gebhart/patrepeval huggingface dataset:
Protein phosphatase 1, regulatory subunit 15B is a survival factor for ERα‐positive breast cancer (2012)

Abstract Breast cancer is a heterogeneous disease at both the clinical and molecular levels. This heterogeneity may give rise to different therapy responses. Molecular profiling has facilitated identification of signatures for stratifying patients who would potentially benefit from given therapies. Previously, we reported on a subset of genes with the potential for predicting response of primary breast cancer to neoadjuvant chemotherapy. Herein, we report that patients with luminal (estrogen receptor α [ERα]‐expressing) breast cancer were enriched for nonresponders. To identify novel factors that contribute to the survival of breast cancer cells, a loss‐of‐function screen was performed with a subset of genes overexpressed in patients with disease resistant to chemotherapy. This approach led us to identify protein phosphatase 1, regulatory subunit 15B (PPP1R15B) as a factor with a potentially essential role in the survival of ERα‐positive breast cancer cells. Functional analyses showed that PPP1R15B depletion results in impaired proliferation due to unsuccessful transition of cells from G1 to S phase of the cell cycle, and apoptosis induction. Moreover, our data revealed a regulatory role for PPP1R15B in activating ERα. Furthermore, a high level of PPP1R15B mRNA expression was associated with poor outcome following tamoxifen‐based therapy. Accordingly, knockdown of PPP1R15B expression sensitized tamoxifen‐resistant MCF‐7 breast cancer cells to tamoxifen while reducing ERα abundance in these cells. Our findings reveal a novel role for PPP1R15B in the survival and therapy response of ERα‐positive breast cancer and may open new avenues for tumor subtype‐specific therapeutic strategies in the era of personalized medicine.
Combinatorial methods: aptamers and aptazymes (1999)

Combinatorial methods have been used to generate nucleic acid molecules with specific characteristics. Aptamers are nucleic acid binding species, and can be modified to directly transduce molecular recognition to optical signals. Aptazymes are allosteric or effector-activated ribyzymes. We have designed or selected aptazymes that are responsive to a variety of ligands. In particular, we have selected a ribozyme ligase that is activated 10,000-fold in the presence of an oligonucleotide effector, and have designed ligases that are up to 1,600-fold dependent on small molecule effectors. Even in those instances where designed constructs were initially unresponsive, we have been able to use selection to optimize their response characteristics.
Was tut sich in der Hochenergiephysik? (1989)

Abstract Neue Teilchenbeschleuniger mit immer gigantischeren Ausmaßen sollen die Struktur der Materie zunehmend feiner auflösen.
Strategies for Prolonged Therapy in Patients With Advanced Non–Small-Cell Lung Cancer (2010)

There are no data to support continuation chemotherapy in advanced NSCLC. Switch-maintenance trials with erlotinib and pemetrexed have demonstrated an improvement in overall survival. Thus far, continuation-maintenance has shown an improvement in progression-free survival, without an overall survival advantage.
Bulk synthesis of silicon nanowires using a low-temperature vapor–liquid–solid method (2001)

Silicon nanowires will find applications in nanoscale electronics and optoelectronics both as active and passive components. Here, we demonstrate a low-temperature vapor–liquid–solid synthesis method that uses liquid-metal solvents with low solubility for silicon and other elemental semiconductor materials. This method eliminates the usual requirement of quantum-sized droplets in order to obtain quantum-scale one-dimensional structures. Specifically, we synthesized silicon nanowires with uniform diameters distributed around 6 nm using gallium as the molten solvent, at temperatures less than 400 °C in hydrogen plasma. The potential exists for bulk synthesis of silicon nanowires at temperatures significantly lower than 400 °C. Gallium forms a eutectic with silicon near room temperature and offers a wide temperature range for bulk synthesis of nanowires. These properties are important for creating monodispersed one-dimensional structures capable of yielding sharp hetero- or homointerfaces.
Enhancement of the Efficacy of Chemotherapy for Lung Cancer by Simultaneous Suppression of Multidrug Resistance and Antiapoptotic Cellular Defense (2004)

