gebhart/patrepeval huggingface dataset:
Measurement of fluid-flow-velocity profile in turbid media by the use of optical Doppler tomography (1997)

Optical Doppler tomography is demonstrated to be a simple, accurate, and noncontact method for measuring the fluid velocity of laminar flow in small-diameter (~0.5-mm) ducts. Studies are described that utilize circular (square) plastic (glass) ducts infused with a moving suspension of polymer microspheres in air and buried in an optically turbid medium. The measurement of Doppler-shifted frequencies of backscattered light from moving microspheres is used to construct a high-resolution spatial profile of fluid-flow velocity in the ducts.
Mumps Outbreaks in Vaccinated Populations: Are Available Mumps Vaccines Effective Enough to Prevent Outbreaks? (2008)

Increased reports of mumps in vaccinated populations prompted a review of the performance of mumps vaccines. The effectiveness of prior vaccination with 1 dose of vaccine ranged from 72.8% to 91% for the Jeryl Lynn strain, from 54.4% to 93% for the Urabe strain, and from 0% to 33% for the Rubini strain. Vaccine effectiveness after 2 doses of mumps vaccine was reported in 3 outbreaks and ranged from 91% to 94.6%. There was evidence of waning immunity, which is a likely factor in mumps outbreaks, aggravated by possible antigenic differences between the vaccine strain and outbreak strains. Inadequate vaccine coverage or use of the Rubini vaccine strain accounted for the majority of outbreaks reviewed; however, some outbreaks could not be prevented, despite high vaccination coverage with 2 doses of the Jeryl Lynn vaccine strain. Our findings indicate the need for more-effective mumps vaccines and/or for review of current vaccination policies to prevent future outbreaks.
Poly-paraphyly of Hirudinidae: many lineages of medicinal leeches (2009)

The family Hirudinidae must be refined to include only the clade containing Hirudo medicinalis (European medicinal leech) and related leeches irrespective of bloodfeeding behavior. A second clade containing Macrobdella decora (North American medicinal leech) and its relatives may yet be recognized in Semiscolecidae in order to avoid paraphyly. The African distribution of species from each of the divergent hirudinid clades suggests that a deep divergence took place in the history of the medicinal leeches hundreds of millions of years ago.
Properties of lucerne transient streak virus, and evidence of its affinity to southern bean mosaic virus (1979)

SUMMARY A virus obtained from naturally infected lucerne ( Medicago sativa ) in New Zealand reacted with antiserum to an Australian isolate of lucerne transient streak virus (LTSV). Some plants infected with New Zealand isolates showed yellow flecks along lateral veins of leaves; symptoms were transient in some lucerne plants but persistent in others. A New Zealand isolate (LTSV‐NZ) infected 14 of 39 plant species tested by mechanical inoculation, but was not transmitted by five aphid species. In sap of Nicotiana clevelandii , LTSV‐NZ was infective after storage for 4 wk at 20 o C, diluting to 10 ‐5 , or heating for 10 min at 70 o C. Purified virus preparations contained a single electrophoretic component and a single sedimenting component (s 20w = 112 S ) which formed a single buoyant density component in CsCl (1.37 g cm ‐3 ) but two density components in Cs 2 SO 4 (1.26 and 1.32 g cm ‐3 ). LTSV‐NZ particles were stable in 10 ITIM EDTA at pH 5, but not at pH 8, being degraded into two sedimenting components of 105 S and 92 S. Particles contained c. 18% RNA in the form of one single‐stranded RNA molecule of mol. wt 1–4 times 10 6 , and a polypeptide of mol. wt c. 32 400. LTSV‐NZ was serologically unrelated to 24 other isometric plant viruses. However, its properties are similar to those of southern bean mosaic virus and allied viruses. The present cryptogram of LTSV is R/l: 1–4/(18):S/S:S/*.
Manganese Blocks Intracellular Trafficking of Shiga Toxin and Protects Against Shiga Toxicosis (2012)

