gebhart/patrepeval huggingface dataset:
Differentiation of intersterility groups and geographic provenances among isolates of Heterobasidion annosum detected by random amplified polymorphic DNA assays (1993)

Random amplified polymorphic DNAs were correlated with the intersterility group and the geographic provenance of 36 isolates of Heterobasidion annosum from North America and Europe and of one herbarium collection of basidiocarps from California. This technique is very precise and yields higher resolution than previous studies implementing techniques such as isozyme electrophoresis and restriction fragment length polymorphisms. Random amplified polymorphic DNAs revealed differentiation among the following geographic groups and intersterility groups: western North American P, eastern North American P, European P, North American S, Scandinavian S, Italian S, and Italian F. This is the first report on differentiation between eastern and western North American P isolates as well as between northern and southern European S isolates. Successful amplification of one dry basidiocarp suggests that random amplified polymorphic DNAs may be used to improve epidemiological and population studies of this pathogen. Key words: species complex, genetic variability, strain typing, forest pathology, polymerase chain reaction.
Combined system of optical coherence tomography and fluorescence spectroscopy based on double-cladding fiber (2008)

We report the development of an all-fiber multimodal system, based on a double-cladding fiber (DCF) and related devices, suitable for simultaneous measurements of optical coherence tomography (OCT) and fluorescence spectroscopy (FS). The DCF together with a DCF coupler and a single-body DCF lens has assisted in the realization of a multimodal but single-unit probe for the combined system. The DCF lens allowed simultaneous focusing of input beams for OCT and FS and also the effective collection of both signal beams from a sample. The DCF coupler could extract the OCT signal via the core channel and the FS signal through the cladding channel. The OCT image and the fluorescence spectra of a plant tissue were then simultaneously measured to validate the performance of the proposed multimodal system.
Deep brain stimulation for Parkinson's disease: Surgical technique and perioperative management (2006)

Deep brain stimulation (DBS) is a widely accepted therapy for medically refractory Parkinson's disease (PD). Both globus pallidus internus (GPi) and subthalamic nucleus (STN) stimulation are safe and effective in improving the symptoms of PD and reducing dyskinesias. STN DBS is the most commonly performed surgery for PD as compared to GPi DBS. Ventral intermediate nucleus (Vim) DBS is infrequently used as an alternative for tremor predominant PD patients. Patient selection is critical in achieving good outcomes. Differential diagnosis should be emphasized as well as neurological and nonneurological comorbidities. Good response to a levodopa challenge is an important predictor of favorable long-term outcomes. The DBS surgery is typically performed in an awake patient and involves stereotactic frame application, CT/MRI imaging, anatomical targeting, physiological confirmation, and implantation of the DBS lead and pulse generator. Anatomical targeting consists of direct visualization of the target in MR images, formula-derived coordinates based on the anterior and posterior commissures, and reformatted anatomical stereotactic atlases. Physiological verification is achieved most commonly via microelectrode recording followed by implantation of the DBS lead and intraoperative test stimulation to assess benefits and side effects. The various aspects of DBS surgery will be presented.
MEDI0639: A Novel Therapeutic Antibody Targeting Dll4 Modulates Endothelial Cell Function and Angiogenesis In Vivo (2012)

The Notch signaling pathway has been implicated in cell fate determination and differentiation in many tissues. Accumulating evidence points toward a pivotal role in blood vessel formation, and the importance of the Delta-like ligand (Dll) 4-Notch1 ligand-receptor interaction has been shown in both physiological and tumor angiogenesis. Disruption of this interaction leads to a reduction in tumor growth as a result of an increase in nonfunctional vasculature leading to poor perfusion of the tumor. MEDI0639 is an investigational human therapeutic antibody that targets Dll4 to inhibit the interaction between Dll4 and Notch1. The antibody cross-reacts to cynomolgus monkey but not mouse species orthologues. In vitro MEDI0639 inhibits the binding of Notch1 to Dll4, interacting via a novel epitope that has not been previously described. Binding to this epitope translates into MEDI0639 reversing Notch1-mediated suppression of human umbilical vein endothelial cell growth in vitro. MEDI0639 administration resulted in stimulation of tubule formation in a three-dimensional (3D) endothelial cell outgrowth assay, a phenotype driven by disruption of the Dll4-Notch signaling axis. In contrast, in a two-dimensional endothelial cell-fibroblast coculture model, MEDI0639 is a potent inhibitor of tubule formation. In vivo, MEDI0639 shows activity in a human endothelial cell angiogenesis assay promoting human vessel formation and reducing the number of vessels with smooth muscle actin-positive mural cells coverage. Collectively, the data show that MEDI0639 is a potent modulator of Dll4-Notch signaling pathway.
High temperature polymer dielectrics from the ring opening metathesis polymerization (ROMP) (2009)

