gebhart/patrepeval huggingface dataset:
The Effect of Photoimmunotherapy Followed by Liposomal Daunorubicin in a Mixed Tumor Model: A Demonstration of the Super-Enhanced Permeability and Retention Effect after Photoimmunotherapy (2013)

In general, de novo solid tumors are composed of phenotypically and functionally heterogeneous malignant cells. This heterogeneity interferes with the effectiveness of targeted molecular cancer therapies. Even if most of the tumor is killed by a targeted treatment, recurrences are common and can be lethal. In this study, a mixed tumor model, which is predominantly a population of epidermal growth factor receptor (EGFR)-positive A431 cells combined with a smaller population of EGFR-negative Balb3T3/DsRed cells, was established. This mixed tumor was then treated with photoimmunotherapy, a newly developed target-cell-selective cancer therapy using a monoclonal antibody (mAb)-photosensitizer (IR700 fluorescence dye) conjugate and exposure of near-infrared light. Although photoimmunotherapy successfully treated EGFR-positive A431 cells in the mixed tumor, EGFR-negative Balb/DsRed cells were not responsive. However, photoimmunotherapy also induced a large increase in tumor permeability, known as the super-enhanced permeability and retention (SUPR) effect, which allowed a 5-fold increase in the accumulation of a liposomal chemotherapy (DaunoXome) and resulted in more effective therapy than either photoimmunotherapy or liposomal daunorubicin alone. The liposomal daunorubicin, administered 1 hour after EGFR-targeted photoimmunotherapy, was homogeneously distributed, allowing delivery to tiny surviving nests of EGFR-negative Balb3T3/DsRed cells, resulting in prolonged survival of mice.
Cardiolipin Switch in Mitochondria:  Shutting off the Reduction of Cytochrome c and Turning on the Peroxidase Activity (2007)

Upon interaction with anionic phospholipids, particularly mitochondria-specific cardiolipin (CL), cytochrome c (cyt c) loses its tertiary structure and its peroxidase activity dramatically increases. CL-induced peroxidase activity of cyt c has been found to be important for selective CL oxidation in cells undergoing programmed death. During apoptosis, the peroxidase activity and the fraction of CL-bound cyt c markedly increase, suggesting that CL may act as a switch to regulate cyt c's mitochondrial functions. Using cyclic voltammetry and equilibrium redox titrations, we show that the redox potential of cyt c shifts negatively by 350-400 mV upon binding to CL-containing membranes. Consequently, functions of cyt c as an electron transporter and cyt c reduction by Complex III are strongly inhibited. Further, CL/cyt c complexes are not effective in scavenging superoxide anions and are not effectively reduced by ascorbate. Thus, both redox properties and functions of cyt c change upon interaction with CL in the mitochondrial membrane, diminishing cyt c's electron donor/acceptor role and stimulating its peroxidase activity.
Cost Analysis of Ethanol Production from Willow Using Recombinant Escherichia coli (1994)

This study comprises a technical and economic analysis of the production of fuel ethanol by fermentation of a pentose-rich hydrolysate with recombinant Escherichia coli, strain KO11. Hydrolysate from steam-pretreated willow was used as raw material in calculations regarding the fermentation. The calculations were based on a feed capacity of 10 metric tons of dry willow per hour to the pretreatment stage, providing 35 metric tons of hydrolysate per hour, consisting of 45 g of sugars/L, to the pentose fermentation plant. A detoxification step was included, since the hydrolysate has been shown to have an inhibitory effect on the E. coli KO11. The technical data used in the calculations were based on a kinetic fermentation model, which was developed from laboratory-scale experiments in a previous study. The economic analysis predicted an ethanol production cost of 48/L in the pentose fermentation plant, indicating potentially good economy. The detoxification cost constitutes 22% of this cost. Sensitivity analyses revealed that if the concentration of sugars in the feed to the fermentation was decreased by 40% to 27 g/L, the ethanol production cost was increased to 54/L. The production cost was increased to 50/L ethanol if the cell mass was recirculated to the fermentation stage 5 times instead of 20.
Human Intervertebral Disc Cell Culture for Disc Disorders (2004)

