gebhart/patrepeval huggingface dataset:
Therapeutic Deep Hypothermic Circulatory Arrest in Dogs (1990)

Early deaths from trauma are often caused by exsanguinating hemorrhage from injuries that appear "irreparable." We explored the limits of deep hypothermic circulatory arrest induced during hemorrhagic shock to enable repair of these injuries in a bloodless field. In 15 dogs, after 30 minutes of hemorrhagic shock (mean arterial pressure, 40 mm Hg), cardiopulmonary bypass (CPB) was used to cool to 15 degrees C in 13-37 minutes. After circulatory arrest of 60 (Group 1), 90 (Group 2), or 120 (Group 3) minutes, reperfusion and rewarming were accomplished by CPB. All dogs survived greater than 72 hours. Best neurologic deficit scores (ND) (0% = normal, 100% = brain death) were 0 +/- 0% (normal) in Group 1, 10 +/- 8% (mild disability) in Group 2, and 27 +/- 24% in Group 3. Outcome in Group 3 dogs ranged from near-normal to comatose. After perfusion-fixation sacrifice, brain histopathologic damage scores correlated with insult time, as did ND scores. Deep hypothermia can allow 60-90 min of circulatory arrest with good neurologic recovery, even after a period of severe hemorrhagic shock. This technique may allow repair of otherwise lethal injuries and survival without brain damage.
Toward an Optimized Dynamic Headspace Method for the Study of Volatiles in Low-Density Polyethylene (1998)

A dynamic headspace technique for detecting C6−C14 volatile organic compounds (VOCs) in low-density polyethylene (LDPE) is discussed in which VOCs are purged with N2, trapped at ambient temperatures on Tenax-GC, and identified by gas chromatography/mass spectrometry. The experimental variables are quantitatively modeled to enhance sensitivity of the technique. The rate of extraction of VOCs from LDPE and the rate of isothermal desorption of VOCs from Tenax-GC are first-order processes with rate constants of 2.79 × 10-5 and 1.53 × 10-3 s-1 respectively. Approximately 4.2% of extractable VOCs are present in the vapor phase at ambient temperature, and 21% of VOCs are liberated instantaneously from Tenax-GC during thermal desorption at 200 °C. The chromatographic peak area associated with each VOC, and the total peak area in the chromatographic window, vary with desorption temperature in accordance with the van't Hoff isochore with an “average” desorption enthalpy of 45.5 kJ mol-1. Keywords: Low-density polyethylene (LDPE); dynamic headspace sampling; gas chromatography/mass spectrometry (GC/MS); volatile organic compounds (VOCs); Tenax-GC; purge and trap; mathematical modeling
Mac‐1: a macrophage differentiation antigen identified by monoclonal antibody (1979)

Abstract We have previously described the derivation of M1/70, a hybrid myeloma line secreting monoclonal rat anti‐mouse cell surface antibody (Springer, T., Galfre, G., Secher, D. S. and Milstein, C, Eur. J. Immunol. 1978. 8 : 539). We have now investigated the cellular distribution of this antigen using a 125 I‐labeled anti‐rat IgG indirect binding assay, the fluorescence‐activated cell sorter, autoradiography and precipitation of cell surface molecules. Screening with a tumor cell panel showed strong reactivity with a macrophage‐like line but no reactivity with B or T lymphoma lines. In normal tissues, M1/70 antigen was found to be present in small amounts on spleen and exudate granulocytes and a subpopulation of bone marrow cells, in moderate amounts on spleen and blood monocytes and expressed in much larger amounts on spleen histiocytes and peritoneal exudate macrophages. In contrast, M1/70 antigen was found to be absent from erythroid and lymphoid cells. M1/70 antibody precipitated two polypeptides of 190 000 and 105 000 mol. wt. which were present in much greater amounts on peritoneal exudate macrophages than on spleen cells. The expression on phagocytes of two other antigens identified by monoclonal antibodies M1/69 and M1/9.3 was also examined. Monocytes and granulocytes expressed large amounts of M1/69 and low amounts of M1/70 antigen, while in peritoneal exudate macrophages this pattern was dramatically reversed. M1/70 thus defines a differentiation antigen on mononuclear phagocytes and granulocytes, the expression of which is specifically increased during monocyte maturation. This antibody is the first to be described which recognizes a discrete molecule specific to phagocytes.
Establishment of a fluorescent polymerase chain reaction method for the detection of the SARS-associated coronavirus and its clinical application. (2003)

