gebhart/patrepeval huggingface dataset:
Full-Thickness Rotator Cuff Tears (1996)

We performed a biomechanical comparison of two rotator cuff repair techniques using fresh-frozen human cadavers. Nine pairs of cadaveric shoulders had standardized full-thickness tears made at the supraspinatus tendon insertion. One of each pair of the cadaveric shoulders was repaired by pulling the tendon into a bone trough in the humeral head using standard sutures. The remaining half of the pairs was repaired using anchor sutures. The repairs were tested using a servohydraulically operated material testing system. The anchor suture repair was significantly stronger than the standard suture technique irrespective of bone quality. Failure occurred predominantly through bone in the suture repairs and as a result of suture breakage in the anchor repairs. The anchors should be placed into the edge of the subchondral bone adjacent to the articular surface. The surgeon should direct the anchor so that the direction of the pull is approximately 90 degrees to the anchor, with the humerus at 30 degrees of abduction.
Selected strategies to augment polynucleotide immunization. (1996)

We sought to amplify the immune response to polynucleotide immunization through co-delivery of complementary DNA (cDNA) encoding a cytokine or co-stimulatory molecule to enhance antigen presentation. In the context of intramuscular immunization, we examined co-delivery of cDNAs for B7-1 and human carcinoembryonic antigen (CEA) within separate plasmids or a dual plasmid with two independent expression cassettes. Intramuscular delivery of the dual expression plasmid produced anti-CEA antibody responses and antitumor effects superior to those generated by plasmid DNA encoding CEA alone. However, co-delivery of cDNAs encoding B7-1 and CEA in the form of two separate plasmids produced no augmentation. The importance of single plasmid delivery suggests the effectiveness of this strategy is contingent upon co-expression of B7-1 and CEA within the same cell. The success of cutaneous polynucleotide immunization by particle bombardment is thought to derive largely from the presence of Langerhans cells within the skin. We hypothesized that co-delivery of plasmid DNA encoding granulocyte-macrophage colony stimulating factor (GM-CSF) by particle bombardment would enhance the antigen presenting capacity of Langerhans cells at the inoculation site similar to its effects in vitro. Augmentation of CEA-specific lymphoblastic transformation and antibody response was observed when plasmid GM-CSF (pGM-CSF) was administered 3 days prior to each dose of plasmid DNA encoding CEA. These strategies for augmentation of immune response to polynucleotide immunization should be applicable to a wide variety of antigenic targets including infectious agents and other tumor-associated antigens.
Cutting Edge: Requirement for Growth Hormone-Releasing Hormone in the Development of Experimental Autoimmune Encephalomyelitis (2003)

Growth hormone (GH)-releasing hormone (GHRH) is a neuropeptide that stimulates secretion of GH from the pituitary gland. Although GHRH and its receptor (GHRHR) are expressed in leukocytes, physiological function of GHRH in the immune system remains unclear. To study the influence of GHRH in autoimmunity, susceptibility to experimental autoimmune encephalomyelitis (EAE) was examined in C57BL/6J-Ghrhr(lit/lit) (lit/lit), mice deficient in the GHRHR gene. We found that lit/lit mice were resistant to myelin oligodendrocyte glycoprotein (MOG)-induced EAE. Splenocytes from MOG-immunized lit/lit mice proliferated normally in response to MOG peptide, suggesting that activation of MOG-specific T cells in GHRHR-deficient mice is not impaired. Our data strongly suggest that GHRH plays a crucial role in the development of EAE and may provide the basis for a novel therapeutic approach protecting from autoimmune diseases.
A Study of øX-174 DNA Torus and Lambda DNA Torus Tertiary Structure and the Implications For DNA Self-Assembly (1986)

