gebhart/patrepeval huggingface dataset:
Human Immunodeficiency Virus (HIV) Seropositivity among Uninfected HIV Vaccine Recipients (2003)

Since 1987, >10,000 individuals worldwide have received immunizations with human immunodeficiency virus (HIV) preventive vaccine constructs. Many constructs elicit antibodies detected by standard serologic tests (enzyme immunoassays, rapid tests, and Western blots) and result in vaccine recipients' serum being identified as reactive and indicative of HIV infection. To determine the frequency of vaccine-induced HIV antibody among uninfected HIV vaccine trial participants and to identify factors associated with these results, serum samples from HIV-uninfected participants from selected United States phase I/II HIV-1 vaccine trials were tested with 6 serologic screening tests. Reactive specimens were tested by use of Western blot. Overall, 490 serum specimens from 461 vaccine recipients were tested; 100 (20.4%) reacted on at least 1 serologic test, and 65 (13%) were determined to be positive by Western blot. Canarypox or vaccinia vaccine recipients' serum with or without HIV envelope glycoprotein (gp120 or gp160) boosts accounted for all positive Western blot results; no positive Western blot results were obtained from gp120 subunit recipients. The potential for vaccine recipients being misclassified as HIV infected increased with vaccine complexity.
A Virulence Locus of Pseudomonas aeruginosa Encodes a Protein Secretion Apparatus (2006)

Bacterial pathogens frequently use protein secretion to mediate interactions with their hosts. Here we found that a virulence locus (HSI-I) of Pseudomonas aeruginosa encodes a protein secretion apparatus. The apparatus assembled in discrete subcellular locations and exported Hcp1, a hexameric protein that forms rings with a 40 angstrom internal diameter. Regulatory patterns of HSI-I suggested that the apparatus functions during chronic infections. We detected Hcp1 in pulmonary secretions of cystic fibrosis (CF) patients and Hcp1-specific antibodies in their sera. Thus, HSI-I likely contributes to the pathogenesis of P. aeruginosa in CF patients. HSI-I-related loci are widely distributed among bacterial pathogens and may play a general role in mediating host interactions.
Mechanisms of growth inhibition by anti-transferrin receptor monoclonal antibodies. (1986)

In previous studies, an immunoglobulin A, anti-transferrin receptor antibody (42/6) inhibited growth of a variety of normal and malignant human hemopoietic cells. To determine its mechanism of growth inhibition, we compared effects of 42/6 and B3/25, an immunoglobulin G anti-transferrin receptor antibody which does not inhibit lymphocyte growth, on transferrin (TF) binding and uptake. As in previous studies, affinity constants of TF and anti-TF receptor antibodies for human TF receptors at 4 degrees C were similar, but the number of calculated binding sites was higher for the antibodies. Antibody B3/25 did not inhibit TF binding at either 4 degrees C or 37 degrees C. At 4 degrees C, antibody 42/6 inhibited TF binding to normal, mitogen-stimulated mononuclear cells. However, TF did not inhibit 42/6 binding, suggesting 42/6 inhibited TF binding by noncompetitive, possibly steric, mechanisms. When cells were simultaneously exposed to labeled TF and unlabeled anti-TF receptor antibodies at 37 degrees C, 42/6 inhibited TF binding only slightly. Initial uptake of antibodies and TF at 37 degrees C was rapid, but when mononuclear cells or HL60 cells were cultured with either 42/6 or B3/25 for 2 days, TF binding and immunoreactive TF receptor sites decreased. However, TF bound to cells cultured with B3/25 continued to enter the cell, whereas cells cultured with 42/6 would no longer take up bound TF. Studies using HL60 cells grown with soluble iron in lieu of TF showed that changes in TF binding sites and TF uptake were not secondary to growth inhibition. We conclude that incubation with both inhibitory (42/6) and noninhibitory (B3/25) anti-TF receptor antibodies results in decreased TF binding sites. However, exposure to 42/6 also inhibits TF uptake and causes growth inhibition by iron deprivation. Monoclonal antibodies to receptors transporting critical nutrient molecules, such as iron, may inhibit cell growth by blocking ligand access to the cell's interior.
Molecular Imaging of Pulmonary Disease In Vivo (2009)

