gebhart/patrepeval huggingface dataset:
Electrospun Poly(ε-caprolactone) Microfiber and Multilayer Nanofiber/Microfiber Scaffolds:  Characterization of Scaffolds and Measurement of Cellular Infiltration (2006)

The physical and spatial architectural geometries of electrospun scaffolds are important to their application in tissue engineering strategies. In this work, poly(epsilon-caprolactone) microfiber scaffolds with average fiber diameters ranging from 2 to 10 microm were individually electrospun to determine the parameters required for reproducibly fabricating scaffolds. As fiber diameter increased, the average pore size of the scaffolds, as measured by mercury porosimetry, increased (values ranging from 20 to 45 microm), while a constant porosity was observed. To capitalize on both the larger pore sizes of the microfiber layers and the nanoscale dimensions of the nanofiber layers, layered scaffolds were fabricated by sequential electrospinning. These scaffolds consisted of alternating layers of poly(epsilon-caprolactone) microfibers and poly(epsilon-caprolactone) nanofibers. By electrospinning the nanofiber layers for different lengths of time, the thickness of the nanofiber layers could be modulated. Bilayered constructs consisting of microfiber scaffolds with varying thicknesses of nanofibers on top were generated and evaluated for their potential to affect rat marrow stromal cell attachment, spreading, and infiltration. Cell attachment after 24 h did not increase with increasing number of nanofibers, but the presence of nanofibers enhanced cell spreading as evidenced by stronger F-actin staining. Additionally, increasing the thickness of the nanofiber layer reduced the infiltration of cells into the scaffolds under both static and flow perfusion culture for the specific conditions tested. The scaffold design presented in this study allows for cellular infiltration into the scaffolds while at the same time providing nanofibers as a physical mimicry of extracellular matrix.
Statistical Methods for Enhanced Metrology in Semiconductor/Photovoltaic Manufacturing (2012)

As semiconductor technology is aggressively scaling to finer feature sizes, manufacturing complexity increases dramatically. This drives the need for extensive control on processing equipment and on the efficiency of the associated metrology. Similarly, in the field of photovoltaic (PV) manufacturing, processing technology is driven by cost reduction while increasing output power per cell. In either case, the variability impact on the final performance is critical. In this thesis, we focus on the application of statistical methods for enhanced metrology in both semiconductor and PV manufacturing. The work falls into three main topics: Wafer-to-Wafer (W2W) Virtual Metrology (VM) via predictive modeling, Site-to-Site (S2S) metrology modeling for Fault Detection and Classification (FDC), and predictive variability modeling for solar PV. The first topic is on creating predictive VM models for W2W control in plasma etching, one of the bottlenecked processes for technology node scaling. The idea is to utilize equipment sensor data to predict the wafer processing results, so that actual wafer measurements can be reduced or eliminated. VM comprises four main steps: data extraction, outlier removal, variable selection, and model creation. They aim to deal with the special characteristics of equipment sensor data which are high dimensional, collinear and non stationary. VM models are trained and tested with approximately one production year worth of wafer data collected from a single plasma etching tool. The best model result is obtained by a hybrid model that utilizes step-wsie parameter selection and Neural Network (NN) based prediction, which achieved a testing R^2?0.75. The second topic aims to develop FDC schemes for wafer-level S2S metrology. We first focus on utilizing spatial and multivariate statistics for detecting outlier wafers. Spatial and multivariate methods are preferred given the temporal and spatial varying nature of wafer level metrology data. We then focus on selecting the optimal measurement sites for process monitoring. Various site selection schemes are evaluated within the FDC application, showing than more than 70% metrology savings with no discernable reduction in performance is possible. The third topic addresses modeling the variability of solar cells. The impact of environmental and manufacturing variability is simulated and discussed. A predictive model for manufacturing variability-induced mismatch power loss is proposed and evaluated with various PV array configurations. Finally, spatial statistics are used to model the non-uniformities of solar cell properties. A SPICE-based distributive solar cell simulator is constructed to estimate electrical performance for various defect distribution patterns. Finally, a statistical model is created in order to correlate the spatial characteristics of defect patterns with the corresponding electrical performance.
Relative efficiency and risk of endomyocardial biopsy: Comparisons in heart transplant and nontransplant patients (1989)