Hydrated torus shaped complexes were examined by transmission electron microscopy in both spermidine-condensed linear and nicked circular phi X-174 DNA and lambda DNA preparations. Freeze-etch replicas of both these torus samples, produced with very low Pt metal deposition levels (9APt/C), were found to have circumferentially wound single DNA double helix size surface fibers in the range of 30A width. Measurements of torus inner and outer circumference as well as ring thickness were performed. Observed differences in the torus dimension distributions from circular phi X-174 DNA and linear phi X-174 DNA may be related to the different topological constraints on DNA folding in these two samples (1). On the basis of annulus thickness measurements phi X-174 DNA toruses, in contrast to lambda DNA toruses, were observed to fall into two classes identified as being formed from monomer DNA condensation and multimer DNA condensation. All of the torus substructure and population dimensions observed here are consistent with the continuous circumferential DNA winding model of torus organization proposed by Marx and Reynolds (1) to explain the micrococcal nuclease cleavage properties of the toruses. End-on view measurements of the torus thickness were made from micrographs obtained by extensive tilting of the object replica. These direct measurements confirmed quaternary structure interpretations made from simple strand packing models. We compared the measured torus properties in this linear DNA size series (5386-48000 bp). With increasing DNA length the pattern of DNA strand self-assembly was found to be more varied producing lambda DNA toruses of varying shape. The relevance of our study to the problem of lambda bacteriophage DNA head packaging was discussed.
A Wavelet-Based ECG Delineator: Evaluation on Standard Databases (2004)

In this paper, we developed and evaluated a robust single-lead electrocardiogram (ECG) delineation system based on the wavelet transform (WT). In a first step, QRS complexes are detected. Then, each QRS is delineated by detecting and identifying the peaks of the individual waves, as well as the complex onset and end. Finally, the determination of P and T wave peaks, onsets and ends is performed. We evaluated the algorithm on several manually annotated databases, such as MIT-BIH Arrhythmia, QT, European ST-T and CSE databases, developed for validation purposes. The QRS detector obtained a sensitivity of Se = 99.66% and a positive predictivity of P+ = 99.56% over the first lead of the validation databases (more than 980,000 beats), while for the well-known MIT-BIH Arrhythmia Database, Se and P+ over 99.8% were attained. As for the delineation of the ECG waves, the mean and standard deviation of the differences between the automatic and manual annotations were computed. The mean error obtained with the WT approach was found not to exceed one sampling interval, while the standard deviations were around the accepted tolerances between expert physicians, outperforming the results of other well known algorithms, especially in determining the end of T wave.
Jonathan Crystal. Unwanted Company: Foreign Investment in American Industries. Ithaca, N.Y.: Cornell University Press, 2003. xii + 230 pp. ISBN 0-8014-4123-4, $30.45 (cloth). (2004)

An abstract is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Cloning and expression of portions of the 34-kilodalton-protein gene of Mycobacterium paratuberculosis: its application to serological analysis of Johne's disease (1993)

Paratuberculosis (Johne's disease), an endemic mycobacteriosis of cattle that is caused by Mycobacterium paratuberculosis, is characterized by incoercible diarrhea and fecal shedding of bacteria. The present work aimed at developing a specific serological test for this disease. We have recently shown that a 34-kDa protein belonging to the major antigen complex A36 of M. paratuberculosis is immunodominant and contains epitopes specific with respect to all mycobacteria tested, including Mycobacterium bovis and the closely related species Mycobacterium avium. From a lambda gt11 genomic library of M. paratuberculosis, three portions of the gene coding for this 34-kDa protein have been isolated. Two of them expressed cross-reacting mycobacterial epitopes. One portion (in clone a362) expressed a polypeptide which cross-reacted with all tested M. paratuberculosis strains but not with 20 other bacteria tested, including many strains of the M. avium-Mycobacterium intracellulare-Mycobacterium scrofulaceum group. The occurrence at the M. paratuberculosis surface of epitopes corresponding to the a362 polypeptide was shown by immune electron microscopy. The recombinant a362 polypeptide was used as reagent for an enzyme-linked immunoassay for paratuberculosis. This assay correctly diagnosed all the tested blood samples from infected cattle at all stages of the disease.
Vitamin E in tardive dyskinesia: time course of effect after placebo substitution. (1993)

