gebhart/patrepeval huggingface dataset:
Assessment of rat sciatic nerve function following acute implantation of high density utah slanted electrode array (25 electrodes/mm2) based on neural recordings and evoked muscle activity (2014)

These studies demonstrate that HD-USEAs provide a useful neural interface without causing a nerve crush injury that would otherwise negate their use in acute preparations (<12 h).
Inhibition of Dll4-mediated signaling induces proliferation of immature vessels and results in poor tissue perfusion (2007)

Vascular development is dependent on various growth factors and certain modifiers critical for providing arterial or venous identity, interaction with the surrounding stroma and tissues, hierarchic network formation, and recruitment of pericytes. Notch receptors and ligands (Jagged and Delta-like) play a critical role in this process in addition to VEGF. Dll4 is one of the Notch ligands that regulates arterial specification and maturation events. In the current study, we have shown that loss of function by either targeted allele deletion or use of a soluble form of Dll4 extracellular domain leads to inhibition of Notch signaling, resulting in increased vascular proliferation but defective maturation. Newly forming vessels have thin caliber, a markedly reduced vessel lumen, markedly reduced pericyte recruitment, and deficient vascular perfusion. sDll4 similarly induced defective vascular response in tumor implants leading to reduced tumor growth. Interference with Dll4-Notch signaling may be particularly desirable in tumors that have highly induced Dll4-Notch pathway.
Low-frequency and high-frequency all-fiber modulators based on birefringence modulation (1999)

In-line optical modulators with low insertion losses and high maximum optical powers are required for Q switching and cavity dumping of fiber lasers as well as for nonlinear optical-fiber experiments. We report the design of polarimetric all-fiber modulators based on optical-fiber birefringence modulation combined with an all-fiber polarizer. Birefringence modulation involves a piezoelectric ceramic tube. This simple technique permits efficient low-frequency and high-frequency harmonic modulation, up to the megahertz range, as well as modulation of pulses shorter than 1 micros.
Long-term oxygen therapy: conference summary. (2000)

With Jan's presentation, the conference concluded. In looking back on it, I think it is obvious that the group heard a very comprehensive, state-of-the-art review of this very important topic. Obviously, LTOT has enormous clinical and financial impact for millions of patients around the world. Indeed, LTOT is one of the few therapies available that has clearly been shown in randomized controlled trials to impact mortality. There are many questions that remain, however. To me, the most important of these questions involve the diagnosis and management of patients who do not have resting hypoxemia but who do have NOD and/or XOD. How aggressively should we "screen" for these conditions? If we find them, do we treat continuously or just during the hypoxemic episodes? What is the role of supplemental oxygen during rehabilitative exercises (including usage in patients who don't become hypoxemic)? The answers to these questions will clearly have substantial clinical and financial impact. Other memorable aspects of this conference included the tireless efforts of Ray Masferrer to pull this conference off, the special camaraderie of the participants that made the discussions so productive, and the lovely location that gave the conference an atmosphere of high quality. I'd like to recognize and thank two important groups. First, the American Association for Respiratory Care did a superb job of organizing the conference and providing the journal Respiratory Care as a forum to publish the proceedings. Second, our 3 industry sponsors not only provided critical funding support but also gave the group important perspectives during many of the discussions. These kinds of industry-profession collaborations benefit everyone. Finally, I'd like to extend my congratulations to all the speakers for jobs well done and to thank them for making my job as summarizer an enjoyable one.
An Algorithm for Path Connections and Its Applications (1961)

The algorithm described in this paper is the outcome of an endeavor to answer the following question: Is it possible to find procedures which would enable a computer to solve efficiently path-connection problems inherent in logical drawing, wiring diagramming, and optimal route finding? The results are highly encouraging. Within our framework, we are able to solve the following types of problems: 1) To find a path between two points so that it crosses the least number of existing paths. 2) To find a path between two points so that it avoids as much as possible preset obstacles such as edges. 3) To find a path between two points so that the path is optimal with respect to several properties; for example, a path which is not only one of those which cross the fewest number of existing paths, but, among these, is also one of the shortest. The minimal-distance solution has been programmed on an IBM 704 computer, and a number of illustrations are presented. The class of problems solvable by our algorithm is given in a theorem in Section III. A byproduct of this algorithm is a somewhat remote, but unexpected, relation to physical optics. This is discussed in Section VI.
Treatment of Ostial Renal-Artery Stenoses with Vascular Endoprostheses after Unsuccessful Balloon Angioplasty (1997)