Characterization and noninvasive measurement of molecular pathways and biochemistry in living cells, animal models, and humans at the cellular and molecular level is now possible using remote imaging detectors. Positron and single photon emission tomography scanners, highly sensitive cameras for bioluminescence and fluorescence imaging, as well as high-magnetic-field magnetic resonance imaging scanners, can be used to study such diverse processes as signal transduction, receptor density and function, host response to pathogens, cell trafficking, and gene transfer. In many cases, images from more than one modality can be fused, allowing structure-function and multifunction relationships to be studied on a tissue-restricted or regional basis. "Molecular imaging" holds enormous potential for elucidating the molecular mechanisms of pulmonary disease and therapeutic response in intact animal models and humans.
Iron requirement of Lactobacillus spp. in completely chemically defined growth media (2000)

A completely chemically-defined growth medium, containing guanine, thymine, cytidine, 2'-deoxyadenosine and 2'-deoxyuridine as DNA precursors, was developed for Lactobacillus johnsonii, on the basis of statistically designed techniques suitable for other lactobacilli. Particular focus was given to the nucleotide composition of different defined media, and to the specific nucleotide requirements of Lact. johnsonii. Most of the lactobacilli tested grew in a medium containing five free bases, four ribonucleosides or five deoxyribonucleosides. Adenine and guanine were replaceable by inosine. The requirement for thymine and cytosine was satisfied with uracil. The presence of inosine and uracil was identified as being essential for the growth of different Lactobacillus species, displaying their inability to synthesize purines and pyrimidines de novo. Defined recipes with different nucleotide composition were used to investigate iron requirements of lactobacilli. Only marginal differences in growth were observed in iron-depleted media supplemented with five free bases, four ribonucleosides or five deoxyribonucleosides; iron depletion had a greater effect on growth when inosine and uracil were supplied as the only nucleotide sources. The results suggest that iron plays a role in the pyrimidine and purine metabolism of lactobacilli. Lactobacillus spp., particularly Lact. johnsonii, require iron under particular environmental conditions with limited or specific nucleotide sources.
Comparative evaluation of a chemiluminescent DNA probe and an exoantigen test for rapid identification of Histoplasma capsulatum (1992)

A chemiluminescent DNA probe (Accuprobe) assay developed by Gen Probe, Inc., for the rapid identification of Histoplasma capsulatum was evaluated and compared with the exoantigen test by using 162 coded cultures including Histoplasma capsulatum var. capsulatum, Histoplasma capsulatum var. duboisii, Histoplasma capsulatum var. farciminosum, Blastomyces dermatitidis, Coccidioides immitis, Paracoccidioides brasiliensis, and morphologically related saprobic fungi. Each test uses a chemiluminescent, acridinium ester-labeled, single-stranded DNA probe that is complementary to the rRNA of the target organism. Lysates of the test cultures were prepared by sonication with glass beads and heat treated. After the rRNA was released from the target organism, the labeled DNA probe combined with the target H. capsulatum rRNA to form a stable DNA-RNA hybrid. A hybridization protection assay was used, and the chemiluminescence of hybrids was measured initially with a Leader 1 luminometer as relative light units and later during the investigation with a probe assay luminometer as probe light units. Of the 162 coded mycelial cultures tested by the Accuprobe assay, 105 were identified as H. capsulatum. The test could be performed with an inoculum of a few square millimeters (1 to 2 mm2) of growth. In the primary evaluation, the Accuprobe identified 103 of the 105 cultures as H. capsulatum within 2 h. The remaining two cultures, contaminated with bacteria, had to be purified before the Accuprobe assay identified them correctly as H. capsulatum. Since each coded culture was concurrently tested for H. capsulatum, B. dermatitidis, and C. immitis exoantigens, the identification of all three dimorphic pathogens was provided simultaneously. Of the 162 coded cultures tested, 105 were identified by the exoantigen test as H. capsulatum, 12 were identified as B. dermatitidis, 13 were identified as C. immitis, and 32 were negative for H. capsulatum, B. dermatitidis, and C. immitis. The bacterial contamination in two isolates did not interfere with the exoantigen testing. The exoantigen test required 7- to 10-day-old colonies and required 48 to 72 h of incubation before definitive identification was obtained.
Proxy Server 2.0 : Proxy Server 2.0の実装とサポート (1999)