Repair of degenerated intervertebral discs by engineered tissue is a clinical challenge in spinal surgery. Prerequisites are cultivation of intervertebral disc cells and determination of their biologic properties. The influence of disc damage in different spinal disorders on the outcome of disc cell cultures has not been discussed previously. This study showed the feasibility of cultivation of cells from damaged human intervertebral discs and the dependence of cellular culture properties on the underlying disc disorder. Human intervertebral disc cells were isolated from disc tissue obtained during surgical procedures for scoliosis, osteochondrosis, and disc herniation. After proliferation in monolayer culture, cells were embedded in a mixed matrix composed of fibrin and hyaluronic acid. Deoxyribonucleic acid content, hydroxyproline content, and proteoglycan synthesis were determined on Days 7, 14, and 21. In a three-dimensional environment only cells obtained from scoliotic and osteochondrotic discs showed significant deoxyribonucleic acid and proteoglycan synthesis. However, hydroxyproline content increased only in cells from scoliotic discs. The results of this study show that the formation of extracellular matrix components under three-dimensional culture conditions is dependent on the nature of intervertebral disc damage of the tissue processed.
Primary CD56 positive lymphomas of the gastrointestinal tract (2001)

These results, together with a literature review, suggest that primary NK cell lymphoma of the GI tract may be considered a distinct clinicopathologic entity. Both primary NK and NK-like T-cell lymphoma pursue an aggressive clinical course. EBER and TCR gene rearrangement are useful in distinguishing NK cell lymphoma from NK-like T-cell lymphoma, particularly when frozen tissue is not available for immunophenotyping.
Isolation and characterization of a syncytium-inducing, macrophage/T-cell line-tropic human immunodeficiency virus type 1 isolate that readily infects chimpanzee cells in vitro and in vivo (1995)

Fresh human immunodeficiency virus type 1 (HIV-1) isolates from patients with AIDS were screened for infectivity in chimpanzee peripheral blood mononuclear cells (PBMC) to identify strains potentially able to generate high virus loads in an inoculated animal. Only 3 of 23 isolates obtained were infectious in chimpanzee cells. Of these three, only one (HIV-1DH12) was able to initiate a productive infection in PBMC samples from all 25 chimpanzees tested. HIV-1DH12 tissue culture infections were characterized by extremely rapid replication kinetics, profound cytopathicity, and tropism for chimp and human PBMC, primary human macrophage, and several human T-cell lines. An infection was established within 1 week of inoculating a chimpanzee with 50 50% tissue culture infective doses of HIV-1DH12; cell-free virus was recovered from the plasma at weeks 1, 2, and 4 and was associated with the development of lymphadenopathy. Virus loads during the primary infection and at 6 months postinoculation were comparable to those reported in HIV-1-seropositive individuals.
Differentially Private High-Dimensional Approximate Range Counting, Revisited (2014)

Locality Sensitive Filters are known for offering a quasi-linear space data structure with rigorous guarantees for the Approximate Near Neighbor search (ANN) problem. Building on Locality Sensitive Filters, we derive a simple data structure for the Approximate Near Neighbor Counting (ANNC) problem under differential privacy (DP). Moreover, we provide a simple analysis leveraging a connection with concomitant statistics and extreme value theory. Our approach produces a simple data structure with a tunable parameter that regulates a trade-off between space-time and utility. Through this trade-off, our data structure achieves the same performance as the recent findings of Andoni et al. (NeurIPS 2023) while offering better utility at the cost of higher space and query time. In addition, we provide a more efficient algorithm under pure ε-DP and elucidate the connection between ANN and differentially private ANNC. As a side result, the paper provides a more compact description and analysis of Locality Sensitive Filters for Fair Near Neighbor Search, improving a previous result in Aumüller et al. (TODS 2022).
DETERMINATION OF RESIDUAL 4‐AMINOMETHYL‐4,5‘,8‐TRIMETHYLPSORALENAND MUTAGENICITY TESTING FOLLOWING PSORALEN PLUS UVA TREATMENT OF PLATELET SUSPENSIONS (1993)