Accurate placement of renal-artery stents is technically feasible without major complications. The favorable early and long-term results suggest that primary stent placement is an effective treatment for renal-artery stenosis involving the ostium.
Lymphoproliferative Disorders with Early Lethality in Mice Deficient in Ctla-4 (1995)

The role of the cell-surface molecule CTLA-4 in the regulation of T cell activation has been controversial. Here, lymph nodes and spleens of CTLA-4-deficient mice accumulated T cell blasts with up-regulated activation markers. These blast cells also infiltrated liver, heart, lung, and pancreas tissue, and amounts of serum immunoglobulin were elevated. The mice invariably became moribund by 3 to 4 weeks of age. Although CTLA-4-deficient T cells proliferated spontaneously and strongly when stimulated through the T cell receptor, they were sensitive to cell death induced by cross-linking of the Fas receptor and by gamma irradiation. Thus, CTLA-4 acts as a negative regulator of T cell activation and is vital for the control of lymphocyte homeostasis.
Structure and Biochemical Properties of the Alkene Producing Cytochrome P450 OleTJE (CYP152L1) from the Jeotgalicoccus sp. 8456 Bacterium (2014)

The production of hydrocarbons in nature has been documented for only a limited set of organisms, with many of the molecular components underpinning these processes only recently identified. There is an obvious scope for application of these catalysts and engineered variants thereof in the future production of biofuels. Here we present biochemical characterization and crystal structures of a cytochrome P450 fatty acid peroxygenase: the terminal alkene forming OleTJE (CYP152L1) from Jeotgalicoccus sp. 8456. OleTJE is stabilized at high ionic strength, but aggregation and precipitation of OleTJE in low salt buffer can be turned to advantage for purification, because resolubilized OleTJE is fully active and extensively dissociated from lipids. OleTJE binds avidly to a range of long chain fatty acids, and structures of both ligand-free and arachidic acid-bound OleTJE reveal that the P450 active site is preformed for fatty acid binding. OleTJE heme iron has an unusually positive redox potential (-103 mV versus normal hydrogen electrode), which is not significantly affected by substrate binding, despite extensive conversion of the heme iron to a high spin ferric state. Terminal alkenes are produced from a range of saturated fatty acids (C12-C20), and stopped-flow spectroscopy indicates a rapid reaction between peroxide and fatty acid-bound OleTJE (167 s(-1) at 200 μm H2O2). Surprisingly, the active site is highly similar in structure to the related P450BSβ, which catalyzes hydroxylation of fatty acids as opposed to decarboxylation. Our data provide new insights into structural and mechanistic properties of a robust P450 with potential industrial applications.
Isolation of PCV3 from Perinatal and Reproductive Cases of PCV3-Associated Disease and In Vivo Characterization of PCV3 Replication in CD/CD Growing Pigs (2020)

Porcine circovirus 3 (PCV3) has been identified as a putative swine pathogen with a subset of infections resulting in stillborn and mummified fetuses, encephalitis and myocarditis in perinatal, and periarteritis in growing pigs. Three PCV3 isolates were isolated from weak-born piglets or elevated stillborn and mummified fetuses. Full-length genome sequences from different passages and isolates (PCV3a1 ISU27734, PCV3a2 ISU58312, PCV3c ISU44806) were determined using metagenomics sequencing. Virus production in cell culture was confirmed by qPCR, IFA, and in situ hybridization. In vivo replication of PCV3 was also demonstrated in CD/CD pigs (<i>n</i> = 8) under experimental conditions. Viremia, first detected at 7 dpi, was detected in all pigs by 28 dpi. IgM antibody response was detected between 7-14 dpi in 5/8 PCV3-inoculated pigs but no IgG seroconversion was detected throughout the study. Pigs presented histological lesion consistent with multi systemic inflammation characterized by myocarditis and systemic perivasculitis. Viral replication was confirmed in all tissues by in situ hybridization. Clinically, all animals were unremarkable throughout the study. Although the clinical relevance of PCV3 remains under debate, this is the first isolation of PCV3 from perinatal and reproductive cases of PCV3-associated disease and in vivo characterization of PCV3 infection in a CD/CD pig model.
Highly Active, Bifunctional Co(III)-Salen Catalyst for Alternating Copolymerization of CO2 with Cyclohexene Oxide and Terpolymerization with Aliphatic Epoxides (2010)