The F-PCR method established may be a rapid, accurate and efficient way for screening and for the early diagnosis of SARS patients.
Endothelial Cell Coculture Within Tissue-Engineered Cardiomyocyte Sheets Enhances Neovascularization and Improves Cardiac Function of Ischemic Hearts (2008)

In vitro engineering of 3-dimensional cardiac tissues with preformed EC networks that can be easily connected to host vessels can contribute to the reconstruction of myocardial tissue grafts with a high potential for cardiac function repair. These results indicate that neovascularization can contribute to improved cardiac function after the transplantation of engineered cardiac tissues.
Effects of amantadine and trihexyphenidyl on memory in elderly normal volunteers (1987)

Anticholinergic drugs impair one's ability to learn new material, even at routine clinically used doses. During the trihexyphenidyl phase of this double-blind crossover trial, elderly normal subjects complained of confusion and memory impairment and demonstrated a pattern of deficits in memory function compatible with that previously reported to result from anticholinergic drugs. The subjects neither complained of nor demonstrated memory impairment while taking amantadine, which is believed to exert its pharmacological effects upon extrapyramidal disorders via dopaminergic mechanisms and does not appear to be associated with memory impairment. Anticholinergic drugs should be avoided whenever possible in the elderly and especially in those suffering dementia.
Polymer Microfluidics: Simple, Low-Cost Fabrication Process Bridging Academic Lab Research to Commercialized Production (2016)

Using polymer materials to fabricate microfluidic devices provides simple, cost effective, and disposal advantages for both lab-on-a-chip (LOC) devices and micro total analysis systems (μTAS). Polydimethylsiloxane (PDMS) elastomer and thermoplastics are the two major polymer materials used in microfluidics. The fabrication of PDMS and thermoplastic microfluidic device can be categorized as front-end polymer microchannel fabrication and post-end microfluidic bonding procedures, respectively. PDMS and thermoplastic materials each have unique advantages and their use is indispensable in polymer microfluidics. Therefore, the proper selection of polymer microfabrication is necessary for the successful application of microfluidics. In this paper, we give a short overview of polymer microfabrication methods for microfluidics and discuss current challenges and future opportunities for research in polymer microfluidics fabrication. We summarize standard approaches, as well as state-of-art polymer microfluidic fabrication methods. Currently, the polymer microfluidic device is at the stage of technology transition from research labs to commercial production. Thus, critical consideration is also required with respect to the commercialization aspects of fabricating polymer microfluidics. This article provides easy-to-understand illustrations and targets to assist the research community in selecting proper polymer microfabrication strategies in microfluidics.
CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications (2016)

Bispecific immunoglobulins (Igs) typically contain at least two distinct variable domains (Fv) that bind to two different target proteins. They are conceived to facilitate clinical development of biotherapeutic agents for diseases where improved clinical outcome is obtained or expected by combination therapy compared to treatment by single agents. Almost all existing formats are linear in their concept and differ widely in drug-like and manufacture-related properties. To overcome their major limitations, we designed cross-over dual variable Ig-like proteins (CODV-Ig). Their design is akin to the design of circularly closed repeat architectures. Indeed, initial results showed that the traditional approach of utilizing (G4S)x linkers for biotherapeutics design does not identify functional CODV-Igs. Therefore, we applied an unprecedented molecular modeling strategy for linker design that consistently results in CODV-Igs with excellent biochemical and biophysical properties. CODV architecture results in a circular self-contained structure functioning as a self-supporting truss that maintains the parental antibody affinities for both antigens without positional effects. The format is universally suitable for therapeutic applications targeting both circulating and membrane-localized proteins. Due to the full functionality of the Fc domains, serum half-life extension as well as antibody- or complement-dependent cytotoxicity may support biological efficiency of CODV-Igs. We show that judicious choice in combination of epitopes and paratope orientations of bispecific biotherapeutics is anticipated to be critical for clinical outcome. Uniting the major advantages of alternative bispecific biotherapeutics, CODV-Igs are applicable in a wide range of disease areas for fast-track multi-parametric drug optimization.
Expression of collagen genes in the liver. (1990)

