gebhart/patrepeval huggingface dataset:
Automatic Segmentation of Kidneys using Deep Learning for Total Kidney Volume Quantification in Autosomal Dominant Polycystic Kidney Disease (2017)

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited disorder of the kidneys. It is characterized by enlargement of the kidneys caused by progressive development of renal cysts, and thus assessment of total kidney volume (TKV) is crucial for studying disease progression in ADPKD. However, automatic segmentation of polycystic kidneys is a challenging task due to severe alteration in the morphology caused by non-uniform cyst formation and presence of adjacent liver cysts. In this study, an automated segmentation method based on deep learning has been proposed for TKV computation on computed tomography (CT) dataset of ADPKD patients exhibiting mild to moderate or severe renal insufficiency. The proposed method has been trained (n = 165) and tested (n = 79) on a wide range of TKV (321.2-14,670.7 mL) achieving an overall mean Dice Similarity Coefficient of 0.86 ± 0.07 (mean ± SD) between automated and manual segmentations from clinical experts and a mean correlation coefficient (ρ) of 0.98 (p < 0.001) for segmented kidney volume measurements in the entire test set. Our method facilitates fast and reproducible measurements of kidney volumes in agreement with manual segmentations from clinical experts.
Hereditary Obesity in the Rat Associated with High Serum Fat and Cholesterol. (1962)

SummaryA rat mutation leading to obesity noticeable by 5 weeks of age and produced on a low fat stock diet is described. It is associated with approximately normal blood sugar levels, but with a spectacular hyper-lipemia, involving a 10-fold rise in total fatty acids, 4-fold rise in cholesterol and lipid phosphorus, and a milky appearance of the blood serum.
Throughput maximization of optical LEO-ground links (2012)

The long-term throughput of optical links between a circular-LEO satellite and a ground station is assessed for systems with fixed and variable data rates. For a fixed data rate, we evaluate the minimum elevation angle above which the link should be established in order to maximize the throughput. The ratio of this optimized constant-data-rate throughput to the throughput of an adaptive transmission with a data rate proportional to the received power is found to depend mainly on the satellite altitude.
Poly-/metal-benzimidazole nano-composite membranes for hydrogen purification (2011)

In this study, a novel scheme to fabricate nano-composite membrane materials containing fully dispersed nano-size zeolitic imidazolate frameworks (ZIFs) has been proposed for the first time. By mixing the as-synthesized ZIF-7 nano-particles without the traditional drying process with polybenzimidazole (PBI), the resultant membranes not only achieve an unprecedented ZIF-7 loading as high as 50 wt%, but also overcome the low permeability nature of PBI. The membranes exhibit characteristics of high transparency and mechanical flexibility, together with enhanced H2 permeability and ideal H2/CO2 permselectivity surpassing both neat PBI and ZIF-7 membranes. Advanced instrument analyses have confirmed the unique ZIF–polymer interface and elucidated the mixed matrix structure that contributes to the high ZIF loading and enhanced gas separation performance superior to the prediction from the Maxwell model. The high thermal stability, good dispersion of ZIF nanoparticles with minimal agglomeration and the attractive gas separation performance at elevated temperatures up to 180 °C indicate the practicability of this nano-composite material for hydrogen production and CO2 capture in realistic industrial applications under harsh and extreme environments.
Susceptibility of dogs to infection with Ehrlichia chaffeensis, causative agent of human ehrlichiosis (1992)

Ehrlichia chaffeensis, the newly recognized agent of human ehrlichiosis, is closely related to E canis, the causative agent of canine ehrlichiosis. Eight pups were inoculated IV with E chaffeensis-, or with E canis-infected DH82 cells, or organisms released from these host cells. Two additional pups served as nonexposed controls. Marked thrombocytopenia was observed in the E canis-infected pups, but not in those infected with E chaffeensis. Homologous serologic response was observed in the E chaffeensis-exposed pups by postinoculation day (PID) 14 and in the E canis-exposed pups by PID 21. Ehrlichia chaffeensis and E canis were reisolated from the respective inoculated pups on each of 8 attempts from PID 7 to 26. One E chaffeensis-exposed pup that was challenge exposed with E canis via blood transfusion, developed fever, anorexia, and thrombocytopenia, suggesting lack of cross protection against E canis.
Substrate Crosstalk Suppression Using Wafer-Level Packaging: Metalized Through-Substrate Trench Approach (2010)