The cobalt(III) complex of a salen ligand bearing one quaternary ammonium salt on the three-position of one aromatic ring is a highly active catalyst for the alternating copolymerization of cyclohexene oxide (CHO) and CO2 to afford the corresponding poly(cyclohexene carbonate) (PCHC) at various temperatures. The cobalt-based catalyst exhibited excellent activity and selectivity for polymer formation at high temperatures up to 120 °C and even under low CO2 pressures of 0.1 MPa. Also, the cobalt(III)-salen complex could operate very efficiently for the terpolymerization of CHO and aliphatic epoxides with CO2 to provide selectively polycarbonates with a narrow polydispersity at high temperatures. The polycarbonates resulting from the terpolymerization of equimolar CHO and propylene oxide (PO) with CO2 have a close content for both cyclohexene carbonate and propylene carbonate units. This is ascribed to the presence of CHO significantly inhibiting the reactivity of PO and thereby causing a matched reactivity for both epoxides during the terpolymerization. The competition coordination of CHO and PO to the electrophilic cobalt(III) ion has no effect on regioselective ring-opening of PO in the terpolymerization.
MIMO Wireless Linear Precoding (2007)

This article provides a tutorial of linear precoding for a frequency- flat, single-user MIMO wireless system, examining both theoretical foundations and practical issues. The article first discusses principles for CSIT (channel-side information at the transmitter) acquisition and develops a dynamic CSIT model, which spans perfectly to statistical CSIT, taking into account channel temporal variation. It then presents the capacity benefits of CSIT and information theoretic arguments for exploiting the CSIT by linear precoding. A precoded system structure is then described, involving an encoder and a linear precoder. Criteria for designing the precoder are then discussed, followed by specific designs for different CSIT scenarios.
Proteolytic cleavage of single-chain pro-urokinase induces conformational change which follows activation of the zymogen and reduction of its high affinity for fibrin. (1985)

A plasminogen activator secreted from human kidney cells was highly purified by affinity chromatography on an anti-urokinase IgG-Sepharose column. The purified plasminogen activator was inactive and had a single-chain structure and a Mr of 50,000. It not only did not incorporate diisopropyl fluorophosphate, which reacts with active site serine residue in urokinase, but also did not bind to p-aminobenzamidine-immobilized CH-Sepharose, to which urokinase bind via its side-chain binding pocket present in active center. The plasminogen activator was converted to the active two-chain form with the same Mr by catalytic amounts of plasmin. Its potential enzymatic activity was quenched completely by anti-urokinase IgG, but not by anti-tissue plasminogen activator Ig. These results indicate that the plasminogen activator is an inactive proenzyme form of human urokinase. Therefore, the plasminogen activator was termed single-chain pro-urokinase. The cleavage of single-chain pro-urokinase by plasmin induced conformational change which followed the generation of reactive serine residue at active site, the increase enzyme activity and the reduction of its high affinity for fibrin. These findings suggest that conformational change occurs in both regions responsible for enzyme activity and affinity for fibrin upon activation of single-chain pro-urokinase.
Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control. (1996)

We have studied the initial development of pluripotent gut endoderm to hepatocytes using a tissue explant system from mouse embryos. We not only find cellular interactions that specify hepatic differentiation but also those that block hepatogenesis in regions of the endoderm that normally give rise to other tissues. The results implicate both positive and negative signaling in early hepatic specification. In vivo footprinting of the albumin enhancer in precursor gut endoderm shows that the transcriptionally silent but potentially active chromatin is characterized by occupancy of an HNF-3 site. Upon hepatic specification, a host of other factors bind nearby sites as the gene becomes active. Genes in pluripotent cells therefore may be marked for potential expression by entry points in chromatin, where additional factors bind during cell type specification. The findings also provide insight into the evolutionary origin of different endodermal cell types.
Selective Depletion of CD4+CD25+Foxp3+ Regulatory T Cells by Low-Dose Cyclophosphamide Is Explained by Reduced Intracellular ATP Levels (2010)