The efficacy of chemotherapy of lung cancer is limited by the development of resistance in cancer cells during treatment. In most lung cancers, this resistance is associated with the overexpression of (a) multidrug resistance-associated protein (MRP) responsible for drug efflux from the cancer cells (pump resistance) and (b) BCL2 protein that activates antiapoptotic cellular defense (nonpump resistance). A novel liposomal proapoptotic anticancer drug delivery system was developed to enhance anticancer efficacy of the well-established drug doxorubicin (DOX). This multicomponent drug delivery system was tested on multidrug-sensitive and -resistant human small-cell lung cancer cells. The drug delivery system includes four components: (a) liposome as a carrier, (b) DOX as an inductor of apoptosis, (c) antisense oligonucleotides (ASOs) targeted to MRP1 mRNA as a suppressor of pump resistance, and (d) ASOs targeted to BCL2 mRNA as a suppressor of nonpump resistance. Intracellular internalization of ASOs and DOX; the influence of the proposed system on the expression of genes and proteins involved in the multidrug resistance, cytotoxicity, and apoptosis induction and antiapoptotic defense; and the activity of caspases were studied. It was found that the proposed liposomal delivery system successfully delivered ASOs and DOX to cell nuclei, inhibited MRP1 and BCL2 protein synthesis, and substantially increased the anticancer action of DOX by stimulating the caspase-dependent pathway of apoptosis in multidrug-resistant human lung cancer cells.
The role of senescence and immortalization in carcinogenesis (2000)

Normal somatic cells are able to divide only a limited number of times before they become senescent. The occurrence of intratumoral cell death and the need for clonal evolution mean that many more cell divisions are required for tumorigenesis than is possible unless cells breach the senescence proliferation barrier and become immortalized. Senescence may therefore be a major tumor suppressor mechanism. During the past decade the study of senescence and immortalization has entered the mainstream of cancer research. A major reason for the current interest in this subject is the observation that most cancers have an activated telomere maintenance mechanism, a marker of immortalization. It has also been found that some of the most common genetic changes known to occur in cancer have a key role in the immortalization process.
Treatment of Prurigo Nodularis With Thalidomide (1980)

A 57-year-old man with prurigo nodularis, was unresponsive to conventional therapy, was successfully treated with thalidomide. The pharmacology and side effects of the drug are briefly reviewed. Why thalidomide is effective for prurigo nodularis is unclear, but possible mechanisms of action are discussed.
Assignment and interpretation of hydrogen out-of-plane vibrations in the resonance Raman spectra of rhodopsin and bathorhodopsin (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAssignment and interpretation of hydrogen out-of-plane vibrations in the resonance Raman spectra of rhodopsin and bathorhodopsinGregory Eyring, Bostick Curry, Albert Broek, Johan Lugtenburg, and Richard MathiesCite this: Biochemistry 1982, 21, 2, 384–393Publication Date (Print):January 19, 1982Publication History Published online1 May 2002Published inissue 19 January 1982https://doi.org/10.1021/bi00531a028RIGHTS & PERMISSIONSArticle Views294Altmetric-Citations140LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A structural model for a homeotic protein-extradenticle-DNA complex accounts for the choice of HOX protein in the heterodimer. (1996)

The genes of the homeotic complex (HOX) encode DNA binding homeodomain proteins that control developmental fates by differentially regulating the transcription of downstream target genes. Despite their unique in vivo functions, disparate HOX proteins often bind to very similar DNA sequences in vitro. Thus, a critical question is how HOX proteins select the correct sets of target genes in vivo. The homeodomain proteins encoded by the Drosophila extradenticle gene and its mammalian homologues, the pbx genes, contribute to HOX specificity by cooperatively binding to DNA with HOX proteins. For example, the HOX protein labial cooperatively binds with extradenticle protein to a 20-bp oligonucleotide that is sufficient to direct a labial-like expression pattern in Drosophila embryos. Here we have analyzed the protein-DNA interactions that are important for forming the labial-extradenticle-DNA complex. The data suggest a model in which labial and extradenticle, separated by only 4 bp, bind this DNA as a heterodimer in a head-to-tail orientation. We have confirmed several aspects of this model by characterizing extradenticle-HOX binding to mutant oligonucleotides. Most importantly, mutations in base pairs predicted to contact the HOX N-terminal arm resulted in a change in HOX preference in the heterodimer, from labial to Ultrabithorax. These results demonstrate that extradenticle prefers to bind cooperatively with different HOX proteins depending on subtle differences in the heterodimer binding site.
Function and Structure in Retinal Transplants (1994)

Embryonic mammalian donor retina transplanted into the subretinal space of a mature host develops into a graft with well-organized, but atypical retinal structure. We tested the effect of this organization on rabbit-to-rabbit graft functional properties, isolating the graft to avoid contamination of graft responses by host retinal activity. Transient ON or ON-OFF spike-like responses and local electroretinograms (L-ERGs) were recorded simultaneously via a single electrode on the graft surface. These response components depended on stimulus diameter, sometimes in a way indicating antagonistic center-surround receptive field organization and spatial tuning (43%). Other times, the responses were an increasing function of stimulus diameter which saturated for large spots (57%). Response amplitudes were a monotonically-increasing function of light intensity over the narrow range tested. The L-ERGs were reminiscent of the proximal negative response or M-wave seen in normal retinas, which reflect light-induced amacrine cell activity. Thus, for the first time, we have shown that these subretinal grafts possess light-transduction and complex functional properties like those in normal retinas. They also possess the cellular complement and synaptic microcircuitry needed to form these physiological properties, Therefore, these results demonstrate a functional ability and capacity in transplants that is required if nerve cell transplantation surgery is to be done with therapeutic aims.
Symptom Profile in Terminally Ill AIDS Patients (1996)