Recently much research has focused on the development of new polymer dielectric materials to fabricate capacitors for use in the inverters of next generation hybrid electric vehicles (HEV). The capacitors used in HEVs inverters will be required to operate at 150°C, 600 V, and have an energy density of 0.9 J/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . Polymer based thin film capacitors are ideal for this application due to their relatively high energy density, low cost, and high dielectric breakdown strength. We have polymerized several ring strained monomers using ring opening metathesis polymerization (ROMP) and have identified a promising polymer system based on N-Phenyl-7-oxanorbornene-5,6-dicarboximide (PhONDI). Several of its copolymers with norbornene have been evaluated for possible use as next generation high temperature polymer dielectrics in thin film capacitors. The copolymers were cast into thin films and Au electrodes were deposited on the polymer film. The electrical properties were evaluated as a function of temperature. The polymer system exhibited very good high temperature dielectric properties and is potentially useful as a high temperature capacitor dielectric.
Customizing lung-protective mechanical ventilation strategies* (2006)

Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, MD Supported, in part, by contracts F32 HL078132, P50 HL073944, and NO1 HR46063 with the National Institutes of Health, National Heart, Lung, and Blood Institute.
Selective Wettability Assisted Nanoliter Sample Generation via Electrowetting-Based Transportation (2007)

A novel method for nanoliter sample generation is demonstrated. In this method, an electrowetting-based platform (EWOD) was used to transport a water droplet which was sandwiched between two hydrophobic plates, and the transportation was carried out by the direct electrical control of planar electrodes on the bottom glass substrate. In contrast to the air environment in ordinary EWOD, silicone oil was employed to surround the water droplet to reduce the surface hysteresis; therefore, the fluidic operations including cutting and transportation became easier to manipulate. While the droplet was moving through the electrodes, a nanoliter sample was produced within the circular hydrophilic area which was patterned on the upper ITO coated plate. Hence, based on the definition of selective wettability areas, the sample volume is capable to be well generated and controlled. Besides, in order to optimize the dimensions of electrode, the dimensional criterion for complete sample generation was investigated. The result shows that larger electrode width permits more flexibility to determine the radius of hydrophilic circle. Upon this mechanism, the hydrophilic circle of 0.25 mm diameter is able to generate the tiny sample of 3.9 nanoliter. Since the dimensions of the hydrophilic circle could be easily patterned in tens microns, this method has the potential to achieve the picoliter sample via similar procedure. Consequently, according to the tiny sample generation and reduction of hysteresis, such method is well-suitable for the versatile applications.
TheXenopusreceptor tyrosine kinase Xror2 modulates morphogenetic movements of the axial mesoderm and neuroectoderm via Wnt signaling (2002)

The Spemann organizer plays a central role in neural induction, patterning of the neuroectoderm and mesoderm, and morphogenetic movements during early embryogenesis. By seeking genes whose expression is activated by the organizer-specific LIM homeobox gene Xlim-1 in Xenopus animal caps, we isolated the receptor tyrosine kinase Xror2. Xror2 is expressed initially in the dorsal marginal zone, then in the notochord and the neuroectoderm posterior to the midbrain-hindbrain boundary. mRNA injection experiments revealed that overexpression of Xror2 inhibits convergent extension of the dorsal mesoderm and neuroectoderm in whole embryos, as well as the elongation of animal caps treated with activin, whereas it does not appear to affect cell differentiation of neural tissue and notochord. Interestingly, mutant constructs in which the kinase domain was point-mutated or deleted (named Xror2-TM) also inhibited convergent extension, and did not counteract the wild-type, suggesting that the ectodomain of Xror2 per se has activities that may be modulated by the intracellular domain. In relation to Wnt signaling for planar cell polarity, we observed: (1) the Frizzled-like domain in the ectodomain is required for the activity of wild-type Xror2 and Xror2-TM; (2) co-expression of Xror2 with Xwnt11, Xfz7, or both, synergistically inhibits convergent extension in embryos; (3) inhibition of elongation by Xror2 in activin-treated animal caps is reversed by co-expression of a dominant negative form of Cdc42 that has been suggested to mediate the planar cell polarity pathway of Wnt; and (4) the ectodomain of Xror2 interacts with Xwnts in co-immunoprecipitation experiments. These results suggest that Xror2 cooperates with Wnts to regulate convergent extension of the axial mesoderm and neuroectoderm by modulating the planar cell polarity pathway of Wnt.
Constitutional Delay of Growth: Expected versus Final Adult Height (1991)