Alpha-tocopherol (vitamin E) has been found to be effective in the treatment of tardive dyskinesia (TD). Studies to date have been short in duration and have not found long-term carryover effects of vitamin E. The present study examined the persistence of the effects of vitamin E after longer term (36-week) treatment was discontinued. Vitamin E significantly improved TD over this period. However, the effects of vitamin E persisted so that TD scores approached baseline only after 12 weeks of placebo substitution.
The Gram Stain after More than a Century (1996)

The Gram stain, the most important stain in microbiology, was described more than a century ago. Only within the past decade, however, has an understanding of its mechanism emerged. It now seems clear that the cell wall of Gram-positive microorganisms is responsible for retention of a crystal violet:iodine complex. In Gram-negative cells, the staining procedures damage the cell surface resulting in loss of dye complexes. Gram-positive microorganisms require a relatively thick cell wall, irrespective of composition, to retain the dye. Therefore, Gram-stainability is a function of the cell wall and is not related to chemistry of cell constituents. This review provides a chronology of the Gram stain and discusses its recently discovered mechanism.
Non Viral Vectors in Gene Therapy- An Overview (2015)

Non-viral vectors are simple in theory but complex in practice. Apart from intra cellular and extracellular barriers, number of other challenges also needs to be overcome in order to increase the effectiveness of non-viral gene transfer. These barriers are categorized as production, formulation and storage. No one-size-fits-all solution to gene delivery, which is why in spite of various developments in liposome, polymer formulation and optimization, new compounds are constantly being proposed and investigated. In this review, we will see in detail about various types of non-viral vectors highlighting promising development and recent advances that had improved the non-viral gene transfer efficiency of translating from "Bench to bedside".
Hypothermia for neuroprotection after cardiac arrest: Systematic review and individual patient data meta-analysis (2005)

Mild therapeutic hypothermia improves short-term neurologic recovery and survival in patients resuscitated from cardiac arrest of presumed cardiac origin. Its long-term effectiveness and feasibility at an organizational level need further research.
An arc‐sequencing algorithm for intensity modulated arc therapy (2007)

Intensity modulated arc therapy (IMAT) is an intensity modulated radiation therapy delivery technique originally proposed as an alternative to tomotherapy. IMAT uses a series of overlapping arcs to deliver optimized intensity patterns from each beam direction. The full potential of IMAT has gone largely unrealized due in part to a lack of robust and commercially available inverse planning tools. To address this, we have implemented an IMAT arc-sequencing algorithm that translates optimized intensity maps into deliverable IMAT plans. The sequencing algorithm uses simulated annealing to simultaneously optimize the aperture shapes and weights throughout each arc. The sequencer enforces the delivery constraints while minimizing the discrepancies between the optimized and sequenced intensity maps. The performance of the algorithm has been tested for ten patient cases (3 prostate, 3 brain, 2 head-and-neck, 1 lung, and 1 pancreas). Seven coplanar IMAT plans were created using an average of 4.6 arcs and 685 monitor units. Additionally, three noncoplanar plans were created using an average of 16 arcs and 498 monitor units. The results demonstrate that the arc sequencer can provide efficient and highly conformal IMAT plans. An average sequencing time of approximately 20 min was observed.
A flexible pattern recognition system for analysis of ECG and related demographics and annotations (2002)

A methodology for structuring information inherent in research data is proposed. Dividing the data according to system, group and temporal levels allows reflecting the information inherent in the data the construction of a flexible analysis system able to handle different research tasks. Two simple examples of the use of these principles are used to illustrate the working principles of the methodology.
Etiology of Parkinson's disease: Genetics and environment revisited (2002)

Idiopathic Parkinson's disease (PD) is the second most common neurodegenerative disorder and affects more than 1 million Americans over the age of 55. The disease selectively affects dopaminergic neurons of the substantia nigra pars compacta, culminating in their demise. After ≈50% of the dopamine neurons and 75–80% of striatal dopamine is lost, patients start to exhibit the classical symptoms of PD including bradykinesia, postural reflex impairment, resting tremor, and rigidity (1, 2). Although there are several treatments that are effective for a number of years, their usefulness wanes over time and is accompanied by unacceptable side effects. New therapies are clearly needed for this disorder.