Psoralens and UVA light have been used in the laboratory to study the inactivation of viruses that may be infrequently present in platelet concentrates that are prepared for transfusion. In order to evaluate safety aspects of the treatment of platelet suspensions with 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), we have investigated the residual levels and mutagenic potential of AMT after UVA phototreatment. 4'-aminomethyl-4,5',8-trimethylpsoralen, at a final concentration of 40 micrograms/mL, was added to platelet suspensions which contained 16% plasma and a synthetic medium. Platelet suspensions containing AMT were irradiated with up to 7.2 J/cm2 UVA light under normal oxygen levels. Residual levels of AMT were determined by HPLC and a bioassay based on bacteriophage phi 6 inactivation. The photodestruction of AMT or its activity by UVA was characterized by a D37 value of 0.6 and 0.3 J/cm2 with HPLC or bioassay, respectively. At 2.4 J/cm2 UVA, which results in approximately 5 log10 inactivation of vesicular stomatitis virus (VSV) and retention of platelet in vitro properties, 12% (HPLC) to 9% (bioassay) AMT remained. Like other psoralens, AMT was found to bind to serum proteins as shown by ultrafiltration. Results are consistent with approximately 36% of the initial drug load binding primarily to serum albumin. It was determined using 3H-AMT that 9 to 18% of radioactivity was bound to platelets in the absence of irradiation. Similar fractions (13 to 18%) of AMT were bound to platelets after 3.6 J/cm2 UVA irradiation, and 8 to 10% of total AMT was associated with saline-washed irradiated platelets and is presumably tightly bound.(ABSTRACT TRUNCATED AT 250 WORDS)
Supporting mobility in MosquitoNet (1996)

The goal of the MosquitoNet project is to provide continuous Internet connectivity to mobile hosts. Mobile hosts must be able to take advantage of the best network connectivity available in any location, whether wired or wireless. We have implemented a mobile IP system that supports seamless switching between different networks and communication devices. In contrast to previous approaches to mobile IP, we believe mobile hosts should not assume any explicit mobility support from the networks they visit, aside from basic Internet connectivity. This decision places extra responsibilities on the mobile hosts themselves. In this paper, we describe the design and implications of such a system. Measurements of our implementation show that the inherent overhead to switch networks (below 10ms) is insignificant compared to the time required to bring up a new communication device. 1. Introduction We envision that ubiquitous network connectivity will someday be a reality. In the future, the Inter...
CD44+CD24− prostate cells are early cancer progenitor/stem cells that provide a model for patients with poor prognosis (2008)

Recent evidence supports the hypothesis that cancer stem cells are responsible for tumour initiation and formation. Using flow cytometry, we isolated a population of CD44+CD24(-) prostate cells that display stem cell characteristics as well as gene expression patterns that predict overall survival in prostate cancer patients. CD44+CD24(-) cells form colonies in soft agar and form tumours in NOD/SCID mice when as few as 100 cells are injected. Furthermore, CD44+CD24(-) cells express genes known to be important in stem cell maintenance, such as BMI-1 and Oct-3/4. Moreover, we can maintain CD44+CD24(-) prostate stem-like cells as nonadherent spheres in serum-replacement media without substantially shifting gene expression. Addition of serum results in adherence to plastic and shifts gene expression patterns to resemble the differentiated parental cells. Thus, we propose that CD44+CD24(-) prostate cells are stem-like cells responsible for tumour initiation and we provide a genomic definition of these cells and the differentiated cells they give rise to. Furthermore, gene expression patterns of CD44+CD24(-) cells have a genomic signature that is predictive of poor patient prognosis. Therefore, CD44+CD24(-) LNCaP prostate cells offer an attractive model system to both explore the biology important to the maintenance and differentiation of prostate cancer stem cells as well as to develop the therapeutics, as the gene expression pattern in these cells is consistent with poor survival in prostate cancer patients.
Proapoptotic BH3-only Bcl-2 family members induce cytochromecrelease, but not mitochondrial membrane potential loss, and do not directly modulate voltage-dependent anion channel activity (2000)

Through direct interaction with the voltage-dependent anion channel (VDAC), proapoptotic Bcl-2 family members such as Bax and Bak induce apoptogenic mitochondrial cytochrome c release and membrane potential (Deltapsi) loss in isolated mitochondria. Using isolated mitochondria, we showed that Bid and Bik, BH3-only proteins from the Bcl-2 family, induced cytochrome c release but not Deltapsi loss. Unlike Bax/Bak, the cytochrome c release induced by Bid/Bik was Ca(2+)-independent, cyclosporin A-insensitive, and respiration-independent. Furthermore, in contrast to Bax/Bak, Bid/Bik neither interacted with VDAC nor directly affected the VDAC activity in liposomes. Consistently, Bid/Bik induced apoptosis without Deltapsi loss, whereas Bax induced apoptosis with Deltapsi loss. These findings indicated the involvement of a different mechanism in BH3-only, protein-induced apoptogenic cytochrome c release.
Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases (2011)

