gebhart/patrepeval huggingface dataset:
Engineering hybrid polymer-protein super-aligned nanofibers via rotary jet spinning (2014)

Cellular microenvironments are important in coaxing cells to behave collectively as functional, structured tissues. Important cues in this microenvironment are the chemical, mechanical and spatial arrangement of the supporting matrix in the extracellular space. In engineered tissues, synthetic scaffolding provides many of these microenvironmental cues. Key requirements are that synthetic scaffolds should recapitulate the native three-dimensional (3D) hierarchical fibrillar structure, possess biomimetic surface properties and demonstrate mechanical integrity, and in some tissues, anisotropy. Electrospinning is a popular technique used to fabricate anisotropic nanofiber scaffolds. However, it suffers from relatively low production rates and poor control of fiber alignment without substantial modifications to the fiber collector mechanism. Additionally, many biomaterials are not amenable for fabrication via high-voltage electrospinning methods. Hence, we reasoned that we could utilize rotary jet spinning (RJS) to fabricate highly aligned hybrid protein-polymer with tunable chemical and physical properties. In this study, we engineered highly aligned nanofiber constructs with robust fiber alignment from blends of the proteins collagen and gelatin, and the polymer poly-ε-caprolactone via RJS and electrospinning. RJS-spun fibers retain greater protein content on the surface and are also fabricated at a higher production rate compared to those fabricated via electrospinning. We measured increased fiber diameter and viscosity, and decreasing fiber alignment as protein content increased in RJS hybrid fibers. RJS nanofiber constructs also demonstrate highly anisotropic mechanical properties mimicking several biological tissue types. We demonstrate the bio-functionality of RJS scaffold fibers by testing their ability to support cell growth and maturation with a variety of cell types. Our highly anisotropic RJS fibers are therefore able to support cellular alignment, maturation and self-organization. The hybrid nanofiber constructs fabricated by RJS therefore have the potential to be used as scaffold material for a wide variety of biological tissues and organs, as an alternative to electrospinning.
Dual mode control of tri-state boost converter for improved performance (2003)

A tri-state boost converter with an additional boost-inductor free-wheeling interval was proposed earlier to eliminate the right-half-plane (RHP) zero that occurs in the control-to output transfer function of a classical boost converter under continuous-conduction mode of operation. A 'constant-D/sub o/' control scheme, in which the 'capacitor-charging' interval of the converter was kept constant, was employed. This resulted in a relatively large inductor current, especially under high line and load conditions, thereby causing high circuit losses. This paper proposes two variations of a novel dual-mode control (DMC) scheme that vary both the 'boost' and the 'capacitor charging' intervals. Control analysis, design, and limitations of the proposed DMC schemes are presented. Through computer simulations and hardware experiments the performance of the tri-state boost converter with DMC schemes are compared with those of the tri-state boost converter with 'constant-D/sub o/' control scheme, and the classical PI-controlled boost converter. The DMC schemes achieve a significant (about 10%) improvement in converter's efficiency for a wide load range over the 'constant-Do' control scheme.
Current State of Interferon Therapy in the Treatment of Chronic Hepatitis B (2002)

Interferon alpha (IFN) has been used in the treatment of chronic hepatitis B for approximately 25 years. Predictors of response include high pretreatment serum levels of alanine aminotransferase (ALT), low serum hepatitis B virus (HBV) DNA levels, and infection in adulthood. However, only one third of patients achieve a durable response to a course of IFN therapy. Predictors of nonresponse include normal serum ALT levels, high serum HBV DNA levels, hepatitis B e antigen (HBeAg)-negative infection, childhood infection, and immunosuppression. IFN is contraindicated in patients with decompensated liver disease. In addition, the need for parenteral administration and a significant incidence of difficult-to-tolerate side effects limit the suitability of IFN for long-term therapy. For most patients with chronic hepatitis B, including those infected neonatally and those with HBeAg-negative disease, safe, tolerable, and effective alternatives to IFN are needed.
The Viability and Regeneration of Artificial Cell Microencapsulated Rat Hepatocyte Xenograft Transplants in Mice (1988)