第１章 Ｍｉｃｒｏｓｏｆｔ Ｐｒｏｘｙ Ｓｅｒｖｅｒ入門 第２章 ＴＣＰ／ＩＰの理解 第３章 Ｐｒｏｘｙ Ｓｅｒｖｅｒの構造 第４章 Ｐｒｏｘｙ Ｓｅｒｖｅｒのインストール 第５章 ＩＩＳのインストール 第６章 インターネットマネージャとＰｒｏｘｙ Ｓｅｒｖｉｃｅ 第７章 アクセス制御 第８章 インターネットとイントラネットアクセス 第９章 複数のＰｒｏｘｙ Ｓｅｒｖｅｒとインターネットアクセス 第１０章 リモートアクセスサービス（ＲＡＳ） 第１１章 監視と調整 第１２章 問題の解明 第１３章 計画と配置
Induction of lymphokine synthesis in peripheral blood mononuclear cells with phorbol ester and calcium ionophore allows precise measurement of individual variations in capacity to produce IL 2. (1986)

Absolute capacity for IL2 production by human peripheral blood mononuclear cells (PBMC) was studied using 12-O-tetradecanoylphorbol 13-acetate (TPA) and calcium ionophore A23187, which act synergistically, to induce lymphokine synthesis. Culture parameters were optimized for the TPA/A23187 stimulation such that maximal IL2 titers were produced with a high degree of reproducibility. Thus, using a synthetic medium, TPA/A23187 at 20/50ng/ml respectively, and a cell concentration of 2.5 X 10(6)/ml, IL2 titers in the cultures increased linearly over a period of 96h, reaching values at least 15-fold higher than with lectin stimulation. This allowed for determinations of IL2 synthetic capacity in individual blood samples. Large fluctuations in normal IL2 production (range 1775-10654 BRMP U/ml at 48h) were observed among 23 normal persons. A statistically significant lower IL2 productive capacity was observed in the age group above 40 as compared to those under 40. The lower rates of IL2 synthesis in a group of patients with Hodgkin's disease was seen only among those who had undergone immunosuppressive therapy; newly diagnosed cases fell within the normal range.
Sunitinib and PF-562,271 (FAK/Pyk2 inhibitor) effectively block growth and recovery of human hepatocellular carcinoma in a rat xenograft model (2009)

The results from this study indicate that the combination of sunitinib and PF-562,271 TKI has the potential to target different aspects of angiogenesis and tumor aggressiveness and may have significantly greater effect than relevant single agent, blocking not only tumor growth, but also impacting the ability of the tumor to recover upon withdrawal of the therapy.
Botulinum Toxin Type A (BOTOX ® ) for the Prophylactic Treatment of Chronic Daily Headache: A Randomized, Double‐Blind, Placebo‐Controlled Trial (2005)

BoNT-A treatment resulted in patients having, on average, approximately seven more (1 week) headache-free days compared to baseline. Although at the primary time point (day 180) the BoNT-A treatment resulted in a 1.5 between-group difference compared to placebo, this difference was not statistically significant. The treatment met secondary efficacy outcome measures, including the percentage of patients experiencing a 50% or more decrease in the frequency of headache days, in addition to statistically significant reductions in headache frequency. BoNT-A was also well tolerated in patients with CDH.
Full-field breast tomosynthesis. (2005)

Breast tomosynthesis is a 3-dimensional (3-D) imaging technology that involves acquiring images of a stationary compressed breast at multiple angles during a short scan. The individual images are then reconstructed into a series of thin high-resolution slices that displayed individually or in a dynamic ciné mode. Tomosynthesis can reduce or eliminate the tissue overlap effect. While holding the breast stationary, images are acquired at a nsumber of different x-ray source angles. Objects at different heights in the breast project differently for each angle. The final step in the tomosynthesis procedure is reconstructing the data to generate images that enhance objects from a given height by appropriate shifting of the projections relative to one another. There are 3 specific areas in tomosynthesis system requirements that warrant a closer review: detector efficiency and dose, field of view, and equipment geometry. The breast is compressed in a standard way. While holding the breast stationary, the x-ray tube is rotated over a limited angular range. A series of low dose exposures are made every few degrees, creating a series of digital images. Typically, the tuben is rotated about +/-15 degrees, and 11 exposures are made every 3 degrees during a total scan of a few seconds. The individual images are projections through the breast at different angles and these arewhat are reconstructed into slices. There are 2 basic tomosynthesis system designs that diiffer in the motion of the detector during acquisition. One method moves the detector in concert with the x-ray tube so as to maintain the shadow of the breast on the detector. An altemate method is to keep the detector stationary relative to the breast platform. The tomosynthesis reconstruction process consists of computing high-resolution images whose planes are parallel to the breast support plates. Typically, these images are reconstructed with slice separation of 1 mm; thus, a 5 cm compressed breast tomosynthesis study will have 50 reconstructed slices. The reconstructed tomosynthesis slices can be displayed similarly to computed tomography (CT) reconstructed slices. Tomosynthesis could resolve many of the tissue overlap reading problems that are a major source of the need for recalls and additional imaging in 2-D mammography exams.
How an Understanding of the Function of the Locus Coeruleus Led to Use of Dexmedetomidine to Treat Agitation in Bipolar Disorder: Example of Rational Development of Psychiatric Medications (2022)