Infections with Shiga toxin (STx)-producing bacteria cause more than a million deaths each year and have no definitive treatment. To exert its cytotoxic effect, STx invades cells through retrograde membrane trafficking, escaping the lysosomal degradative pathway. We found that the widely available metal manganese (Mn(2+)) blocked endosome-to-Golgi trafficking of STx and caused its degradation in lysosomes. Mn(2+) targeted the cycling Golgi protein GPP130, which STx bound in control cells during sorting into Golgi-directed endosomal tubules that bypass lysosomes. In tissue culture cells, treatment with Mn(2+) yielded a protection factor of 3800 against STx-induced cell death. Furthermore, mice injected with nontoxic doses of Mn(2+) were completely resistant to a lethal STx challenge. Thus, Mn(2+) may represent a low-cost therapeutic agent for the treatment of STx infections.
Anti-DR5 mAb Ameliorate Adjuvant Arthritis Rats Through Inducing Synovial Cells Apoptosis (2009)

This study shows that anti-DR5 mAb can ameliorate arthritic symptoms. The mechanisms of the treatment are related to the increase in synovial cell apoptosis by regulating the mRNA expression of DR5 and apoptosis-related genes, prolonging the duration of the cell cycle by modulation of the mRNA expression of cell cycle-related genes, and the protein expression of the molecules in the caspase pathway and RANKL, JNK2, and c-Jun.
Inferior Sagittal Osteotomy With Hyoid Bone Suspension for Obese Patients With Sleep Apnea (1996)

An inferior sagittal osteotomy with a sliding mandibular osteotomy and hyoid bone suspension, combined with a uvulopalatopharyngoplasty, tends to improve obstructive sleep apnea in obese patients.
aarC, an essential gene involved in density-dependent regulation of the 2'-N-acetyltransferase in Providencia stuartii (1997)

The 2'-N-acetyltransferase [AAC(2')-Ia] in Providencia stuartii has a dual function where it is involved in the acetylation of peptidoglycan and certain aminoglycosides. A search for negative regulators of the aac(2')-Ia gene has resulted in the identification of aarC. A missense allele (aarC1) resulted in an 8.9-fold increase in beta-galactosidase accumulation from an aac(2')-lacZ transcriptional fusion. Northern blot analysis demonstrated an increase in aac(2')-Ia mRNA accumulation that was specific to cells at high density. In addition, the aarC1 allele also resulted in a substantial increase in the expression of aarP, a transcriptional activator of the aac(2')-Ia gene. The wild-type aarC gene was isolated by complementation and encodes a predicted protein of 365 amino acids with a molecular mass of 39,815 Da. The predicted AarC protein exhibited 88% amino acid homology to the previously identified GcpE protein of Escherichia coli and 86% homology to a gene product from Haemophilus influenzae. The E. coli gcpE gene was able to functionally complement the aarC1 allele in P. stuartii. The aarC1 allele was identified as a T to G transversion that resulted in a valine to glycine substitution at position 136 in the AarC protein. The aarC gene appears to be essential for cell viability as construction of a disrupted copy (aarC::lacZ) was possible only in cells that carried an episomal copy of aarC or gcpE.
An off-line breath sampling and analysis method suitable for large screening studies (2007)

We present a new, off-line breath collection and analysis method, suitable for large screening studies. The breath collection system is based on the guidelines of the American Thoracic Society for the sampling of exhaled NO. Breath containing volatile gases is collected in custom-made black-layered Tedlar bags and analyzed by proton-transfer reaction mass spectrometry (PTR-MS). The collection method and data analysis is validated for its accuracy, precision, selectivity, limits of detection, sensitivity and reproducibility. Consecutive fillings of five bags by the same person gave reproducible results to within 12% relative standard deviation (RSD) for methanol, acetaldehyde, acetone and water content from breath, whereas isoprene was constant to within 30% RSD. In an exploratory small-scale case-control study, we monitor the exhaled breath of 11 lung cancer patients on the day before surgery. The control group consisted of 57 age-matched subjects, the so-called 'healthy smokers'. This study is used as an example of the use of the system presented here.
Modified Toxicity Probability Interval Design: A Safer and More Reliable Method Than the 3 + 3 Design for Practical Phase I Trials (2013)