A study protocol to record prospectively, frequency and intensity of symptoms in terminally ill AIDS patients was developed. Other information included mode of transmission, active intravenous drug use, regular visits of family/friends to the ward, the use of symptom-control drugs, and death without family or partner. The study population was selected from patients admitted to the wards or followed in the Clinic or Day Center of the Department of Infectious Diseases of the Catholic University, Rome. Inclusion criteria were diagnosis of AIDS prior to 12 months and advanced stage AIDS (defined with standardized criteria). To standardize the analysis of data, the terminal phase was considered to start 3 months before death (T1). From January 1, 1993 to December 12, 1993, 266 patients (208 males, 58 females) were enrolled. By June 30, 1995 168 patients had died and were considered for analysis. The most frequent symptoms at T1 were anorexia (63.1%), fatigue (60.1%), pain (60.1%), fever (47.6%), and cough (37.5%). At the end week (T6) the most frequent symptoms were fever (81.5%), fatigue (70.2%), dyspnea (68.1%), and pain (58.9%). In two-thirds of the patients, symptom-control drugs were used, most frequently nonopioid analgesics (39.9% at T1 and 56.5% at T6) and antipyretics (38.7% at T1 and 53.6% at T6). Opioid analgesics were used in 19% of patients at T1 and in 28.6% at T6. Almost one-third of the patients (29.2%) died alone without having family, their partner, or a friend near. Considering the high frequency of treatable symptoms in terminally ill AIDS patients, the use of palliative therapy should be emphasized. Flexibility and patient-directed care should be used in deciding care plans to avoid overhospitalization and promote alternative care.
Integration of isoelectric focusing with multi-channel gel electrophoresis by using microfluidic pseudo-valves (2007)

Two-dimensional (2D) protein separation is achieved in a plastic microfluidic device by integrating isoelectric focusing (IEF) with multi-channel polyacrylamide gel electrophoresis (PAGE). IEF (the first dimension) is carried out in a 15 mm-long channel while PAGE (the second dimension) is in 29 parallel channels of 65 mm length that are orthogonal to the IEF channel. An array of microfluidic pseudo-valves is created for introducing different separation media, without cross-contamination, in both dimensions; it also allows transfer of proteins from the first to the second dimension. Fabrication of pseudo-valves is achieved by photo-initiated, in situ gel polymerization; acrylamide and methylenebisacrylamide monomers are polymerized only in the PAGE channels whereas polymerization does not take place in the IEF channel where a mask is placed to block the UV light. IEF separation medium, carrier ampholytes, can then be introduced into the IEF channel. The presence of gel pseudo-valves does not affect the performance of IEF or PAGE when they are investigated separately. Detection in the device is achieved by using a laser induced fluorescence imaging system. Four fluorescently-labeled proteins with either similar pI values or close molecular weight are well separated, demonstrating the potential of the 2D electrophoresis device. The total separation time is less than 10 minutes for IEF and PAGE, an improvement of 2 orders of magnitude over the conventional 2D slab gel electrophoresis.
Joint beamforming strategies in OFDM-MIMO systems (2002)

Orthogonal Frequency Division Multiplexing (OFDM) has been recently established for several systems such as HIPERLAN/2 and Digital Video and Audio Broadcasting. The success of this modulation is due to the easy implementati9n of the modulator and demodulator, including the equalization process. Moreover, in last years also increasing interest has been put on the study of Multi-Input-Multi-Output (MIMO) channels, based on the use of arrays of antennas at both the transmitter and the receiver. In this paper we propose two new and low computational cost joint beamforming strategies for communication systems that combine OFDM and MIMO channels. An asymptotic analysis of the proposed methods is carried out, providing a complete comparative study among other classical strategies. To demonstrate the potential of the proposed techniques, we present MonteCarlo simulation results of the system BER and make comparisons with other methods.
An Alternative Splicing Product of the Lamin A/C Gene Lacks Exon 10 (1996)