This column reviews >50 years of research on the functions subsumed by the locus coeruleus (LC) (also called the central adrenergic system). A major role of the LC is monitoring acid-base balance in the brain and responding by regulating blood-brain permeability to water and other small molecules and cerebral blood flow. The LC, through its downward projections, also regulates and coordinates respiratory and cardiac functions. Through its effect regionally or more globally depending on the stimulus and its magnitude, the LC can regulate the extracellular space in the brain, which in turn can alter ionic concentrations and thus the sensitivity of neurons to signaling. As a result of these far-reaching effects, the LC has been implicated in brain functions ranging from sleep and wakefulness to psychiatric conditions such as hyperarousal/hypervigilance, fear, agitation, anxiety, and panic attacks. This understanding of the brain functions subsumed by the LC has, in turn, led to the most recent development in the use of dexmedetomidine, an alpha-2 adrenergic agonist, to treat agitation in patients with bipolar disorder. This column also illustrates a theme discussed in a series of previous columns concerning the successful development of novel psychiatric/central nervous system drugs on the basis of an understanding of relatively simple circuits or mechanisms that underlie pathologic behavior.
A Prospective Double-Blind Evaluation of Cocaine, Phenylephrine with Xylocaine and Oxymetazoline with Xylocaine for Topical Intranasal Use (1989)

A prospective, double-blind evaluation using 3 ml of 10% cocaine, 0.5% phenylephrine with 5% Xylocaine, and 0.05% oxymetazoline with 5% Xylocaine was conducted to compare the anesthetic, decongestant, and systemic effects of each of the drugs. Degree of anesthesia was measured by placing a probe on the nasal mucosa in the area of Kisselbach's plexus and passing an electric current until a sensation could just be felt. Decongestant properties were assessed using anterior rhinomanometry. Systemic effects were determined by continuous blood pressure and pulse recordings and by recording subject comments. Cocaine showed better anesthesia, slower onset of vasoconstriction, significant blood pressure elevation, and multiple subjective side effects. Phenylephrine mixtures showed almost no unpleasant side effects, more rapid vasoconstriction than cocaine, and statistically significant anesthesia. Oxymetazoline mixture did not offer any advantages in anesthesia or vasoconstriction and produced the most unpleasant side effects. Cocaine appears to be the drug of choice for long surgical procedures in patients with normal cardiorespitatory systems. Phenylephrine with Xylocaine may be used as the drug of choice for shorter office procedures for those patients with cocaine sensitivity.
Current guidelines in the management of interstitial cystitis. (2015)

Interstitial cystitis (IC) is a heterogeneous chronic disease of unknown etiology that impacts a very large number of women. Symptoms are highly variable: patients may suffer from pelvic pain that is exacerbated by bladder filling, and can be associated with a variety of lower urinary tract symptoms including frequency and urgency. Given the varying presentations and severities of corresponding treatment must be tailored to each specific patient. Current American Urological Association (AUA) guidelines separate the IC treatment recommendations into six tiers of increasing invasive therapies. These treatment guidelines begin with education and lifestyle modifications and progress through levels of physical, pharmacological, and ultimately surgical therapies for those that fail the less invasive therapies. The purpose of this review is to outline the recommendations for the treatment of IC and the evidence from which these recommendations arise. Furthermore, we examine the most up to date literature so that we may recognize future directions in the treatment of IC.
Measurements and models for 38-GHz point-to-multipoint radiowave propagation (2000)