The demand for miniaturization technology has been increasing over the last decades. Consumer electronics end-users often, if not always, go for more functionality and practicality. This is translated into systems that are more complex and yet smaller in size such as smart cellular phones and portable audio/video systems. System on Chip (SoC) is still a solution preferred by many. The SoC comprises of many different circuit blocks that fall into two categories namely analog/RF and digital. The integration of the analog/RF circuitry and digital circuitry on the same silicon substrate has yet another challenge to cope with. The noise generated from the switching activity of the digital circuitry is injected into the silicon substrate, which then can propagate to the sensitive analog/RF circuitry. Such substrate noise can significantly degrade the functionality of the analog/RF circuitry, thus deteriorating the performance of the entire electronic system. In this thesis, a method to isolate the noise generating circuit block from the noise sensitive circuit block is proposed and demonstrated. The proposed method is based on through-substrate trench isolation scheme to suppress the substrate noise. The idea behind this isolation scheme is to create a full through-substrate trench that physically separates the noise agressor from the victim. This idea is very simple and effective. The through-substrate trench is achieved by means of wafer-level packaging (WLP) technology and consists of only a few additional fabrication steps that can readily be incorporated in the WLP processing flow. In a few words, it can be described as follows: the silicon substrate is first bonded to a spacer substrate, e.g. AF-45 glass or High-Resistivity Polycrystalline Silicon (HRPS). Then, the bonded wafer stack is turned upside down before being thinned down. The next step is to create the through-substrate trench by means of KOH etching. At this stage, we now have an air-filled through-substrate trench. This isolation scheme can be further improved by metalizing the trench resulting in a backside metal plane. The backside metal can then be connected to ground to drain the substrate noise. This is called grounded-metalized through-substrate trench. In this work, we have successfully fabricated and measured several devices, i.e. control device (without isolation), air-filled trench device, and metalized trench device. At 50 MHz air-filled trench provides around 55 dB isolation with respect to control device, whereas the metalized-trench provides additional isolation of 7 dB. At 10 GHz air-filled trench provides around 10 dB isolation with respect to control device, whereas the metalized-trench provides additional isolation of 23 dB. At 40 GHz air-filled trench provides around 2 dB isolation with respect to control device, whereas the metalized-trench provides additional isolation of 20 dB.
Endothelial-borne platelet-activating factor and interleukin-8 rapidly immobilize rolling neutrophils (1997)

The kinetics of the response of integrins to activating signal(s) must be rapid to ensure that rolling neutrophils are localized at the sites of inflammation. From video records, we analyzed the adhesion of individual neutrophils in a flow-based in vitro model of endothelial hypoxia and reoxygenation. There were numerous rolling interactions between flowing neutrophils and P-selectin on human umbilical vein endothelial cells after hypoxia, but 90% lasted for < 1 s, with approximately 30% converted to stationary attachment via beta 2-integrin(s). Interleukin-8 (IL-8) and platelet-activating factor (PAF) were responsible for neutrophil activation in this model [G. E Rainger, A. Fisher, C. Shearman, and G. B. Nash. Am. J. Physiol. 269 (Heart Circ. Physiol. 38): H1398-H1406, 1995]. In the presence of a PAF-receptor antagonist, IL-8 acting alone induced conversion of rolling to stationary adhesion in as little as 80 ms after the initial attachment of a neutrophil, with a median response time of 240 ms. In the presence of a monoclonal antibody that neutralized IL-8 activity, PAF acting alone required a minimum duration of rolling of 560 ms to promote stationary adhesion, with a significantly longer median duration of 720 ms. In a reconstituted model, treatment of endothelial cells with hydrogen peroxide induced short-lived rolling of neutrophils supported by P-selectin. Exogenously added IL-8 and/or PAF bound to the endothelial surface and successfully induced the immobilization of neutrophils. Rapid and distinct kinetics of the conversion to stationary adhesion were observed again for IL-8 or PAF. Thus although endothelial-presented signals differed in their rate of action, neutrophils could be localized within one or two endothelial cell diameters of their initial adhesive contact point.
Pattern dependent alignment technique for mix-and-match electron-beam lithography with optical lithography (1998)