Viable hepatocytes were microencapsulated within artificial cells to form a bio-artificial liver. Trypan blue stain exclusion testing generally showed that 60% of the encapsulated hepatocytes remained viable immediately after encapsulation. To determine if xenogeneic hepatocytes can be successfully transplanted, encapsulated rat hepatocytes were implanted intra-peritoneally into mice and galactosamine induced liver failure mice. After 29 days of implantation in mice and 8 days of implantation in liver failure induced mice there was no significant change observed in the number of hepatocytes within the free floating microcapsules recovered from the peritoneal cavity. The percentage viability of the hepatocytes inside the recovered microcapsules increased from 62% to nearly 100% after 29 days of implantation in mice. The percentage viability of the encapsulated hepatocytes implanted in the liver failure induced mice was followed for 8 days. The percentage viability of the hepatocytes inside the microcapsule also increased from 42% to nearly 100%. In mice implanted with free rat hepatocytes, no viable hepatocytes were observed as early as 4 and 5 days after implantation. Instead a larger number of lymphoid cells and remnants of hepatocytes were recovered from the peritoneal cavity. In all cases the viability of the rat hepatocytes were determined with trypan blue stain.
Block transmission over dispersive channels: transmit filter optimization and realization, and MMSE-DFE receiver performance (1996)

Optimal transmit filters for packet-based data transmission on dispersive Gaussian-noise linear time-invariant channels are derived by maximizing the mutual information, subject to a fixed input power budget. A quasi-stationary approximation to the optimal nonstationary input covariance process is derived and shown to exhibit negligible mutual information loss from the optimal case, for situations of most practical interest. Moreover, this quasi-stationary approximation results in efficiently computed lattice or pole-zero implementations of the transmit filter. By considering the popular finite-impulse-response minimum-mean-square-error decision-feedback equalizer (FIR MMSE-DFE) as a receiver structure, we show that transmitter optimization results in an appreciable improvement in the decision-point signal-to-noise ratio. Finally, we show that, as the output blocklength becomes infinite, the optimum finite-dimensional nonstationary input covariance process converges to a stationary process whose power spectrum obeys the well-known water-pouring distribution.
Pressure driven digital logic in PDMS based microfluidic devices fabricated by multilayer soft lithography (2012)

Advances in microfluidics now allow an unprecedented level of parallelization and integration of biochemical reactions. However, one challenge still faced by the field has been the complexity and cost of the control hardware: one external pressure signal has been required for each independently actuated set of valves on chip. Using a simple post-modification to the multilayer soft lithography fabrication process, we present a new implementation of digital fluidic logic fully analogous to electronic logic with significant performance advances over the previous implementations. We demonstrate a novel normally closed static gain valve capable of modulating pressure signals in a fashion analogous to an electronic transistor. We utilize these valves to build complex fluidic logic circuits capable of arbitrary control of flows by processing binary input signals (pressure (1) and atmosphere (0)). We demonstrate logic gates and devices including NOT, NAND and NOR gates, bi-stable flip-flops, gated flip-flops (latches), oscillators, self-driven peristaltic pumps, delay flip-flops, and a 12-bit shift register built using static gain valves. This fluidic logic shows cascade-ability, feedback, programmability, bi-stability, and autonomous control capability. This implementation of fluidic logic yields significantly smaller devices, higher clock rates, simple designs, easy fabrication, and integration into MSL microfluidics.
Development of the New Lung Allocation System in the United States (2006)

This article reviews the development of the new U.S. lung allocation system that took effect in spring 2005. In 1998, the Health Resources and Services Administration of the U.S. Department of Health and Human Services published the Organ Procurement and Transplantation Network (OPTN) Final Rule. Under the rule, which became effective in 2000, the OPTN had to demonstrate that existing allocation policies met certain conditions or change the policies to meet a range of criteria, including broader geographic sharing of organs, reducing the use of waiting time as an allocation criterion and creating equitable organ allocation systems using objective medical criteria and medical urgency to allocate donor organs for transplant. This mandate resulted in reviews of all organ allocation policies, and led to the creation of the Lung Allocation Subcommittee of the OPTN Thoracic Organ Transplantation Committee. This paper reviews the deliberations of the Subcommittee in identifying priorities for a new lung allocation system, the analyses undertaken by the OPTN and the Scientific Registry for Transplant Recipients and the evolution of a new lung allocation system that ranks candidates for lungs based on a Lung Allocation Score, incorporating waiting list and posttransplant survival probabilities.
Transforming growth factor beta as endogenous growth inhibitor of chronic lymphocytic leukemia B cells. (1994)