Right ventricular endomyocardial biopsy remains the gold standard for the diagnosis of acute rejection of the cardiac allograft. Among 704 consecutive procedures performed in 39 transplant recipients (2,842 myocardial samples), endomyocardial biopsy by either the right internal jugular (n = 661) or the femoral venous (n = 43) approach was compared with 243 consecutive procedures performed in nontransplant patients (n = 149 and n = 94, internal jugular and femoral approach, respectively). The internal jugular vein could not be located in only 0.61% (4/661) of heart transplant versus 5% (7/149) of nontransplant procedures (P less than 0.001). Vascular access plus sufficient myocardial sampling was obtained in all but 0.61% (4/661) internal jugular procedures performed in heart transplant patients and in all but 7% (11/149) of those performed in nontransplant patients (P less than 0.0001). (Vascular access was achieved in all femoral venous procedures performed in both transplant and nontransplant patients; sampling was successful after vascular access in all heart transplant recipients and all but two [2.1%] nontransplant procedures.) Cardiac complications occurred in nontransplant patients after one internal jugular procedure (cardiac perforation with tamponade) and after one femoral venous procedure (pericardial effusion). No cardiac complications occurred in transplant recipients, but 2 other complications were observed: One local abscess and one superior vena caval perforation with hemothorax associated with hypotension, both after an internal jugular approach. The overall efficiency (no safety problem; vascular access and adequate sample) was higher among transplant than nontransplant procedures (99% vs 93%, respectively, P less than 0.0001). These observations continue to support routine application of endomyocardial biopsy for monitoring rejection in cardiac transplant patients.(ABSTRACT TRUNCATED AT 250 WORDS)
Cotranslational folding of proteins (1995)

Many unfolded polypeptides are capable of refolding into their native structure upon the removal of the denaturant. However, the folding of the mature protein during renaturation does not accurately reflect the folding process of nascent proteins in the interior of the cell. This view resulted from the discovery of molecular chaperones known to modulate protein folding. Recent publications discussing the possible role and mechanisms of chaperone action suggest that folding in vivo may be a posttranslational process. Here we discuss data that indicate the final native structure and biological activity can be attainted can be nascent protein on the ribosome, thus supporting the cotranslational folding hypothesis.
Allelic loss on chromosome 8p12-21 in microdissected prostatic intraepithelial neoplasia. (1995)

The development and progression of human prostate cancer is associated with genetic abnormalities in tumor cells. Inactivation of tumor suppressor genes due to allelic loss is thought to be an important mechanism of gene alteration in prostatic neoplasms. In this study we examined allelic loss on chromosome 8p12-21 in microdissected samples of normal prostatic epithelium, high grade prostatic intraepithelial neoplasia (PIN), and invasive prostate carcinoma from the same patients. Tissue microdissection under direct microscopic visualization procures pure populations of cells of interest, including small lesions such as PIN. Among 30 patients with concomitant cancer and PIN, we found loss of heterozygosity on chromosome 8p12-21 in 63% (34 of 54) of foci of PIN examined and 90.6% (29 of 32) of tumors, suggesting that abnormalities on chromosome 8p12-21 may be important in the early stages of prostatic carcinoma development. Several cases in which multiple foci of PIN from the same patient were sampled showed different patterns of allelic loss. Fifty-five % (16 of 29) of the prostate carcinomas contained a potential precursor PIN focus based on allelic loss pattern. Our results are consistent with the hypothesis that PIN arises multifocally within the prostate gland, and that a subset of these lesions progress to become carcinoma.
In Vivo Mammalian Brain Imaging Using One- and Two-Photon Fluorescence Microendoscopy (2004)