Sequence homology indicates the existence of three human cytosolic acyl protein thioesterases, including APT1 that is known to depalmitoylate H- and N-Ras. One of them is the lysophospholipase-like 1 (LYPLAL1) protein that on the one hand is predicted to be closely related to APT1 but on the other hand might also function as a potential triacylglycerol lipase involved in obesity. However, its role remained unclear. The 1.7 Å crystal structure of LYPLAL1 reveals a fold very similar to APT1, as expected, but features a shape of the active site that precludes binding of long-chain substrates. Biochemical data demonstrate that LYPLAL1 exhibits neither phospholipase nor triacylglycerol lipase activity, but rather accepts short-chain substrates. Furthermore, extensive screening efforts using chemical array technique revealed a first small molecule inhibitor of LYPLAL1.
Direct Identification of Staphylococcus aureus from Positive Blood Culture Bottles (2003)

Fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes targeting Staphylococcus aureus 16S rRNA is a novel method for direct identification of S. aureus from positive blood culture bottles. The test (S. aureus PNA FISH) is performed on smears made directly from positive blood culture bottles with gram-positive cocci in clusters (GPCC) and provides results within 2.5 h. A blinded comparison of S. aureus PNA FISH with standard identification methods was performed in collaboration with eight clinical microbiology laboratories. A total of 564 routine blood culture bottles positive for GPCC recovered from both aerobic and anaerobic media from three different manufacturers (ESP, BACTEC, and BacT/Alert) were included in the study. The sensitivity and specificity of S. aureus PNA FISH were 100% (57 of 57) and 99.2% (116 of 117), respectively, with 174 GPCC-positive ESP blood culture bottles, 98.5% (67 of 68) and 98.5% (129 of 131), respectively, with 200 GPCC-positive BACTEC blood culture bottles, and 100% (74 of 74) and 99.1% (115 of 116), respectively, with 190 GPCC-positive BacT/Alert blood culture bottles. It is concluded that S. aureus PNA FISH performs well with commonly used continuously monitoring blood culture systems.
Sequence Homology Between Certain Viral Proteins and Proteins Related to Encephalomyelitis and Neuritis (1985)

Post-infectious or post-vaccinal demyelinating encephalomyelitis and neuritis may be due to immunological cross-reactions evoked by specific viral antigenic determinants (epitopes) that are homologous to regions in the target myelins of the central and peripheral nervous systems. Such homologies have been found by computer searches in which decapeptides in two human myelin proteins were compared with proteins of viruses known to infect humans. These viruses include measles, Epstein-Barr, influenza A and B, and others that cause upper respiratory infections. Several regions identified in myelin basic protein and P2 protein can be related to experimental allergic encephalomyelitis or neuritis in laboratory animals.
Genomic Alterations in Human Breast Cancer: A Review (1989)

We review and discuss data on the genetic alterations documented in human breast carcinomas at the molecular level. These alterations may result in: 1) deletion of genetic material (chromosome 11p, 13q, 3p, 1q, 17p); 2) amplification of genes or entire chromosomal segments (c-myc, c-erb-B2, locus DF3/PUM, loci on 11q13); 3) rearrangements (c-myc); 4) point mutations (c-ras). Presently available informations do not allow the development of cohesive pathogenetic models but indicate that the molecular basis of human breast cancer is heterogeneous.
Vaccination of Renal Cell Cancer Patients with Modified Vaccinia Ankara Delivering Tumor Antigen 5T4 (TroVax) Administered with Interleukin 2: A Phase II Trial (2008)

TroVax in combination with IL-2 was safe and well tolerated in all patients. The high frequency of 5T4-specific immune responses and good clinical response rate are encouraging and warrant further investigation.
On the constricted neon positive column (1995)

The axial electric field strength, electron temperature, and radially averaged electron density in a medium pressure and current, constricted neon plasma column of a direct current glow discharge have been measured by electric methods. The ion loss and production rate coefficients and the loss terms have been calculated and the ratio between recombination loss and diffusion loss evaluated. The steady-state equilibrium between ion production and ion loss shows that, though electron-impact ionization of metastable species is an important ion-production channel, electron-impact ionization via the resonance and higher excited neon levels and associative ionization are also important ion-production channels.
Modulation of the Immune Response by Antigen-Reactive Lymphocytes after Cultivation with Gangliosides (1975)