An alignment technique for electron-beam (EB) lithography that corrects the writing pattern to match the pattern-dependent lens distortion of an optical stepper is proposed. In mix-and-match EB and optical lithography, precise measurement of positional distortion caused by the stepper lens is necessary. However, recent research in optical lithography has shown that the lens distortion differs depending on the pattern features. Thus, we have enhanced the measurement method to reflect the pattern-feature dependence of positional distortion in optical lithography. To measure the various types of distortions more effectively, we modified the marks used for distortion and overlay measurement. The measured pattern dependence of the lens distortion was in good agreement with our simulation results and the overlay accuracy in mix-and-match lithography was improved with this method.
Current understanding of fatty acid biosynthesis and the acyl carrier protein (2010)

Volume 430 (2010), pp. 1–19The URL linking to Supplementary Movies S1–S3 is incorrect in the print version of this Review Article. The correct URL is http://www.BiochemJ.org/bj/430/bj4300001add.htm. The online version of the journal is not affected.
Translation and processing of Bacillus amyloliquefaciens extracellular RNase (1989)

Bacillus amyloliquefaciens extracellular RNase has been previously cloned and expressed in Bacillus subtilis. Site-specific mutagenesis experiments have identified codon -39 as the start site of translation. We have determined the primary signal peptide cleavage site of preprobarnase and propose a pathway for the conversion of probarnase to mature barnase.
Immunologic studies in asymptomatic hemophilia patients. Relationship to acquired immune deficiency syndrome (AIDS). (1983)

Asymptomatic hemophilia patients receiving Factor VIII concentrate were found to have normal natural killer (NK) cells and B cells, and an inverted T helper/suppressor ratio due to an increase in cells of T suppressor phenotype. In contrast, a hemophilia patient with acquired immune deficiency syndrome (AIDS) exhibited nonfunctional NK cells, low B cells, and an inverted T helper/suppressor ratio due to very low numbers of T helper cells. Hemophilia patients on cryoprecipitate therapy exhibited normal immune parameters. A high percentage of hemophilia patients on both treatments had antibody to hepatitis B virus. The isolated finding of elevated levels of T suppressor cells in hemophilia patients receiving Factor VIII concentrate has not been recognized as an early indicator of impending AIDS, and longitudinal studies will be required to determine its clinical significance.
Nonlinear behavior of piezoelectric lead zinc niobate-lead titanate single crystals under AC electric fields (2003)

The nonlinear behavior of the dielectric and piezoelectric resopnse of &lt;001&gt; oriented Pb(Zn<sub>1/3</sub>Nb<sub>2/3</sub>)O<sub>3</sub>-xPbTiO<sub>3</sub> (PZN-PT) single crystals for x=4.5% and x=8% have been investigated as a function of AC electric fields and DC bias field. At relatively low applied fields, the polarization and strain of PZN-PT single crystals poled along the &lt;001&gt; direction show little hysteresis and have a linear dependence on the applied field, which is a consequence of engineered domain stability. Hence, the dielectric and piezoelectric coefficients of the material do not exhibit any field dependence. However, when the applied electric field exceeds a threshold value, the strain and dielectric responses become nonlinear. The dielectric and piezoelectric constants are a function of the applied field, and hysteresis loops are observed. The results suggest that the observed nonlinear behavior in the PZN-PT single crystals is caused by domain motion/switching in response to the large AC fields. Applying a positive DC bias can effectively stabilize the domain configuration in the crystals and enhance linear responses. The threshold field, at the onset of nonlinearity, is found to have a linear relation with DC bias field in the field range investigated.
Discovery of (<i>S</i>)-2-Cyclopentyl-<i>N</i>-((1-isopropylpyrrolidin2-yl)-9-methyl-1-oxo-2,9-dihydro-1<i>H</i>-pyrrido[3,4-<i>b</i>]indole-4-carboxamide (VU0453379): A Novel, CNS Penetrant Glucagon-Like Peptide 1 Receptor (GLP-1R) Positive Allosteric Modulator (PAM) (2014)