Chronic lymphocytic leukemia (CLL) B cells are hyporesponsive or refractory to mitogens and growth factors in vitro. This study examined whether transforming growth factor beta (TGF-beta), a potent inhibitor of lymphocyte proliferation may play a role in the growth regulation of CLL B cells. CLL B cells from all donors treated expressed detectable TGF-beta 1 mRNA. In vitro release of TGF-beta by unstimulated cultures, or cultures stimulated by antibody to cell surface immunoglobulin (anti-mu) plus phorbol 12-myristate 13-acetate (PMA) was higher in CLL than in normal B cells. High levels of TGF-beta activity were also detected in plasma samples of CLL patients. The role of TGF-beta in growth regulation of CLL B cells was tested in assays using different B cell activators. Purified neoplastic B cells from most CLL patients proliferated in response to anti-mu, or the combination of anti-mu plus PMA. Levels of CLL B cell proliferation were lower than observed in normal B cells. Some CLL were refractory to these stimuli. Antibody to CD40 induced proliferation of CLL B cells from all donors tested when presented on Fc gamma RII (CDw32)-expressing L cells. Neutralizing antibodies to TGF-beta increased CLL B cell proliferation in the absence or presence of additional stimuli. These effects were dose dependent and specific. Exogenous TGF-beta completely inhibited CLL B cell proliferation induced by anti-mu, PMA, and anti-TGF-beta. CLL B cell proliferation induced by anti-CD40 was reduced by exogenous TGF-beta. However, even at high doses, TGF-beta did not completely inhibit the anti-CD40 effect. In summary, TGF-beta is overexpressed in CLL. CLL B cells are sensitive to TGF-beta and this cytokine functions as an autocrine growth inhibitor accounting at least in part for reduced proliferative responses of these leukemic cells and for the slow progression of the malignant process in vivo.
Reactivity of 2‐substituted imidazo[1,2‐b]pyridazines: Preparation of 3‐nitro, nitroso and chloro derivatives (2002)

Abstract The synthesis of 2‐substitutedimidazo[1,2‐ b ]pyridazines and their reactivity towards electrophilic substitutions are reported. The nitration was shown to be very dependent on the nature of the 2 substituent. Nitrosation using sodium nitrite in acetic acid media as a general method failed in all cases whereas chlorination was observed in warm hydrochloric acid. In order to ascertain the structure of some chloro derivatives, chlorination using N ‐chlorosuccinimide was also reported. Depending of the nature of the substituent, the reaction occurred at the C‐3 imidazolic position and/or at the substituent on position 2. The 3‐nitroso‐2‐phenyl derivative was finally obtained using an alternative synthetic pathway by direct condensation of 3‐amino‐6‐chloropyridazine to ω‐chloro‐ω‐nitrosoacetophenone. The structural determinations were ascertained using high field l H and 13 C‐NMR.
Proteolytic cleavage and cell wall anchoring at the LPXTG motif of surface proteins in Gram‐positive bacteria (1994)

Many surface proteins are thought to be anchored to the cell wall of Gram-positive bacteria via their C-terminus. Cell wall anchoring requires a specific sorting signal, normally located at the predicted C-terminus of surface proteins. Here we show that when placed into the middle of a polypeptide chain, the sorting signal causes the specific cleavage of the precursor as well as the cell wall anchoring of its N-terminal fragment, while the C-terminal fragment remains within the cytoplasm. N-terminal sequencing of the C-terminal cleavage fragment suggests that the cleavage site is located between threonine (T) and glycine (G) of the LPXTG motif, the signature sequence of cell wall sorting signals. All surface proteins harbouring an LPXTG sequence motif may therefore be cleaved and anchored by a universal mechanism. We also propose a novel hypothesis for the cell wall linkage of surface proteins in Gram-positive bacteria.
Immunological evidence for the association of p53 with a heat shock protein, hsc70, in p53-plus-ras-transformed cell lines. (1987)

