the well‐known tumour suppressor p53 via a pathway independent from the oncogene Mdm2, which is the main p53 down‐regulator, with its anticancer potentiality being probably connected with the binding of its amino acid residues 11 to 18 to p53. However, the p28 mode of action has not been completely elucidated yet, mostly because the details of the p28 interaction with p53 are still unknown. In the present study, computational docking modelling supported by cluster analysis, molecular dynamics simulations and binding free energy calculations have been performed to model the interaction between the DNA‐binding domain (DBD) of p53 and the p28 fragment. Since the folding state of p28 when interacting with p53 inside the cell is not known, both the folded and the unfolded structures of this peptide have been taken into consideration. In both the cases, we have found that p28 is able to form with DBD a complex characterized by favourable negative binding free energy, high shape complementarity, and the presence of several hydrogen bonds at the interface. These results suggest that p28 might exert its anticancer action by hampering the binding of ubiquitin ligases to DBD, susceptible to promoting the p53 proteasomal degradation. Copyright © 2011 John Wiley & Sons, Ltd.
Incidence of Common Transfusion Transmitted Diseases Among Blood Donors

Transfusion transmitted diseases are one of the major health problem in Bangladesh. This study was carried out among 12,270 voluntary and directed donors in the transfusion medicine department of Khulna Medical College Hospital (KMCH), a teaching hospital of southern Bangladesh during the period from 1st July 2007 to 30th June 2008 to see the incidence of HIV, HCV, HBV, Syphilis & Malaria. All were voluntary and relative/directed donors. No professional donors had taken part in this donation system. Blood samples were collected in sterile dry plain test tube after predonation consent. Serum of each donor was collected by proper centrifugation within 6 hours of collection. Tests of all the samples were done within 24 hours of collection. The methods used were latex agglutination Immunochromatographic test (ICT) and reconfirmed by ELISA techniques. For malaria thick and thin film studies under microscope were done. On analyzing the results, 171 (1.39%) were found positive for HBsAg, 03 (0.024%) were positive for anti HCV, 01 was positive for anti HIV (0.008%). None found positive for Malarial parasite (MP) none were reactive for RPR test. Donation from professional blood donors are completely stopped in the transfusion medicine unit of KMCH. Mandatory screening of donated blood should be done for HIV, HBV, HCV, Syphilis and Malaria to reduce their transmission by transfusion. Key Words: Transfusion transmitted diseases, Blood donors. doi: 10.3329/jafmc.v5i1. 2840 JAFMC Bangladesh. Vol 5, No 1 (June) 2009 pp.4-6
Output and (kQclin,Qmsrfclin,fmsr) correction factors measured and calculated in very small circular fields for microDiamond and EFD-3G detectors

The purpose of this work was to obtain factors for microDiamond and EFD-3G detectors in very small (less than 5 mm) circular fields. We also investigated the impact of possible variations in microDiamond detector design schematics on the calculated factors. Output factors (OF’s) of 6 MV beams from TrueBeam linac collimated with 1.27–40 mm diameter cones were measured with EBT3 films, microDiamond and EFD-3G detectors as well as calculated (in water) using Monte Carlo (MC) methods. Based on EBT3 measurements and MC calculations factors were derived for these detectors. MC calculations were performed for microDiamond detector in parallel and perpendicular orientations relative to the beam axis. Furthermore, factors were calculated for two microDiamond detector models, differing by the presence or absence of metallic pins. The measured OFs agreed within 2.4% for fields ⩾10 mm. For the cones of 1.27, 2.46, and 3.77 mm maximum differences were 17.9%, 1.8% and 9.0%, respectively. MC calculated output factors in water agreed with those obtained using EBT3 film within 2.2% for all fields. MC calculated factors for microDiamond detector in fields ⩾10 mm ranged within 0.975–1.020 for perpendicular and parallel orientations. MicroDiamond detector factors calculated for the 1.27, 2.46 and 3.77 mm fields were 1.974, 1.139 and 0.982 with detector in parallel orientation, and these factors were 1.150, 0.925 and 0.914 in perpendicular orientation. Including metallic pins in the microDiamond model had little effect on calculated factors. EBT3 and MC obtained factors agreed within 3.7% for fields of ⩾3.77 mm and within 5.9% for smaller cones. Including metallic pins in the detector model had no effect on calculated factors. Our results show that microDiamond and EFD-3G detectors can be used in very small (1.27–3.77 mm) fields once corrections determined in this work are applied. Expected uncertainty of such measurements will be in the range of 8%–2.5%.
Kinetic and mechanistic differences in the interactions between caldendrin and calmodulin with AKAP79 suggest different roles in synaptic function

The kinetic and mechanistic details of the interaction between caldendrin, calmodulin and the B‐domain of AKAP79 were determined using a biosensor‐based approach. Caldendrin was found to compete with calmodulin for binding at AKAP79, indicating overlapping binding sites. Although the AKAP79 affinities were similar for caldendrin (KD = 20 n m) and calmodulin (KD = 30 n m), their interaction characteristics were different. The calmodulin interaction was well described by a reversible one‐step model, but was only detected in the presence of Ca2+. Caldendrin interacted with a higher level of complexity, deduced to be an induced fit mechanism with a slow relaxation back to the initial encounter complex. It interacted with AKAP79 also in the absence of Ca2+, but with different kinetic rate constants. The data are consistent with a similar initial Ca2+‐dependent binding step for the two proteins. For caldendrin, a second Ca2+‐independent rearrangement step follows, resulting in a stable complex. The study shows the importance of establishing the mechanism and kinetics of protein–protein interactions and that minor differences in the interaction of two homologous proteins can have major implications in their functional characteristics. These results are important for the further elucidation of the roles of caldendrin and calmodulin in synaptic function. Copyright © 2012 John Wiley & Sons, Ltd.