This article presents results of a wide-band measurement campaign conducted at 38 GHz. The objective of the research was to determine multipath and time varying channel behavior of short-hop millimeter-wave point-to-multipoint radio links during various weather events. 73963 power delay profiles (PDPs) were captured on three links, each comparable to proposed local multipoint distribution systems (LMDS) in a campus environment. Multipath was observed in unobstructed LOS links during rain but not during clear weather. Short-term variation of the received signal over 1-2 min observation periods is described by a Rician distribution with a K factor which varies as a function of rain rate. Measured rain attenuation exceeds Crane's (1996) model predictions by several decibels. A novel prediction technique is presented that applies canonical antenna patterns and site specific information to estimate worst case multipath channel characteristics including relative power, time of arrival (TOA), and angle of arrival (AOA) of each multipath component. New metrics, the excess delay zone and relative power zone, are defined and contour plots are developed to determine potential reflectors from an area site map. These results and models provide useful guidelines for the design of millimeter-wave wireless communication systems.
Porter: a new, accurate server for protein secondary structure prediction (2004)

gianluca.pollastri@ucd.ie.
A novel pitch-lag search method using adaptive weighting and median filtering (2003)

This paper presents a novel method to estimate the pitch-lag in a speech codec. The pitch-lag is related to the fundamental frequency of the speech signal and an accurate estimation of this parameter is important for the subjective quality of the synthesised speech. A common problem in speech codecs is that the estimation of the pitch-lag often produces a multiple or a sub-multiple of the true pitch value. When these incorrect pitch-lag values are used in speech synthesis the subjective quality of the speech is degraded. This paper presents an improved method where the estimation of the pitch-lag parameter is biased towards the pitch-lag values of the previous speech segments resulting in a consistent set of consecutive pitch-lag values and a high quality reconstructed signal. The classification of speech into voiced and unvoiced parts is used when tracking the pitch-lag values and adapting the pitch track centered weighting function.
TWEAK stimulation of astrocytes and the proinflammatory consequences (2000)

Astrocytes exert many active roles in brain homeostasis, potentially including the regulation of immune reactions. They possess a substantial aptitude for plasticity and, indeed, functional and phenotypic changes are frequently encountered in reactive gliosis observed in brain injuries. The significance of reactive astrocytes is still poorly defined, but it is clear that these cells are an important source of cytokines in inflamed brain. How tumor necrosis factor (TNF) and TNF-receptor family members contribute to this reaction is an interesting issue that is currently being explored. It was previously shown that reactive astrocytes express high levels of Fas (CD95) and respond to Fas ligand (CD95L) by apoptosis or IL-8 production. TWEAK (Apo-3 ligand) is a recently identified member of the TNF family that is produced mainly by leukocytes that can infiltrate the inflamed brain and thus influence astrocyte behavior. Here we show that human astrocytes derived from different regions of the brain specifically bind TWEAK and are totally resistant to TWEAK mediated apoptosis. In addition, high amounts of IL-8 and IL-6 were secreted by astrocytes after TWEAK exposure. Finally, expression of cell surface molecules involved in the propagation and/or maintenance of brain inflammation was determined. TWEAK significantly increased ICAM-1 expression on astrocytes, whereas no modification was detected in the expression of Fas, TNFRI, B7-1, or MHC molecules. In conclusion, the proinflammatory effects induced by TWEAK on astrocytes in culture recapitulate many characteristics of reactive astrocytes observed in vivo, suggesting that TWEAK could play a significant role in brain inflammation.
Characterization of the Mouse Adeno-Associated Virus AAVS1 Ortholog (2004)

The nonpathogenic human adeno-associated virus (AAV) has developed a mechanism to integrate its genome into human chromosome 19 at 19q13.4 (termed AAVS1), thereby establishing latency. Here, we provide evidence that the chromosomal signals required for site-specific integration are conserved in the mouse genome proximal to the recently identified Mbs85 gene. These sequence motifs can be specifically nicked by the viral Rep protein required for the initiation of site-specific AAV DNA integration. Furthermore, these signals can serve as a minimal origin for Rep-dependent DNA replication. In addition, we isolated the mouse Mbs85 proximal promoter and show transcriptional activity in three mouse cell lines.