CD4(+)CD25(+)Foxp3(+) regulatory T (Treg) cells have been shown to play important roles in mediating cancer development. Although cyclophosphamide (CY) has shown promise as a drug to selectively target Treg cells with low-dose in vivo, the underlying molecular mechanism remains unclear. In this report, we provide evidence that ATP, the energy molecule and signal element, accounts for the selective depletion of Treg cells by low-dose CY. Relative to conventional T cells or other cell types, ATP levels were much lower in Treg cells. This was due to Treg cells that downregulate one microRNA, miR-142-3p, and upregulate ecto-nucleoside triphosphate diphosphohydrolase CD39. The transfection of miR-142-3p or the blockade of CD39 could increase intracellular ATP levels of Treg cells, consequently decreasing the sensitivity of Treg cells to low-dose CY. On the other hand, the transfection of miR-142-3p inhibitor or the addition of soluble CD39 to the cultured CD4(+)CD25(-) T cells resulted in the decrease of intracellular ATP levels and increase of sensitivity of conventional T cells to low-dose CY. Furthermore, we found that the low levels of ATP attenuated the synthesis of glutathione, leading to the decrease of CY detoxification, thus increasing the sensitivity of Treg cells to low-dose CY. Therefore, we here identify a molecular pathway through which low-dose CY selectively ablates Treg cells. Our findings also imply that low levels of ATP are probably related to Treg cell function.
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules (2003)

The new prediction model is implemented at http://zlab.bu.edu/SMM. The underlying matrix and pair coefficients are also available as supplementary materials.
Nanostructure Modified Gas Sensor Detection Matrix for NO Transient Conversion of NO to NO2 (2011)

Porous silicon (PS) conductometric gas sensors are used to create a sensitivity matrix for the room temperature detection of NOx (NO, NO2). "P-type" nanopore coated microporous silicon is treated with tin, nickel, copper, and gold, electrolessly deposited onto the PS surface to form SnOx, NiO, CuxO, and AuxO nanostructured centers as confirmed by XPS measurements. The relative sensitivities of these modified PS gas sensor surface sites have been measured under 1–5 ppm NO exposure. An improved sensitivity of up to 10 times that of untreated PS is observed for a 1 ppm exposure. The choice of deposits is based on the hard to soft acid character of the nanostructured metal oxide islands that are fractionally deposited on the semiconductor interface and their effect on the physisorption of NO, a weak base, dictated by an inverse pattern (IHSAB) to the hard-soft acid base concept. NO, a free radical, can interact with oxygen sites on the modified PS sensor interfaces, to effect a transient NO2 signal unique to PS-based NO sensors, which is not observed as other basic analytes including NH3, PH3, H2S, SO2, and CO interact with "p-type" PS.A comparison is made between the current PS sensor systems which operate at room temperature and electrochemical and traditional metal oxide sensors.
Annals of Surgery (2005)

From the American College of Surgeons, Chicago, IL. Reprints: Thomas R. Russell, MD, American College of Surgeons, 633 North Saint Clair St., Chicago, IL 60611-3211. E-mail: [email protected].
Rapid bench-top fabrication of poly(dimethylsiloxane)/polystyrene microfluidic devices incorporating high-surface-area sensing electrodes (2015)

The development of widely applicable point-of-care sensing and diagnostic devices can benefit from simple and inexpensive fabrication techniques that expedite the design, testing, and implementation of lab-on-a-chip devices. In particular, electrodes integrated within microfluidic devices enable the use of electrochemical techniques for the label-free detection of relevant analytes. This work presents a novel, simple, and cost-effective bench-top approach for the integration of high surface area three-dimensional structured electrodes fabricated on polystyrene (PS) within poly(dimethylsiloxane) (PDMS)-based microfluidics. Optimization of PS-PDMS bonding results in integrated devices that perform well under pressure and fluidic flow stress. Furthermore, the fabrication and bonding processes are shown to have no effect on sensing electrode performance. Finally, the on-chip sensing capabilities of a three-electrode electrochemical cell are demonstrated with a model redox compound, where the high surface area structured electrodes exhibit ultra-high sensitivity. We propose that the developed approach can significantly expedite and reduce the cost of fabrication of sensing devices where arrays of functionalized electrodes can be used for point-of-care analysis and diagnostics.
Whole-genome resequencing reveals loci under selection during chicken domestication (2010)

Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.
Treatment of Rheumatoid Arthritis with Gammalinolenic Acid (1993)

Gammalinolenic acid in doses used in this study is a well-tolerated and effective treatment for active rheumatoid arthritis. Gammalinolenic acid is available worldwide as a component of evening primrose and borage seed oils. It is usually taken in far lower doses than used in this trial. It is not approved in the United States for the treatment of any condition and should not be viewed as therapy for any disease. Further controlled studies of its use in rheumatoid arthritis are warranted.