The 3 + 3 design is the most common choice among clinicians for phase I dose-escalation oncology trials. In recent reviews, more than 95% of phase I trials have been based on the 3 + 3 design. Given that it is intuitive and its implementation does not require a computer program, clinicians can conduct 3 + 3 dose escalations in practice with virtually no logistic cost, and trial protocols based on the 3 + 3 design pass institutional review board and biostatistics reviews quickly. However, the performance of the 3 + 3 design has rarely been compared with model-based designs in simulation studies with matched sample sizes. In the vast majority of statistical literature, the 3 + 3 design has been shown to be inferior in identifying true maximum-tolerated doses (MTDs), although the sample size required by the 3 + 3 design is often orders-of-magnitude smaller than model-based designs. In this article, through comparative simulation studies with matched sample sizes, we demonstrate that the 3 + 3 design has higher risks of exposing patients to toxic doses above the MTD than the modified toxicity probability interval (mTPI) design, a newly developed adaptive method. In addition, compared with the mTPI design, the 3 + 3 design does not yield higher probabilities in identifying the correct MTD, even when the sample size is matched. Given that the mTPI design is equally transparent, costless to implement with free software, and more flexible in practical situations, we highly encourage its adoption in early dose-escalation studies whenever the 3 + 3 design is also considered. We provide free software to allow direct comparisons of the 3 + 3 design with other model-based designs in simulation studies with matched sample sizes.
Texture classification using rotated wavelet filters (2000)

We propose an approach to the texture classification problem using a set of two-dimensional (2-D) wavelet filters that are nonseparable and oriented for improved characterization of diagonally oriented textures. Channel energies are estimated at the output of both the new filter bank and a standard discrete wavelet frames (DWF) filter bank. Classification results obtained using each individual method and in combination are presented. The results show that the oriented filter set results in finer discrimination providing complementary texture information to the DWF by making use of its orientation selectivity. As a result, a combination of the features from the output of two filter banks improved the classification accuracy significantly with a smaller number of features.
CD36 is a receptor for oxidized low density lipoprotein (1993)

The oxidation of low density lipoprotein (LDL) in the arterial wall is thought to contribute to human atherosclerotic lesion formation, in part by the high affinity uptake of oxidized LDL (OxLDL) by macrophages, resulting in foam cell formation. We have utilized cloning by expression to identify CD36 as a macrophage receptor for OxLDL. Transfection of a CD36 clone into 293 cells results in the specific and high affinity binding of OxLDL, followed by its internalization and degradation. An anti-CD36 antibody blocks 50% of the binding of OxLDL to platelets and to human macrophage-like THP cells. Furthermore, like mouse macrophages, 293 cells expressing CD36 recognize LDL which has been oxidized only 4 h, whereas more extensive oxidation of the LDL is required for recognition by the other known OxLDL receptors, the acetylated LDL (AcLDL) receptor and Fc gamma RII-B2. CD36 may play a role in scavenging LDL modified by oxidation and may mediate effects of OxLDL on monocytes and platelets in atherosclerotic lesions.
Cams and Pincer Impingement Are Distinct, Not Mixed: The Acetabular Pathomorphology of Femoroacetabular Impingement (2010)

Before performing surgery for cam-type femoroacetabular impingement, surgeons should consider measuring the acetabular depth. The cam acetabulum is shallower than normal and may be rendered pathologically shallow by acetabular rim resection leading to early joint failure.
Label-Free Cell-Based Functional Assays (2008)

Label-free technologies based on electrical impedance or refractive index are new tools for measuring a cell-based functional response. Although the technologies are relatively new to high throughput screening cell-based applications, they are rapidly generating interest in that they are able to measure a phenotypic response using cells natively expressing the target protein without using dyes or cellular extracts. In addition, one can measure the cellular response using a kinetic mode resulting in an assay potentially rich in content. This article will describe these technologies and their applications in measuring cell proliferation, cell attachment and spreading, cell apoptosis and their application for several receptor target classes, including receptor tyrosine kinases and G protein-coupled receptors. The potential utility and drawbacks of these tools for high throughput screening, directed screening and compound profiling will also be discussed.
Adverse events associated with mTOR inhibitors (2012)