Constitutional delay of growth and puberty is believed to represent a variation of normal growth, and it is expected that children with this condition will grow for a longer duration than average and reach a height that is normal for their genetic potential. The records of children with constitutional delay of growth and puberty who were initially seen in the Pediatric Endocrine Clinic at the Oregon Health Sciences University between 1975 and 1983 were retrospectively reviewed. Criteria for study included a height more than 2 SD below the mean, a significantly delayed bone age, and a normal growth velocity on follow-up. Forty-two subjects were located and final adult height measurements were obtained. AT contact, the 29 male subjects (mean age = 23.9 years) were 169.5 +/- 4.5 cm tall (mean +/- SD), and the 13 female subjects (mean age = 20.5 years) were 156 +/- 3.8 cm tall. Adult height predictions during follow-up, using either the Bayley-Pinneau or Roche-Wainer-Thissen method, were close to final adult heights. The males were 1.2 SD and the females 1.3 SD below the 50th percentile as adults. This finding was not fully explained by genetic short stature; the males fell 5.1 cm and the females 5.3 cm below target heights based on midparental heights. It is concluded that this discrepancy is most likely explained by a selection bias of the shortest children referred to and observed in a subspecialty clinic, although a defect in human growth hormone secretion or function in children at the far end of the spectrum of constitutional delay of growth and puberty cannot be excluded.
Effect of Plasma on Characteristics of Zirconium Oxide Films Deposited by Plasma-Enhanced Atomic Layer Deposition (2005)

The effect of plasma on the deposition of films was investigated using plasma-enhanced atomic layer deposition. Plasma pulse width and oxidant gas composition were varied to examine the effect on film characteristics. Characteristics such as impurity content, dielectric constant, and electric field-current density curve were strongly dependent on the plasma pulse width. The relative dielectric constants of films deposited at 150°C were greatly increased from 11.2 to 31.3 with increasing plasma pulse width from 0.2 to 1.5 s. The addition of gas to the plasma had only a slight effect on film characteristics.
Retrovirus-expressed hemagglutinin protects against lethal influenza virus infections (1988)

An influenza virus hemagglutinin gene, H7, has been expressed in a replication-competent Schmidt-Ruppin Rous sarcoma virus-derived vector. This virus, P1/H7, expressed a glycosylated precursor of the H7 protein which was processed to a mature form and transported to the cell surface. The expressed H7 glycoprotein could not be detected in P1/H7 virus particles. A P1/H7 stock which expressed 5 to 10% of the level of H7 observed in influenza virus-infected chicken embryo fibroblasts was used to immunize 1-month-old chickens. This immunization resulted in low or undetectable levels of hemagglutination-inhibiting and neutralizing antibody. Despite the low serum response, challenge with a highly pathogenic H7N7 virus revealed complete protection against lethal infection.
Effect of whole body vibration on muscular performance, balance, and bone (2012)