A duplexed, functional multiaddition high throughput screen and subsequent iterative parallel synthesis effort identified the first highly selective and CNS penetrant glucagon-like peptide-1R (GLP-1R) positive allosteric modulator (PAM). PAM (S)-9b potentiated low-dose exenatide to augment insulin secretion in primary mouse pancreatic islets, and (S)-9b alone was effective in potentiating endogenous GLP-1R to reverse haloperidol-induced catalepsy.
myo-Inositol-1-phosphate synthase. Characteristics of the enzyme and identification of its structural gene in yeast. (1981)

A purification procedure for L-myo-inositol-1-phosphate synthase (EC 5.5.1.4) from yeast is described. The method routinely produces enrichments of 500-fold with 20-40% yields. In addition, a procedure for obtaining highly specific and purified antibody against the protein is described. The molecular weight of the native enzyme as determined by gel filtration is approximately 240,000. A single subunit of approximately Mr = 62,000 is detected upon sodium dodecyl sulfate-gel electrophoresis of the purified enzyme. The purified antibody was used to assay crude extracts of wild type and inositol-requiring mutants for the presence of cross-reacting material. Mutant ino1-13 produces an inactive but fully cross-reacting protein of a molecular weight identical with the wild type enzyme subunit. Mutant ino1-16 produces low levels of a fully active enzyme which appears to be more susceptible to proteolytic degradation. Mutants representing other unlinked loci (ino2 and ino4) do not produce cross-reacting protein. Based on this analysis, the ino1 locus is identified as the structural gene for the enzyme. Furthermore, it is shown that the Mr = 62,000 subunit is largely absent from crude extracts prepared from wild type yeast grown in the presence of repressing concentrations of inositol.
Advances in membrane receptor screening and analysis (2004)

During the last decade there has been significant progress in the development of analytical techniques for the screening of ligand binding to membranes and membrane receptors. This review focuses on developments using label-free assays that facilitate ligand-membrane-receptor screening without the need for chemical-, biological- or radiological-labelled reagents. These assays include acoustic, optical surface plasmon resonance biosensing, sedimentation (analytical ultracentrifugation), chromatographic assays, isothermal titration calorimetry and differential scanning calorimetry. The merits and applications of cell-based screening systems and of different model membrane systems, including planar supported lipid layers, bead-supported membranes and lipid micro-arrays, are discussed. Recent advances involving more established techniques including intrinsic fluorescence, FRET spectroscopy, scintillation proximity assays and automated patch clamping are presented along with applications to peripheral membrane proteins, ion channels and G protein-coupled receptors. Novel high-throughput assays for determination of drug- and protein-partitioning in membranes are also highlighted. To aid the experimenter, a brief synopsis of the techniques commonly employed to purify and reconstitute membranes and membrane receptors is included.
Investigation of Barite "Sag" in Weighted Drilling Fluids in Highly Deviated Wells (1990)

ABSTRACT Significant mud weight variations greater than 4 Ibm/gal have been measured in flowline returns when circulating bottoms up after trips. This phenomenon, called "sag", has preceded pack off, lost circulation, failure to get logging tools to bottom, stuck pipe, and other drilling problems on some directional wells. Two key findings have emerged from an extensive project to investigate and minimize sag in highly deviated wells. First, the density variations are caused by the slumping of beds which form when weight material settles to the low side of the hole. Second, most of the bed formation occurs while the mud is circulating. Previous efforts to investigate sag have focused on static settling. Case histories, results from laboratory flow-loop studies, and operational guidelines to minimize sag and its consequences are presented in this paper.
Infection Associated with Tunneled Hemodialysis Catheters (2008)