Despite many years of focused research, the causes of this disease remain to be elucidated. Understanding the cause of PD is critical as that knowledge could lead to directed research that will develop new and potent therapies. The relative contributions of genetic versus environmental factors regarding the cause of PD have been hotly debated. In an attempt to define a cause for this disease, early epidemiological studies examining twins suggested an absence of genetic factors (3). However, these studies were not definitive and could never account for differences in disease progression between twin pairs that could account for discordance in diagnosis. The discovery that the protoxin n -methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) causes parkinsonism in both humans and nonhumans further strengthened the hypothesis that PD had an environmental etiology. Other environmental toxins have been shown to induce a parkinsonian state as well, supporting this view (4). However, the recent discovery of inherited forms of PD shifted the emphasis back to genetic factors. Among the different genetic forms of PD, mutations in the gene encoding for α-synuclein have received the most attention. Mutations in this gene cause rare forms of PD. Furthermore, α-synuclein is also present in the …
MATLAB-based automated patch-clamp system for awake behaving mice (2015)

Automation has been an important part of biomedical research for decades, and the use of automated and robotic systems is now standard for such tasks as DNA sequencing, microfluidics, and high-throughput screening. Recently, Kodandaramaiah and colleagues (Nat Methods 9: 585-587, 2012) demonstrated, using anesthetized animals, the feasibility of automating blind patch-clamp recordings in vivo. Blind patch is a good target for automation because it is a complex yet highly stereotyped process that revolves around analysis of a single signal (electrode impedance) and movement along a single axis. Here, we introduce an automated system for blind patch-clamp recordings from awake, head-fixed mice running on a wheel. In its design, we were guided by 3 requirements: easy-to-use and easy-to-modify software; seamless integration of behavioral equipment; and efficient use of time. The resulting system employs equipment that is standard for patch recording rigs, moderately priced, or simple to make. It is written entirely in MATLAB, a programming environment that has an enormous user base in the neuroscience community and many available resources for analysis and instrument control. Using this system, we obtained 19 whole cell patch recordings from neurons in the prefrontal cortex of awake mice, aged 8-9 wk. Successful recordings had series resistances that averaged 52 ± 4 MΩ and required 5.7 ± 0.6 attempts to obtain. These numbers are comparable with those of experienced electrophysiologists working manually, and this system, written in a simple and familiar language, will be useful to many cellular electrophysiologists who wish to study awake behaving mice.
Image Alignment and Stitching: A Tutorial (2007)

This tutorial reviews image alignment and image stitching algorithms. Image alignment algorithms can discover the correspondence relationships among images with varying degrees of overlap. They are ideally suited for applications such as video stabilization, summarization, and the creation of panoramic mosaics. Image stitching algorithms take the alignment estimates produced by such registration algorithms and blend the images in a seamless manner, taking care to deal with potential problems such as blurring or ghosting caused by parallax and scene movement as well as varying image exposures. This tutorial reviews the basic motion models underlying alignment and stitching algorithms, describes effective direct (pixel-based) and feature-based alignment algorithms, and describes blending algorithms used to produce seamless mosaics. It ends with a discussion of open research problems in the area.
Phenotypic and Biochemical Analyses of BACE1- and BACE2-deficient Mice (2005)