GM1 ganglioside isolated from mouse brain was found to be capable of inhibiting the thymocytotoxicity of AKR anti-Thy 1.2 antiserum and to a lesser extent anti-BAtheta antiserum. GD1b ganglioside of mouse brain and thymocytes inhibited the thymocytotoxicity of rabbit anti-BAtheta anti-serum for mouse thymocytes. When GM1 ganglioside, in the form of cholesterol-lecithin liposomes, was incubated with spleen cell cultures in the presence of SRBC, depressed anti-SRBC hemolytic plaque responses were observed. This effect could be neutralized by first absorbing the GM1 liposomes with anti-Thy-1.2 antibodies. The kinetics of GM1 numbers when the ganglioside was added even as late as the 4th day of culture. Results of experiments in which GM1 ganglioside was incubated with either bone marrow cells or with thymocytes suggest that the target cell for GM1 liposomes is the B lymphocytes.
Evaluation of the retrieval of total suspended matter concentration in Taihu Lake, China from CBERS-02B CCD (2010)

遥感技术被用来确定全部的推迟的事集中(C TSM ) 。在这研究，我们使用了遥远地察觉到的数据为泰胡·莱克，检索 C TSM 中国，并且特别为 CBERS-02B 电荷耦合器件数据开发了一个大气的修正算法。我们模仿了在原处使用在秋天 2004 在泰胡·莱克上在巡航做的观察的电荷耦合器件乐队的遥感反射(R rs ) ，从哪个一个检索模型与模仿的 R rs (830 ) 被建立并且测量了 C TSM。另外，我们使用了大气的修正算法和检索模型在 2008 在湖上处理电荷耦合器件数据并且检索 C TSM。在从 MODIS 并且从 CCD 图象检索的 C TSM 之间的 RMS 相对错误是大约 42.9% ，显示在这份报纸描述的算法能被用于在监视在泰胡·莱克的 C TSM 分发的电荷耦合器件数据的应用程序。
Source control using VM/SP and CMS (1988)

This paper describes the Source Control System (SCS), an automated system which runs under IBM VM/SP with CMS. It is designed to manage source code data in medium-sized software development environments.
Thrombin‐induced increase in albumin permeability across the endothelium (1986)

We studied the effect of thrombin on albumin permeability across the endothelial monolayer in vitro. Bovine pulmonary artery endothelial cells were grown on micropore membranes. Morphologic analysis confirmed the presence of a confluent monolayer with interendothelial junctions. Albumin permeability was measured by the clearance of 125I-albumin across the endothelial monolayer. The control 125I-albumin clearance was 0.273 +/- 0.02 microliter/min. The native enzyme, alpha-thrombin (10(-6) to 10(-10) M), added to the luminal side of the endothelium produced concentration-dependent increases in albumin clearance (maximum clearance of 0.586 +/- 0.08 microliter/min at 10(-6) M). Gamma (gamma) thrombin (10(-6) M and 10(-8) M), which lacks the fibrinogen recognition site, also produced a concentration-dependent increase in albumin clearance similar to that observed with alpha-thrombin. Moreover, the two proteolytically inactive forms of the native enzyme, i-Pr2 P-alpha-thrombin and D-Phe-Pro-Arg-CH2-alpha-thrombin, increased the 125I-albumin clearance (0.610 +/- 0.09 microliter/min and 0.609 +/- 0.02 microliter/min for i-Pr2 P-alpha-thrombin and D-Phe-Pro-Arg-CH2-alpha-thrombin at 10(-6) M, respectively). Since the modified forms of thrombin lack the fibrinogen recognition and active serine protease sites, the results indicate that neither site is required for increased albumin permeability. The increase in albumin clearance with alpha-thrombin was not secondary to endothelial cell lysis because lactate dehydrogenase concentration in the medium following thrombin was not significantly different from baseline values. There was also no morphological evidence of cell lysis. Moreover, the increase in 125I-albumin clearance induced by alpha-thrombin was reversible by washing thrombin from the endothelium. The basis for the increased albumin permeability following the addition of alpha-thrombin appears to be a reversible change in endothelial cell shape with formation of intercellular gaps.