A rabbit antiserum was prepared against the C-terminal peptide of 21 amino acids from the human heat shock protein hsp70. These antibodies were shown to be specific for this highly inducible heat shock protein (72 kilodaltons [kDa] in rat cells), and for a moderately inducible, constitutively expressed heat shock protein, hsc70 (74 kDa). In six independently derived rat cell lines transformed by a murine cDNA-genomic hybrid clone of p53 plus an activated Ha-ras gene, elevated levels of p53 were detected by immunoprecipitation by using murine-specific anti-p53 monoclonal antibodies. In all cases, the hsc70, but not the hsp70, protein was coimmunoprecipitated with the murine p53 protein. Similarly, antiserum to heat shock protein coimmunoprecipitated p53. Western blot (immunoblot) analysis demonstrated that the hsc70 and p53 proteins did not share detectable antigenic epitopes. The results provide clear immunological evidence for the specific association of a single heat shock protein, hsc70, with p53 in p53-plus-ras-transformed cell lines. A p53 cDNA clone, p11-4, failed to produce clonable cell lines from foci of primary rat cells transfected with p11-4 plus Ha-ras. A mutant p53 cDNA clone derived from p11-4, SVKH215, yielded a 2- to 35-fold increase in the number of foci produced after transfection of rat cells with SVKH215 plus Ha-ras. When cloned, 87.5% of these foci produced transformed cell lines. SVKH215 encodes a mutant p53 protein that binds preferentially to the heat shock proteins of 70 kDa compared with binding by the parental p11-4 p53 gene product. These data suggest that the p53-hsc70 protein complex could have functional significance in these transformed cells.
HIDDEN OR UNSUSPECTED BRONCHIECTASIS IN THE ASTHMATIC PATIENT (1952)

Chronic irritation causes muscle spasm, and prolonged muscle spasm augments chronic irritation. The bronchial musculature is not excepted from this inter-reactive phenomenon. The classical symptoms of bronchiectasis—cough, hemoptysis, and production of purulent sputum—are irritative factors that can, and frequently do, produce bronchospasm. Conversely, chronic or recurrent bronchospasm can produce bronchial obstruction and resultant infection. Whether it be the inaugurative or the secondary source of infection, bronchiectasis not only joins but also maintains this vicious disease cycle, although, unfortunately, its identity may be hidden behind the paroxysms of dyspnea and wheeze (often called bronchial asthma). The asthmatic patients we have seen at the Overholt Thoracic Clinic are classified as medical failures, since they have not responded favorably to conservative therapy. Their previous medical treatment has included bronchodilatory and expectorant drugs, desensitization measures, changes in climate, psychotherapy, antibiotics, corticotropin (ACTH), and cortisone. In addition, several have had surgical measures for asthma, such
IMG/M 4 version of the integrated metagenome comparative analysis system (2013)

IMG/M (http://img.jgi.doe.gov/m) provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of reference genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG/M's data content and analytical tools have expanded continuously since its first version was released in 2007. Since the last report published in the 2012 NAR Database Issue, IMG/M's database architecture, annotation and data integration pipelines and analysis tools have been extended to copewith the rapid growth in the number and size of metagenome data sets handled by the system. IMG/M data marts provide support for the analysis of publicly available genomes, expert review of metagenome annotations (IMG/M ER: http://img.jgi.doe.gov/mer) and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP: http://img.jgi.doe.gov/imgm_hmp).
A SNP panel for identification of DNA and RNA specimens (2018)

This first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.
1/fFlux Noise in Josephson Phase Qubits (2007)

We present a new method to measure 1/f noise in Josephson quantum bits (qubits) that yields low-frequency spectra below 1 Hz. A comparison of the noise taken at positive and negative bias of a phase qubit shows the dominant noise source to be flux noise and not junction critical-current noise, with a magnitude similar to that measured previously in other systems. Theoretical calculations show that the level of flux noise is not compatible with the standard model of noise from two-level state defects in the surface oxides of the films.
Bidirectional passive optical network for the transmission of WDM channels with digital broadcast video signals (2003)