One of the major limitations in the current set of techniques available to neuroscientists is a dearth of methods for imaging individual cells deep within the brains of live animals. To overcome this limitation, we developed two forms of minimally invasive fluorescence microendoscopy and tested their abilities to image cells in vivo. Both one- and two-photon fluorescence microendoscopy are based on compound gradient refractive index (GRIN) lenses that are 350-1,000 microm in diameter and provide micron-scale resolution. One-photon microendoscopy allows full-frame images to be viewed by eye or with a camera, and is well suited to fast frame-rate imaging. Two-photon microendoscopy is a laser-scanning modality that provides optical sectioning deep within tissue. Using in vivo microendoscopy we acquired video-rate movies of thalamic and CA1 hippocampal red blood cell dynamics and still-frame images of CA1 neurons and dendrites in anesthetized rats and mice. Microendoscopy will help meet the growing demand for in vivo cellular imaging created by the rapid emergence of new synthetic and genetically encoded fluorophores that can be used to label specific brain areas or cell classes.
Mutation of Unique Region of Bruton's Tyrosine Kinase in Immunodeficient XID Mice (1993)

The cytoplasmic tyrosine kinase, Bruton's tyrosine kinase (Btk, formerly bpk or atk), is crucial for B cell development. Loss of kinase activity results in the human immunodeficiency, X-linked agammaglobulinemia, characterized by a failure to produce B cells. In the murine X-linked immunodeficiency (XID), B cells are present but respond abnormally to activating signals. The Btk gene, btk, was mapped to the xid region of the mouse X chromosome by interspecific backcross analysis. A single conserved residue within the amino terminal unique region of Btk was mutated in XID mice. This change in xid probably interferes with normal B cell signaling mediated by Btk protein interactions.
Read Bulk Data From Computational RFIDs (2015)

Without the need of local energy supply, computational RFID (CRFID) sensors are emerging as important platforms enabling a variety of sensing and computing applications. Nevertheless, the data throughput of CRFIDs is very low. This paper aims at efficiently reading bulk data from CRFIDs using commodity RFID readers. We carry out thorough experiment studies to investigate the root cause of the low data throughput of CRFIDs. The experiment results suggest that the fundamental problem of data transfer stems from the mismatch between the stringent timing requirement of commodity standard and the limited packet handling capability of CRFIDs. We further propose several simple yet effective techniques to allow CRFIDs to meet stringent timing requirement of commodity RFID readers and achieve efficient data transfer. We implement a prototype system based on the WISP CRFIDs and commercial off-the-self RFID readers. We carry out extensive experiments on the prototype systems, which show that the proposed scheme works well with the commodity RFID readers.
Gene expression changes with age in skin, adipose tissue, blood and brain (2013)

Skin showed the most age-related gene expression changes of all the tissues investigated, with many of the genes being previously implicated in fatty acid metabolism, mitochondrial activity, cancer and splicing. A significant proportion of age-related changes in gene expression appear to be tissue-specific with only a few genes sharing an age effect in expression across tissues. More research is needed to improve our understanding of the genetic influences on aging and the relationship with age-related diseases.
Interactions of the Human T-cell Leukemia Virus Type-II Integrase with the Conserved CA in the Retroviral Long Terminal Repeat End (2001)

Retroviral integrases (INs) interact with termini of retroviral DNA in the conserved 5'-C(A/G)T. For most integrases, modifications of critical moieties in the major and minor grooves of these sequences decrease 3'-processing. However, for human immunodeficiency virus type-2 (HTLV-2) IN, the replacement of the guanine with 6-methylguanine or hypoxanthine not only reduced 3'-processing, but also promoted cleavage at a second site. This novel cleavage activity required an upstream ACA, unique to the HTLV-2 U5 end. 3'-Processing assays with additional isosteric modifications at Gua and filter binding experiments revealed that the mechanism of the second site cleavage differed among the major groove, minor groove, and mismatch modifications. Importantly, the decrease in 3'-processing activity noted with the minor groove and mismatch modifications were attributed to a decrease in binding. Major groove modifications, however, decreased the level of 3'-processing, but did not affect binding. This suggests that integrase binds the viral end through the minor groove, but relies on major groove contacts for 3'-processing. Several modifications were also examined in strand transfer and disintegration substrates. HTLV-2 IN showed reduced activity with strand transfer and disintegration substrates containing major groove, but not minor groove modifications. This suggests major groove interactions at guanine also provide an important role in these reactions.
Immunotherapy with interleukin-10 depends on the CXC chemokines inducible protein-10 and monokine induced by IFN-gamma. (2002)