Tässä väitöskirjatutkimussarjassa tutkittiin vibraatiokuormituksen vaikutuksia nuorten ihmisen (turvallisuussyyt) luustoon, suorituskykyyn ja tasapainoon, ja sitä kautta pyrittiin löytämään uusia keinoja kaatumisten ja osteoporoottisten murtumien ehkäisyyn.\n\nTutkimus koostui viidestä osatyöstä (Vibra I-V), joista I ja II selvittivät, kuinka paljon ja miten yksittäinen, 4 minuutin vibraatioaltistus (seisominen vibraatiolevyllä) kuormittaa elimistöä (suorituskykymittaukset ja EMG-rekisteröinnit alaraajojen lihaksista). Vibraatioaltistus oli Vibra I:ssä ja II:ssa erilainen värinän frekvenssin ja amplitudin suhteen. Vibra III:ssa selvitimme 4 kk kestävän vibraatiokuormituksen vaikutukset fyysiseen suorituskykyyn ja tasapainoon (suorituskykymittaukset). Vibra IV puolestaan tutki 8 kk kestävän kuormituksen vaikutuksia sekä fyysiseen suorituskykyyn (suorituskykymittaukset) että luustoon (pQCT, DXA, MRI, verianalyysit) satunnaistetussa, randomisoidussa koeasetelmassa. Lisäksi selvitettiin kehittyykö elimistössä vibraatiokuormituksen kautta kompensatorisia mekanismeja, joilla olisi suotuisia vaikutuksia kaatumisten ja niistä johtuvien osteoporoottisten murtumien ehkäisyyn. Vibra V oli seurantatutkimus neljännelle työlle ja siinä tutkittiin pitkäaikaisen vibraatiokuormituksen seurauksena mahdollisesti syntyneiden luu- ja suorituskykyvaikutusten pysyvyyttä.\n\nTutkimussarja onnistui hyvin ja vibraatiokuormitus todettiin turvalliseksi käyttää. Sillä ei ollut vaikutuksia luun massaan, rakenteeseen tai lujuuteen missään mitatussa luustopisteessä. Luumarkkerit eivät myöskään muuttuneet intervention aikana. Sen sijaan vibraatiokuormitus (sekä kerta-altistus että pitkäaikaiskuormitus) aikaansai merkittävän nettohyödyn hyppykorkeuteen kontrolliryhmään verrattuna. Muihin suorituskyky- tai tasapainotesteihin vibraatiokuormituksella ei sensijaan ollut selviä vaikutuksia.\n\nVaikka tämän randomoidun, kontrolloidun kliinisen tutkimuksen tulokset eivät olleet yhtä positiiviset kuin äskettäin julkaistujen eläinkokeiden tulokset, tässä tutkimuksessa käytetty vibraatiokuormitus voi kuitenkin olla sekä turvallinen että tehokas harjoittelu- ja kuntoutusmuoto, ei pelkästään urheilijoille vaan myös ikäihmisille, sillä alaraajojen räjähtävällä voimalla sekä suorituskyvyllä on tärkeä merkitys kaatumisten ehkäisyssä. Toisaalta tämä tutkimus jätti myös paljon kysymyksiä ilmaan koskien vibraatiokuormituksen vaikutuksia luuhun ja suorituskykyyn, ja lisätutkimukset ovatkin ehdottomasti tarpeen, ennen kuin minkäänlaisia kliinisiä suosituksia vibraatiokuormitukselle voidaan antaa. Jatkotutkimuksissa voidaan vaihdella vibraatiokuormituksen laatua, voimakkuutta, taajuutta ja kestoa, ja näin yrittää löytää mahdollisimman tehokas kuormitusmuoto. Mielenkiintoista olisi myös tutkia vibraatiokuormituksen vaikutuksia ihmisillä, joiden suorituskyky ja/tai luukudos ovat syystä tai toisesta heikentyneet.
A Drosophila gene is subject to glucose repression (1987)

Amylase-specific cDNA probes were used to assay amylase mRNA levels in third-instar larvae of Drosophila melanogaster. It is shown that there is a difference, of the order of 100-fold, in the mRNA levels between larvae that are fed 10% glucose and larvae of the same wild-type strain that are fed an equivalent diet lacking glucose. In fact, the glucose-fed larvae have barely detectable levels of amylase mRNA. This large difference in transcript abundance indicates that the glucose effect, which we previously characterized at the level of enzyme activity, probably reflects a change in the transcriptional activity of the amylase gene.
Performance of Endosonography-Guided Fine Needle Aspiration and Biopsy in The Diagnosis of Pancreatic Cystic Lesions (2003)

EUS-guided FNA is a valuable tool in the preoperative diagnostic assessment of pancreatic cystic lesions.
Inhibition of lung tumor colonization by leech salivary gland extracts from Haementeria ghilianii. (1983)