Abstract The use of tunneled dialysis catheters to deliver hemodialysis treatment may be associated with major problems. For this reason their use should be minimized as much as possible. Infection is the most serious of these problems. This complication causes very significant morbidity and mortality and has emerged as the primary barrier to long‐term catheter use. Bacteremia is the most serious type of infection associated with catheter use. It can result in metastatic infection and even lead to death of the patient. Prophylaxis is important to decrease the risk of infection. The use of an antibiotic ointment at the exit site until it has healed and the long‐term use of a dressing to cover the exit site are effective in decreasing the incidence of exit‐site infection. With optimal catheter‐use management, it should be possible to reduce the incidence of catheter‐related bacteremia (CRB) to a level in the range of 1/1000 catheter days. Antibiotic and antimicrobial locking solutions show promise and may, if verified in appropriate clinical studies, prove to be important adjuncts to the management of catheter‐dependent patients. Aspirin has been shown to have anti‐staphylococcal activity and warrants further clinical evaluation. The diagnosis of CRB is based upon positive blood cultures in association with typical clinical features. If a simple routine blood culture is positive, along with a high clinical probability based upon the patient’s signs and symptoms, the sensitivity and specificity of the diagnosis is greater than 75%. CRB is in reality a biofilm infection and must be treated as such. Treatment needs to focus on appropriate systemic antibiotics which should be continued for a minimum of 3 weeks and catheter management to remove the biofilm. Catheter exchange has been shown to be effective and should be performed based upon the clinical presentation of the patient. While treatment with a combination of systemic antibiotics and antibiotic locking solution may be effective for gram‐negative infections, this approach does not appear to be a good choice for Staphylococcus aureus CRB.
Quantitative Immunohistochemistry by Measuring Cumulative Signal Strength Accurately Measures Receptor Number (2003)

We previously demonstrated that quantitative immunohistochemistry (Q-IHC) performed by measuring the cumulative signal strength of the digital file encoding an image can be used to determine the absolute amount of chromogen present per pixel. We now show that Q-IHC so performed can be used to accurately determine the amount of peptide hormone receptor of interest in archived tissues. To do this we transfected Balb 3T3 fibroblasts with the cDNA encoding the human receptor for gastrin-releasing peptide (GRP), and selected six cell lines stably expressing between 10(2) and 10(6) receptors/cell. These cell lines were fixed in formalin, embedded in paraffin, and treated with antipeptide antibodies against the GRP receptor, followed by DAB chromogen to identify bound antibody. Images were acquired using a 4.9 million pixel digital scanning 24-bit RGB camera, saved in TIFF format, and used for subsequent analysis. Q-IHC was performed after digitally dissecting out the relevant portion of the image for analysis, and processing using a program written in C (available at http://www.uic.edu/com/dom/gastro/Freedownloads.html). Under the conditions defined here, chromogen quantity as determined by Q-IHC tightly correlated with GRP receptor number (r(2)=0.867) in these cell lines. Using the conversion factor identified as a result of these studies, we then determined GRP receptor number on eight randomly selected, archived human colon cancers. Overall GRP receptor expression in colon cancer depended on the degree to which cells within any particular tumor were differentiated, with well-differentiated cells expressing the greatest numbers of receptors (approximately 55,000 +/- 10,000 sites/cell). These studies indicate that Q-IHC can be used to determine receptor quantity in archived tissues and other samples of limited quantity.
Effect of head-down bedrest on blood/plasma density after intravenous fluid load. (1992)

Using the mechanical oscillator technique, the mass density of antecubital venous blood and plasma samples was measured in 6 men before and after infusion of 22 ml/kg isotonic NaCl solution before, on day 7 during, and on day 3 after ten days of 6 degrees head-down bedrest. We studied 1) the distribution volumes of the infused NaCl solution, 2) the magnitude and time-course of induced fluid shifts to the extravascular spaces after rapid volume expansion, and 3) the protein concentration of the translocated fluid. The NaCl distribution volume was 16.7 +/- 2.9% body weight (BW) before, 15.0 +/- 3.0% BW during (P less than 0.05) and 13.0 +/- 1.3% BW after the head-down tilt (HDT) period (P less than 0.01). The volume of fluid shifted 120 min after infusion was not different in the control (12.9 +/- 7.4% plasma volume and 8.3 +/- 3.2% blood volume), during HDT (14.7 +/- 3.8% plasma volume and 7.4 +/- 5.6% blood volume), during HDT HDT conditions (14.6 +/- 2.2% plasma volume, and 8.2 +/- 1.3% blood volume, respectively). The density of the shifted fluid which reflects protein concentration was also unchanged (1004.2 +/- 4.2 g/l, 1002.6 +/- 4.3 g/l and 1003.9 +/- 8.2 g/l in the control, during, and after HDT periods, respectively). The mass density of red cells did not change with any condition. It is concluded that the distribution volume of isotonic saline solution decreases with diminished body mass. Densitometry provides a means of monitoring volume changes and protein shifts under the circumstances of our study.