The cytokine interleukin (IL)-10 has potent antitumor activity in many model systems when expressed locally at very high levels from the time of tumor transplantation. We now demonstrate that systemic administration of recombinant human IL-10 to animals bearing established highly malignant mammary tumors also leads to significant growth inhibition. We had shown previously that expression of the CXC chemokines Mig (monokine induced by IFN-gamma) and IP-10 (inducible protein 10) is observed in IL-10 transduced but not neo-vector control tumors. We now demonstrate that treatment of IL-10-tumor-bearing mice with antibodies to either chemokine partially reverses the therapeutic effect of IL-10. Tumor growth in animals treated with both antibodies is comparable with that of vector control tumors. Direct transduction of Mig cDNA into the parental tumor cell line before transplantation also results in smaller tumors. This tumor growth inhibition is associated with increased numbers of CD4+ cells, consistent with a T-cell chemoattractant activity for Mig. No change in vascularization, as indicated by CD31+ cells, was observed in either Mig or IL-10-transfected tumors. Thus, an antiangiogenic activity for either cytokine could not be confirmed. Mig and IP-10 are critical to the therapeutic response resulting from high levels of IL-10, and, furthermore, Mig as a single agent also has tumor-inhibitory activity in a model of breast cancer.
Freestanding SiGe/Si/Cr and SiGe/Si/SixNy/Cr microtubes (2004)

We report on hybrid microtubes and rings fabricated from rolled-up strained metal–semiconductor SiGe/Si/Cr and metal–insulator–semiconductor SiGe/Si/SixNy/Cr films. For making suspended microtubes, a method of directional rolling of the patterned films by anisotropic underetching of silicon substrate was introduced. It is shown quantitatively that Cr and SixNy layers are highly strained, the tensile stress being sufficient to cause the rolling-up of the hybrid films into microtubes of preset diameter. The proposed controllable and reproducible technology is promising for fabricating cylindrical-shaped microcapacitors, induction coils, transistors, and building blocks of microelectromechanical devices.
Pharmacokinetics of Pilocarpine in Subjects with Varying Degrees of Renal Function (2000)

Data from three separate single-center studies were combined to assess the pharmacokinetics of orally administered pilocarpine. Pilocarpine concentration-time data were used to generate a data set including 42 subjects (34 males, 8 females) with varying degrees of renal function (average of two estimated creatinine clearance rates of 10 to 112 mL/min). Age ranged from 19 to 88 years. Subjects received single oral doses (range: 2.5-20 mg) of pilocarpine. Plasma samples were collected at time 0; at 20 and 40 minutes; and at 1, 1.5, 2, 3, 4, 6, 8, 12, 16, and 24 hours following dose administration. Cmax and AUC were normalized to a 5 mg exposure in those subjects who received doses other than 5 mg. Plasma pilocarpine concentrations were determined by gas chromatography/mass spectrometry. The pharmacokinetic parameters (elimination rate constant, Cmax, tmax, AUC, Vd/F, and Cl/F) in subjects with impaired renal function were similar to results found in other pharmacokinetic studies involving normal healthy volunteers with only Cmax being significantly higher (p < 0.05). No significant regression relationships were noted between creatinine clearance and pilocarpine elimination rate constant, tmax, Vd/F, Cl/F, or AUC. Pilocarpine clearance does not appear to be impaired in patients with varying degrees of renal insufficiency.
Tests of Functional Form and Heteroscedasticity (2003)