Hepatic production of type I collagen is markedly increased in liver cirrhosis. Previous studies using primary liver cell cultures have demonstrated that hepatocytes, lipocytes and endothelial cells are all capable of producing collagen. In this study in situ hybridization and hepatic cell sorting have been used to identify which cells are expressing the type I collagen gene, alpha 1(I), in normal rat liver. Northern blotting of mRNAs from purified hepatic cell populations demonstrated that both hepatocytes and several types of non-parenchymal cells express the collagen alpha 1(I) gene. Calculations based on cell numbers, yields of mRNA, and cellular mRNA concentration demonstrated that the majority of collagen alpha 1(I) mRNA originates from the hepatocytes in the normal liver. Localization of a collagen alpha 1(I) mRNA by in situ hybridization confirmed that both hepatocytes and non-parenchymal cells express this gene. Furthermore, collagen alpha 1(I) gene expression in hepatocytes was obtained by transfecting a reporter gene driven by the collagen alpha (I) 5' regulatory segment in primary liver cell cultures. Future experiments will further characterize the regulation of collagen alpha 1(I) gene expression in the liver.
Detection and removal of barcode swapping in single-cell RNA-seq data (2018)

Barcode swapping results in the mislabelling of sequencing reads between multiplexed samples on patterned flow-cell Illumina sequencing machines. This may compromise the validity of numerous genomic assays; however, the severity and consequences of barcode swapping remain poorly understood. We have used two statistical approaches to robustly quantify the fraction of swapped reads in two plate-based single-cell RNA-sequencing datasets. We found that approximately 2.5% of reads were mislabelled between samples on the HiSeq 4000, which is lower than previous reports. We observed no correlation between the swapped fraction of reads and the concentration of free barcode across plates. Furthermore, we have demonstrated that barcode swapping may generate complex but artefactual cell libraries in droplet-based single-cell RNA-sequencing studies. To eliminate these artefacts, we have developed an algorithm to exclude individual molecules that have swapped between samples in 10x Genomics experiments, allowing the continued use of cutting-edge sequencing machines for these assays.
Role of Right Atrial Endocardial Structures as Barriers to Conduction During Human Type I Atrial Flutter (1995)

ICE enabled the correlation of functional electrophysiological properties with specific anatomic landmarks, identifying the CT and ER as barriers to conduction during human atrial flutter.
Binding of heparan sulfate to type V collagen (1989)

The functions and molecular interactions of type V collagen in the pericellular matrix are unclear. Our studies show that type V collagen adsorbed on a surface binds heparin/heparan sulfate with apparent higher affinity than do collagen types I, II, III, IV, or VI, fibronectin, or laminin. Therefore, heparin-like molecules may mediate interactions between cells and type V collagen. Hence, type V collagen may act as an anchor for proteoglycans in the extracellular matrix and function as a substrate for glycosaminoglycan-mediated cell attachment. This model is supported by studies showing that Chinese hamster ovary (CHO) cell mutants which are deficient in glycosaminoglycan synthesis attach poorly to type V collagen substrates compared to wild-type cells, whereas attachment of CHO cell mutants to fibronectin substrates is not affected. Also, exogenous heparin reduces attachment of CHO, endothelial, and smooth muscle cells to type V collagen but does not affect cell attachment to fibronectin. The inhibitory activity of the exogenous heparin/heparan sulfate depends on the size and sulfate content of the polysaccharide chains. At tested concentrations, chondroitin sulfate does not affect the attachment of CHO cells or the binding of biotin-conjugated heparan sulfate to wells coated with type V collagen. These data suggest that a certain degree of structural specificity is involved in glycosaminoglycan binding to type V collagen.
Noncovalent Immobilization of Proteins on a Solid Surface by Cucurbit[7]uril-Ferrocenemethylammonium Pair, a Potential Replacement of Biotin−Avidin Pair (2007)