Beta-secretase (BACE1) is the rate-limiting protease for the generation of the amyloid beta-peptide (Abeta) in Alzheimer disease. Mice in which the bace1 gene is inactivated are reported to be healthy. However, the presence of a homologous gene encoding BACE2 raises the possibility of compensatory mechanisms. Therefore, we have generated bace1, bace2, and double knockout mice. We report here that BACE1 mice display a complex phenotype. A variable but significant number of BACE1 offspring died in the first weeks after birth. The surviving mice remained smaller than their littermate controls and presented a hyperactive behavior. Electrophysiologically, subtle alterations in the steady-state inactivation of voltage-gated sodium channels in BACE1-deficient neurons were observed. In contrast, bace2 knockout mice displayed an overall healthy phenotype. However, a combined deficiency of BACE2 and BACE1 enhanced the bace1-/- lethality phenotype. At the biochemical level, we have confirmed that BACE1 deficiency results in an almost complete block of Abeta generation in neurons, but not in glia. As glia are 10 times more abundant in brain compared with neurons, our data indicate that BACE2 could indeed contribute to Abeta generation in the brains of Alzheimer disease and, in particular, Down syndrome patients. In conclusion, our data challenge the general idea of BACE1 as a safe drug target and call for some caution when claiming that no major side effects should be expected from blocking BACE1 activity.
Spatial and molecular organization of lymph node T cell cortex: a labyrinthine cavity bounded by an epithelium-like monolayer of fibroblastic reticular cells anchored to basement membrane-like extracellular matrix (2001)

Naive T cells encounter antigen-presenting cells within the cortex of lymph nodes to initiate primary immune responses. Within this T cell cortex is the reticular network (RN)--a system of collagen fibers and extracellular matrix (ECM) wrapped by fibroblastic reticular cells (FRC). We have investigated the distribution of various molecules, including ECM proteins and proteoglycans, in the T cell cortex of both human and rodent lymph node. We confirm and extend reports of matrix elements in the RN. In addition, we find that staining for the laminin-alpha3 chain and for tenascin reveals a 'hollow' reticular pattern, consistent with localization to the basement membrane-like covering of reticular fibers. In contrast, keratan sulfate is observed in a fine linear pattern within the RN, suggesting it is localized to the core of the fibers. Staining with the marker ER-TR7 indicates that FRC cover all identifiable ECM surfaces of the T cell cortex. Based on these findings and previous reports, we conclude that cortical lymphocytes migrate within a 'labyrinthine cavity' free of fibrillar ECM, distinguishing the T cell cortex from other loose connective tissues, and that the FRC lining of the cavity constitutes an epithelium-like boundary. We propose that this spatial organization facilitates ameboid leukocyte crawling along preformed paths of least resistance and that the basement membrane-like ECM of the FRC may facilitate fluid transport within the RN by limiting leakage from the fiber.
Development of a P1 phagemid system for the delivery of DNA into Gram-negative bacteria (2002)

The inability to transform many clinically important Gram-negative bacteria has hampered genetic studies addressing the mechanism of bacterial pathogenesis. This report describes the development and construction of a delivery system utilizing the broad-host-range transducing bacteriophage P1. The phagemids used in this system contain a P1 pac initiation site to package the vector, a P1 lytic replicon to generate concatemeric DNA, a broad-host-range origin of replication and an antibiotic-resistance determinant to select bacterial clones containing the recircularized phagemid. Phagemid DNA was successfully introduced by infection and stably maintained in members of the families Enterobacteriaceae (Escherichia coli, Shigella flexneri, Shigella dysenteriae, Klebsiella pneumoniae and Citrobacter freundii) and Pseudomonadaceae (Pseudomonas aeruginosa). In addition to laboratory strains, these virions were used successfully to deliver phagemids to a number of strains isolated from patients. This ability to deliver genetic information to wild-type strains raises the potential for use in antimicrobial therapies and DNA vaccine development.
Whole blood angiopoietin-1 and -2 levels discriminate cerebral and severe (non-cerebral) malaria from uncomplicated malaria (2009)

These results suggest that whole blood ANG-1/2 levels are promising clinically informative biomarkers of disease severity in malarial syndromes.