This paper considers tests of misspecification in a heteroscedastic transformation model. We derive Lagrange multiplier (LM) statistics for (i) testing functional form and heteroscedasticity jointly, (ii) testing functional form in the presence of heteroscedasticity, and (iii) testing heteroscedasticity in the presence of data transformation. We present LM statistics based on the expected information matrix. For cases (i) and (ii), this is done assuming the Box-Cox transformation. For case (iii), the test does not depend on whether the functional form is estimated or pre-specified. Small-sample properties of the tests are assessed by Monte Carlo simulation, and comparisons are made with the likelihood ratio test and other versions of LM test. The results show that the expected-information based LM test has the most appropriate finite-sample empirical size
Fundemental principles and diagnostic applications of molecular biology (1993)

B.D.M. Theophilus, Ralph Rapley and Matthew R. Walker, 'Fundamental principles and diagnostic applications of molecular biology' in M.R Walker and R Rapley Eds., Molecular & Antibody Probes in Diagnosis (Chichester: John Wiley & Sons, 1993)
SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments (1995)

Recently a new method called the self-optimized prediction method (SOPM) has been described to improve the success rate in the prediction of the secondary structure of proteins. In this paper we report improvements brought about by predicting all the sequences of a set of aligned proteins belonging to the same family. This improved SOPM method (SOPMA) correctly predicts 69.5% of amino acids for a three-state description of the secondary structure (a-helix. (3-sheet and coil) in a whole database containing 126 chains of non-homologous (less than 25% identity) proteins. Joint prediction with SOPMA and a neural networks method (PHD) correctly predicts 82.2% of residues for 74% of co-predicted amino acids.
Write amplification reduction in NAND Flash through multi-write coding (2010)

The block erase requirement in NAND Flash devices leads to the need for garbage collection. Garbage collection results in write amplification, that is, to an increase in the number of physical page programming operations. Write amplification adversely impacts the limited lifetime of a NAND Flash device, and can add significant system overhead unless a large spare factor is maintained. This paper proposes a NAND Flash system which uses multi-write coding to reduce write amplification. Multi-write coding allows a NAND Flash page to be written more than once without requiring an intervening block erase. We present a novel two-write coding technique based on enumerative coding, which achieves linear coding rates with low computational complexity. The proposed technique also seeks to minimize memory wear by reducing the number of programmed cells per page write. We describe a system which uses lossless data compression in conjunction with multi-write coding, and show through simulations that the proposed system has significantly reduced write amplification and memory wear.
Immunochemical analysis of the modulation of human melanoma-associated antigens by DNA recombinant immune interferon. (1985)

By utilizing the human melanoma cell line Colo 38, a panel of monoclonal antibodies, and a combination of serologic and immunochemical assays, the effect of recombinant immune interferon (IFN-gamma) on the synthesis, expression, and shedding of a cytoplasmic melanoma-associated antigen (MAA) and of the membrane-bound high m.w. MAA (HMW-MAA), 115K MAA, and 100K MAA has been investigated. IFN-gamma increased the synthesis and shedding of the cytoplasmic MAA, but reduced the synthesis and cell surface expression of the HMW-MAA and of the 100K MAA. The cell surface expression of the 115K MAA on IFN-gamma-treated melanoma cells was reduced, although its synthesis was not markedly changed. The effects were dose-dependent and were related to the incubation time of cells with IFN-gamma. Among the three membrane-bound MAA analyzed, the 100K MAA was the most susceptible to modulation by IFN-gamma. The effects of IFN-gamma preparations are not mediated by contaminants in IFN-gamma preparations because removal of IFN-gamma by affinity chromatography on anti-IFN-gamma monoclonal antibodies abolished its modulating activity. The effects of IFN-gamma on the cytoplasmic MAA are similar to those of leukocyte and fibroblast interferons, whereas those on the membrane-bound MAA are significantly different. The potential implications of the marked changes in the antigenic profile of melanoma cells treated with IFN-gamma are discussed in view of the changes in the immunogenicity of IFN-gamma-treated melanoma cells.