Expression of the A-type lamins was studied in the lung adenocarcinoma cell line GLC-A1. A-type lamins, consisting of lamin A and C, are two products arising from the same gene by alternative splicing. Northern blotting showed in GLC-A1 a relatively low expression level of lamin C and an even lower expression level of lamin A as compared to other adenocarcinoma cell lines. Immunofluorescence studies revealed highly irregular nuclear inclusions of lamin A, suggesting protein or gene expression abnormalities. Reverse transcriptase-polymerase chain reaction-based cDNA analysis followed by sequencing indicated the presence of an as yet unidentified alternative splicing product of the lamin A/C gene. This product differs from lamin A by the absence of the 5' part of exon 10 (90 nucleotides). Therefore we propose to designate this product lamin Adelta10. Deletion of the 30 amino acids encoded by exon 10 was predicted to result in a shift in pI of the protein from 7.4 to approximately 8.6, which was confirmed by two-dimensional immunoblotting. mRNA analysis in a variety of cell lines, normal colon tissue as well as carcinomas demonstrated the presence of lamin Adelta 10 in all samples examined, suggesting its presence in a variety of cell types.
Large Core−Shell Poly(methyl methacrylate) Colloidal Clusters: Synthesis, Characterization, and Tracking (2010)

We present a multistep procedure yielding large (diameter > 2 μm) monodisperse, fluorescently labeled core-shell poly(methyl methacrylate) (PMMA) latex particles via dispersion polymerization. The particles' physical properties were controlled by adjusting two reaction parameters, the initiator and chain transfer agent concentrations, which influence the molecular weight of the PMMA. Under certain conditions, particles with the requisite properties for fabricating colloidal clusters were synthesized. The resulting clusters represent a new type of nonspherical colloid that can be dispersed in a density- and refractive index-matching solvent, making them ideal for quantitative studies using confocal microscopy. To demonstrate the utility of our clusters, we measured the translational and rotational diffusion coefficients of a tetrahedral cluster by tracking the motion of its constituent particles in three-dimensional space. More broadly, our findings provide new insights concerning PMMA dispersion polymerization in apolar media.
The Treatment of Wet Age-Related Macular Degeneration (2009)

With the advent of the antivascular endothelial growth factor (anti-VEGF) therapy, the prognosis of choroidal neovascularization has changed dramatically. Visual acuity can actually be improved, but, in most cases, the improvement can only be sustained with repeated intravitreal injections.
Virtual machine images as structured data: the mirage image library (2011)

The rise of infrastructure-as-a-service (IaaS) clouds, both private and public, has created new problems in managing large collections of virtual-machine (VM) images. VM images must be kept up-to-date with security patches and scanned for malicious or improperly licensed software. Because images are bulky, attention must be paid to the latencies of deployment and capture. Large collections of VM images also present new opportunities which, while not completely realized today, do not exist with collections of physical machines. Users can search for images that contain the software they want, configured as they want it. Collections can be mined for patterns in order to answer questions like “which database management systems does our company use?” Images can be compared with one another. This paper describes Mirage, an image library that addresses these problems and opportunities and is pluggable into various clouds. Mirage stores images in a format that indexes their filesystem structure, instead of as opaque disk images. Like other libraries, Mirage provides features for image capture and deployment. In addition, Mirage maintains a provenance tree that records how each image was derived from other images; allows operations, like patching and scanning, that normally require a VM instance to execute offline; and enables analyses such as image search and comparison. Other papers have used Mirage [16, 13, 17] or described parts of the system [8]. This paper is the first overview of the complete system. It also describes three novel features that reduce the costs of translating between disk images and the Mirage format: a content-addressed store optimized for VM image data; a simple yet flexible indexer that supports a variety of filesystem and image types; and delta deployment, which uses precomputed deltas between images to speed up format conversions. Finally, we relate our experience with Mirage in the IBM Workload Deployer product (IWD) [3], which serves images to a customer’s own private cloud, and in the Research Compute Cloud (RC2) [10], which is a production IaaS cloud.
Comparison of 10-kHz High-Frequency and Traditional Low-Frequency Spinal Cord Stimulation for the Treatment of Chronic Back and Leg Pain (2016)

IPG, implantable pulse generatorMCID, minimal clinically important differencePI, permanent implantODI, Oswestry Disability IndexSCS, spinal cord stimulationVAS, Visual Analog Scale.
Alternative splicing of ERCC1 and cisplatin-DNA adduct repair in human tumor cell lines. (1998)

Alternative splicing is a common natural tool for the inhibition of function of full length gene products. We explored whether there was evidence that alternative splicing of ERCC1 may serve such a function for nucleotide excision repair. The ratio of alternatively spliced species to full length species was assessed for the protein and/or for the mRNA, for a series of human cell lines and tissues. This ratio was plotted against the amount of cisplatin-DNA adduct repair in each cell line (n=9), as measured by atomic absorbance spectrometry. As the percentage of alternatively spliced protein and/or mRNA increased, the amount of cisplatin-DNA adduct that was repaired was reduced. This inverse relationship was associated with a substantial amount of scatter (r=0.635), particularly at low levels of repair. These data demonstrate an association between alternative splicing of ERCC1, and reduction in cellular capability to repair cisplatin-DNA adduct.