A better prevention and management of mTORi-related side effects requires the identification of alterations in related biological pathways that will help to delineate therapeutic targets.
Small molecules based on 2,7-carbazole for efficient solution-processed organic solar cells (2013)

A series of small molecules (DTCz-TBT, DTCz-2TBT and DTCz-3TBT) with 2,7-carbazole as a center core donor, benzothiadiazole as acceptor units and oligothiophenes as end-capping units were synthesized and characterized. Their thermal, optical, electrochemical and photovoltaic properties were examined. With increasing the number of the terminal thiophene units and conjugation length, these molecules exhibit red-shifted absorption (529–594 nm), up-shifted HOMO levels (−5.27 to −5.08 eV), and reduced optical band gaps (2.04 to 1.80 eV). Solution processed organic solar cells (OSCs) based on DTCz-TBT/PC71BM exhibit a power conversion efficiency of 2.26% with a high open-circuit voltage up to 1.02 V, while the OSCs based on DTCz-2TBT/PC71BM and DTCz-3TBT/PC71BM exhibit power conversion efficiencies of 3.44% and 3.90% without any post-treatment.
Estradiol Effects on Proliferation, Messenger Ribonucleic Acid for Collagen and Insulin-like Growth Factor-I, and Parathyroid Hormone-Stimulated Adenylate Cyclase Activity in Osteoblastic Cells from Calvariae and Long Bones (1989)

Estradiol (E2) replacement therapy effectively prevents or delays postmenopausal bone loss, but the mode of E2 action on bone is still unknown. Recently, the presence of E2 receptors was described for bone-derived cells. In this study we examined the estrogen responsiveness of osteoblastic cells using the experimentally immortalized calvarial cell lines RCT-1 and RCT-3 as well as primary cultures of calvarial and trabecular bone cells. E2 treatment reduced PTH-stimulated adenylate cyclase activity by 20-30% in RCT cells; the maximum effect was observed after treatment with 1 nM E2 for 4 h or longer. In trabecular cells E2 decreased PTH-stimulated adenylate cyclase activity by 60-80%. After a lag period of at least 48 h, E2 treatment (0.01-10 nM) increased cell number and [3H]thymidine incorporation in both RCT-3 cells and primary cultures of trabecular cells to 20-60% above control values. Half-maximal effects were observed at about 1 nM E2. Antibodies against insulin-like growth factor-I (IGF-I) inhibited the E2-induced proliferation in a dose-dependent manner without affecting basal growth. Furthermore, E2 treatment increased the steady state levels of IGF-I mRNA 2- to 2.5-fold in calvarial and RCT-3 cells compared to control levels. In addition, E2 (10 nM) increased the level of collagen mRNA more than 2-fold and opposed the suppression of collagen mRNA produced by PTH treatment. The E2 effects were specific to 17 beta-E2, since they were not observed with the biologically less active stereoisomer 17 alpha-E2 and were blocked by the E2 antagonist tamoxifen (1 microM). Thus, for osteoblastic cells in culture, E2 can directly stimulate proliferation as well as collagen and IGF-I mRNA while decreasing PTH responsiveness; these effects could explain the anabolic and anticatabolic effects of E2 on bone.
Optimal load balancing algorithms for Jacksonian networks with acknowledgement delays (2003)

The load-balancing problem for centralized Jacksonian networks is investigated. The networks are subject to end-to-end flow control with nonzero acknowledgement delay. To analyze these networks, a closed queuing network controlled by a queue with a variable service rate is investigated. The load balancing problem is reduced to one of combined routing and flow control. The objective is to maximize the throughput of the network such that the end-to-end expected time delay does not exceed an upper bound. The optimal routing balances the traffic in the network, and the optimal flow-control policy guarantees the upper bound constraint. Iterative algorithms that derive the optimal routing and flow-control parameters are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Laminin–a glycoprotein from basement membranes. (1979)