A novel noncovalent method to immobilize a protein on a solid surface using the cucurbit[7]uril (CB[7])-ferrocenemethylammonium ion (FA) pair, which exhibits exceptionally high binding affinity (K approximate to 10(12) M-1), is reported. This method involves (1) anchoring CB[7] units on an alkanethiolate self-assembled monolayer (SAM) on gold, (2) attachment of FA units to a protein to be immobilized, and (3) immobilization of the "ferrocenylated" protein to the CB[7]-attached SAM on gold. As a proof of concept, the immobilization of ferrocenylated glucose oxidase (FA-GOx) on a CB[7]-anchored gold substrate, and its use as a glucose sensor, were demonstrated. In principle, this approach can be applied to the immobilization of any biomolecules including nucleic acids on any surfaces including glass, silicon, silica, and polymers. The synthetic host-guest pair with exceptional affinity, chemical robustness, simple preparation, and easy handling may replace the biotin-avidin system not only in the immobilization of biomolecules on solid surfaces, but also in other applications such as affinity chromatography and immunoassay.
Soluble Repulsive Guidance Molecule c/Hemojuvelin Is a Broad Spectrum Bone Morphogenetic Protein (BMP) Antagonist and Inhibits both BMP2- and BMP6-mediated Signaling and Gene Expression (2010)

Inactivating mutations in hemojuvelin/repulsive guidance molecule c (HJV/RGMc) cause juvenile hemochromatosis (JH), a rapidly progressive iron overload disorder in which expression of hepcidin, a key liver-derived iron-regulatory hormone, is severely diminished. Several growth factors in the bone morphogenetic protein (BMP) family, including BMP2 and BMP6, can stimulate production of hepcidin, a biological effect that may be modified by RGMc. Here we demonstrate that soluble RGMc proteins are potent BMP inhibitors. We find that 50- and 40-kDa RGMc isoforms, when added to cells as highly purified IgG Fc fusion proteins, are able to block the acute effects of both BMP2 and BMP6 at the levels of Smad induction and gene activation, and thus represent a potentially unique class of broad-spectrum BMP antagonists. Whole transcript microarray analysis revealed that BMP2 and BMP6 each stimulated expression of a nearly identical cohort of approximately 40 mRNAs in Hep3B cells and demonstrated that 40-kDa RGMc was an effective inhibitor of both growth factors, although its potency was less than that of the known BMP2-selective antagonist, Noggin. We additionally show that JH-linked RGMc mutant proteins that retain the ability to bind BMPs are also able to function as BMP inhibitors, and like the wild type soluble RGMc species, can block BMP-activated hepcidin gene expression. The latter results raise the question of whether disease severity in JH will vary depending on the ability of a given mutant RGMc protein to interact with BMPs.
High-Speed Tracking with Kernelized Correlation Filters (2014)

The core component of most modern trackers is a discriminative classifier, tasked with distinguishing between the target and the surrounding environment. To cope with natural image changes, this classifier is typically trained with translated and scaled sample patches. Such sets of samples are riddled with redundancies-any overlapping pixels are constrained to be the same. Based on this simple observation, we propose an analytic model for datasets of thousands of translated patches. By showing that the resulting data matrix is circulant, we can diagonalize it with the discrete Fourier transform, reducing both storage and computation by several orders of magnitude. Interestingly, for linear regression our formulation is equivalent to a correlation filter, used by some of the fastest competitive trackers. For kernel regression, however, we derive a new kernelized correlation filter (KCF), that unlike other kernel algorithms has the exact same complexity as its linear counterpart. Building on it, we also propose a fast multi-channel extension of linear correlation filters, via a linear kernel, which we call dual correlation filter (DCF). Both KCF and DCF outperform top-ranking trackers such as Struck or TLD on a 50 videos benchmark, despite running at hundreds of frames-per-second, and being implemented in a few lines of code (Algorithm 1). To encourage further developments, our tracking framework was made open-source.
Efficient generation of transgenic pigs using equine infectious anaemia virus (EIAV) derived vector (2004)