Salivary gland extract from the South American leech Haementeria ghilianii, administered i.v. on the same day as the i.v. inoculation of T241 sarcoma cells, completely suppresses colonization of the mediastinal lymph nodes and markedly reduces the number and size of lung tumor colonies produced by this tumor. Additional studies indicate that the extract contains various types of proteinase inhibitors and has the capacity to inhibit clotting and platelet aggregation by tumor material and collagen. Although not yet proved by direct evidence, these activities may be involved in the inhibitory effect of lung tumor colonization by the leech extract.
Convenient Synthesis of 2-Arylbenzimidazoles and 2,2′-Diaryl-bisbenzimidazoles (2003)

Abstract 2-Aryl-benzimidazoles and 2,2′-diaryl-5,5′-bisbenzimidazoles were synthesized conveniently by treating of trifluoromethyl aryl ketones with ortho-diamines in polar solvents with good to excellent yields. The reaction condition is mild and tolerant to most function groups.
Learning The Discriminative Power-Invariance Trade-Off (2007)

We investigate the problem of learning optimal descriptors for a given classification task. Many hand-crafted descriptors have been proposed in the literature for measuring visual similarity. Looking past initial differences, what really distinguishes one descriptor from another is the tradeoff that it achieves between discriminative power and invariance. Since this trade-off must vary from task to task, no single descriptor can be optimal in all situations. Our focus, in this paper, is on learning the optimal tradeoff for classification given a particular training set and prior constraints. The problem is posed in the kernel learning framework. We learn the optimal, domain-specific kernel as a combination of base kernels corresponding to base features which achieve different levels of trade-off (such as no invariance, rotation invariance, scale invariance, affine invariance, etc.) This leads to a convex optimisation problem with a unique global optimum which can be solved for efficiently. The method is shown to achieve state-of-the-art performance on the UIUC textures, Oxford flowers and Cal- tech 101 datasets.
The duobinary technique for high-speed data transmission (1963)

A new data transmission technique has been evolved, which has the speed capability of the quaternary systems and, at the same time, promising performance. An important advantage of this technique is that the amount of circuitry required and the degree of complexity are relatively low, being not much more than for a straight binary system and much less than for a typical quaternary system. The process is sufficiently general so that it is applicable to serial transmission over wire lines and parallel transmission over high-frequency radio circuits.
Smart community: an internet of things application (2011)

In this article, we introduce an Internet of Things application, smart community, which refers to a paradigmatic class of cyber-physical systems with cooperating objects (i.e., networked smart homes). We then define the smart community architecture, and describe how to realize secure and robust networking among individual homes. We present two smart community applications, Neighborhood Watch and Pervasive Healthcare, with supporting techniques and associated challenges, and envision a few valueadded smart community services.
HPID: The Human Protein Interaction Database (2004)

http://www.hpid.org.
Anti-glucosaminidase monoclonal antibodies as a passive immunization for methicillin-resistant Staphylococcus aureus (MRSA) orthopedic infections (2011)

Recently, methicillin-resistant Staphylococcus aureus (MRSA) has surpassed HIV as the most deadly pathogen in the United States, accounting for over 100,000 deaths per year. In orthopedics, MRSA osteomyelitis has become the greatest concern in patient care, despite the fact that improvements in surgical technique and aggressive antibiotic prophylaxis have decreased the infection rate for most procedures to less than 5%. This great concern is largely due to the very poor outcomes associated with MRSA osteomyelitis, which includes 30-50% failure rates for revision surgery. Thus, there is a need to develop additional therapeutic interventions such as passive immunization, particularly for immunocompromised patients and the elderly who are typically poor responders to active vaccines. Using a novel murine model of implant-associated osteomyelitis in which a stainless steel pin is coated with bioluminescent S. aureus and implanted transcortically through the tibial metaphysis, we discovered that mice protect themselves from this infection by mounting a specific IgG2b response against the peptidoglycan hydrolase, glucosaminidase (Gmd), an enzyme involved in cell wall digestion during binary fission. Since this subunit of S. aureus autolysin is essential for bacterial growth, and no genetic variation has been identified among clinical strains, we propose that monoclonal antibodies against this enzyme would have multiple mechanisms of action, including promotion of opsonophagocytosis and direct inhibition of enzyme function. Here we review the field of MRSA osteomyelitis and our research to date on the development of an anti-Gmd passive immunotherapy.