We have demonstrated a bidirectional PON for the transmission of 2.5-Gbps WDM channels and >70 digital broadcast video signals. This network could be implemented cost-effectively using a single strand of fiber for bidirectional transmission, LEDs for upstream channels, and one receiver for the detection of both the video and baseband signals (5622 Mbps). In addition, the capacity of the proposed network could be upgraded easily by changing the RF filter or using an additional WDM filter and a receiver.
Research on the Relationship between Grades and Borrowing Log Based on Data Mining (2012)

The traditional library data mining that generally uses only a single data source is likely to lose a number of important factors in the mining results. This paper attempts to overcome the drawback by utilizing multiple data sources, specifically, the library circulation information and grade information of the students from two departments. The use of association rule algorithm to explore the relationships in data preprocessing finds some circulation rules about literature books and language books, etc. Through analyses we draw a conclusion from the perspective of providing a useful reference for management, which is very helpful to guide the students' reading behavior.
The advantages of PD1 activating chimeric receptor (PD1-ACR) engineered lymphocytes for PDL1(+) cancer therapy. (2015)

Tumors exploit immunoregulatory checkpoints to attenuate T cell responses as a means of circumventing immunologic rejection. By activating the inhibitory costimulatory pathway of Programmed Death 1 (PD1)/PDL1 which provides tumor cells an escape mechanism from immune surveillance, Programmed Death Ligand1 (PDL1)(+) tumors hamper activated tumor-specific T cell functions and render them functionally exhausted. To overcome the inhibitory costimulatory effects of PDL1 on the adoptively transferred T cells, we sought to convert PD1 to a T cell costimulatory receptor by exchanging its transmembrane and cytoplasmic tail with CD28 and 4-1BB signaling domains (PD1-CD28-4-1BB, PD1-ACR), anticipating the genetically modified effector T lymphocytes expressing PD1-ACR would exhibit enhanced functional attributes. And the results showed that PD1-ACR expressed T cells retained the ability to bind PDL1, resulting in T cell activation as evidenced by the elevated activity of phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt), the augmentation of cytokine secretion and the increased proliferative capacity. Moreover, when systemically administered in the mouse model of glioblastoma metastases, PD1-ACR T cells localized at the area of U87 invasive tumor, which results in suppressed tumor growth and enhanced survival of mice with established U87 glioblastoma. Together, these data demonstrated that PD1-ACR has a high potential to serve as a novel strategy to overcome PDL1 mediated immunosuppression of T cells for cancer therapy.
Human cartilage glycoprotein‐39 as a candidate autoantigen in rheumatoid arthritis (1997)

These data indicate that HC gp-39 is a target of the immune response in RA. Consequently, HC gp-39 is a candidate for antigen-specific immunotherapy.
P-selectin glycoprotein ligand regulates the interaction of multiple myeloma cells with the bone marrow microenvironment (2011)

Interactions between multiple myeloma (MM) cells and the BM microenvironment play a critical role in the pathogenesis of MM and in the development of drug resistance by MM cells. Selectins are involved in extravasation and homing of leukocytes to target organs. In the present study, we focused on adhesion dynamics that involve P-selectin glycoprotein ligand-1 (PSGL-1) on MM cells and its interaction with selectins in the BM microenvironment. We show that PSGL-1 is highly expressed on MM cells and regulates the adhesion and homing of MM cells to cells in the BM microenvironment in vitro and in vivo. This interaction involves both endothelial cells and BM stromal cells. Using loss-of-function studies and the small-molecule pan-selectin inhibitor GMI-1070, we show that PSGL-1 regulates the activation of integrins and downstream signaling. We also document that this interaction regulates MM-cell proliferation in coculture with BM microenvironmental cells and the development of drug resistance. Furthermore, inhibiting this interaction with GMI-1070 enhances the sensitization of MM cells to bortezomib in vitro and in vivo. These data highlight the critical contribution of PSGL-1 to the regulation of growth, dissemination, and drug resistance in MM in the context of the BM microenvironment.