We have isolated a large noncollagenous glycoprotein, laminin, from a mouse tumor that produces basement membrane. The protein consists of at least two polypeptide chains (Mr = 220,000 and Mr = 440,000) joined to each other by disulfide bonds. Laminin and type IV collagen are major constituents of the tumor. Laminin is distinctly different from fibronectin, another component of basement membranes, in amino acid composition and immunological reactivity. Pepsin digestion of laminin releases a large, cystine-rich fragment which retains most of the antigenicity of the original protein. Immunological studies using purified antibody against laminin show that it is produced by a variety of cultured cells. In addition, these antibodies react with the basement membranes of normal tissues, suggesting that this protein or an immunologically related protein is a constituent of the basement membranes of these tissues.
Hemorrhage Without Tissue Trauma Produces Immunosuppression and Enhances Susceptibility to Sepsis (1987)

To determine whether hemorrhage without major tissue trauma can itself produce immunosuppression, the effect of hemorrhage on the lymphocyte response to T-cell mitogen in endotoxin-resistant C3H/HEJ mice was measured. The mice were bled to achieve a mean blood pressure of 35 mm Hg, maintained at that level for one hour, and then adequately resuscitated. On days 1 through 10 thereafter, the proliferative responses of the splenocytes to concanavalin A were measured and allogeneic mixed lymphocyte reaction was performed. The proliferative responses to mitogen stimulation as well as the results of mixed lymphocyte reaction studies indicated that marked immunosuppression occurred at day 1. Immunosuppression persisted for at least five days following hemorrhage, as evidenced by mitogen stimulation assay. Another group of mice was subjected to sepsis three days after hemorrhage and resuscitation. The mortalities in the sham-hemorrhage and hemorrhage groups following sepsis were 58% and 100%, respectively. Thus, a significant depression of cellular immunity occurred following simple hemorrhage despite adequate resuscitation, and this immunosuppression enhanced the susceptibility to sepsis.
Disialoganglioside GD2 on human neuroblastoma cells: target antigen for monoclonal antibody-mediated cytolysis and suppression of tumor growth. (1987)

A murine monoclonal antibody 14.18 specifically recognizes disialoganglioside GD2, the major ganglioside expressed on the surface of human neuroblastoma cells. This monoclonal antibody (Mab) is of immunoglobulin G3 isotype, has an affinity constant (KA) of 3.5 X 10(8) M-1, and reacts preferentially with tumor cells and fresh frozen tumor tissues of neuroectodermal origin in enzyme-linked immunosorbent assay and immunoperoxidase assays, respectively. Mab 14.18 effectively lyses a number of human neuroblastoma cell lines by two distinct mechanisms, i.e., antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. There is a good correlation between the average number of antibody-binding sites per neuroblastoma cell and the amount of cell lysis observed in complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity. In addition, Mab 14.18 suppresses establishment as well as growth of progressively growing, established human neuroblastoma tumors in nude mice when injected 24 h and 9 days, respectively, after the initial s.c. inoculation of tumor cells. These data suggest that Mab 14.18 can mediate tumor cell killing in vivo and in vitro and may thereby prove useful for immunotherapy of human neuroblastoma.
Potentiation of oncogenicity of adenovirus type 12 grown in African green monkey kidney cell cultures preinfected with SV40 virus. Persistence of both T antigens in the tumors and evidence for possible hybridization. (1966)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Novel Potential Anticancer Naphthyl Phosphoramidates of BVdU:  Separation of Diastereoisomers and Assignment of the Absolute Configuration of the Phosphorus Center (2005)

We have previously reported our SAR optimization of the anticancer agent thymectacin. Tuning of the parent ProTide structure initially involved the amino acid and, subsequently, the aromatic masking group on the phosphate moiety. Herein, derivatives bearing the combined modifications are reported and biological evaluation is described. Moreover, separation of the diastereoisomeric final product mixture shows a different cytostatic activity for the two diastereoisomers. Through computational and NMR studies, the absolute stereochemistry of the phosphorus center of the two diastereoisomers has been suggested.