Traditional methods of transgene delivery in livestock are inefficient. Recently, human immunodeficiency virus (HIV-1) based lentiviral vectors have been shown to offer an efficient transgene delivery system. We now extend this method by demonstrating efficient generation of transgenic pigs using an equine infectious anaemia virus derived vector. We used this vector to deliver a green fluorescent protein expressing transgene; 31% of injected/transferred eggs resulted in a transgenic founder animal and 95% of founder animals displayed green fluorescence. This compares favourably with results using HIV-1 based vectors, and is substantially more efficient than the standard pronuclear microinjection method, indicating that lentiviral transgene delivery may be a general tool with which to efficiently generate transgenic mammals.
Requirement of CD9 on the Egg Plasma Membrane for Fertilization (2000)

CD9 is an integral membrane protein associated with integrins and other membrane proteins. Mice lacking CD9 were produced by homologous recombination. Both male and female CD9-/- mice were born healthy and grew normally. However, the litter size from CD9-/- females was less than 2% of that of the wild type. In vitro fertilization experiments indicated that the cause of this infertility was due to the failure of sperm-egg fusion. When sperm were injected into oocytes with assisted microfertilization techniques, however, the fertilized eggs developed to term. These results indicate that CD9 has a crucial role in sperm-egg fusion.
Molecular-level modeling of the viscoelasticity of crosslinked polymers: Effect of time and temperature (1997)

We present a new molecular-level picture of chain dynamics for describing the viscoelasticity of crosslinked polymers. The associated mathematical model consists of a time-dependent momentum balance on a representative polymer segment in the crosslinked network, plus phenomenological expressions for forces acting on the segments. These include a cohesive force that accounts for intermolecular attraction, an entropic force describing the thermodynamics governing chain conformations, and a frictional force that captures the temperature dependence of relative chain motion. We treat the case of oscillatory uniaxial deformation. Solution of the model equations in the frequency domain yields the dynamic moduli as functions of temperature and frequency. The model reproduces all of the qualitative features of experimental dynamic modulus data across the complete spectrum of time and temperature, spanning the glassy zone, the β transition, the dynamic glass transition, and the rubbery zone. All of the model parameters can be evaluated through the use of independent experimental data. Comparison of model predictions with experimental data yields good quantitative agreement outside of the glass transition region.
HINGE: long-read assembly achieves optimal repeat resolution (2017)

Long-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge. Aggressive approaches to repeat resolution often produce misassemblies, and conservative approaches lead to unnecessary fragmentation. We present HINGE, an assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding "hinges" to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers. HINGE was evaluated on the long-read bacterial data sets from the NCTC project. HINGE produces more finished assemblies than Miniasm and the manual pipeline of NCTC based on the HGAP assembler and Circlator. HINGE also allows us to identify 40 data sets where unresolvable repeats prevent the reliable construction of a unique finished assembly. In these cases, HINGE outputs a visually interpretable assembly graph that encodes all possible finished assemblies consistent with the reads, while other approaches such as the NCTC pipeline and FALCON either fragment the assembly or resolve the ambiguity arbitrarily.
Ion Channels — Basic Science and Clinical Disease (1997)

Ion channels constitute a class of proteins that is ultimately responsible for generating and orchestrating the electrical signals passing through the thinking brain, the beating heart, and the contracting muscle. Using the methods of molecular biology and patch-clamp electrophysiology, investigators have recently cloned, expressed, and characterized the genes encoding many of these proteins. Ion-channel proteins are under intense scrutiny in an effort to determine their roles in pathophysiology and as potential targets for drugs.Defective ion-channel proteins are responsible for cystic fibrosis,1 the long-QT syndrome,2 heritable hypertension (Liddle's syndrome),3,4 familial persistent hyperinsulinemic hypoglycemia of infancy,5,6 hereditary nephrolithiasis (Dent's . . .