gebhart/patrepeval huggingface dataset:
Photodynamic Therapy Synergizes with Irinotecan to Overcome Compensatory Mechanisms and Improve Treatment Outcomes in Pancreatic Cancer (2016)

Abstract The ability of tumor cells to adapt to therapeutic regimens by activating alternative survival and growth pathways remains a major challenge in cancer therapy. Therefore, the most effective treatments will involve interactive strategies that target multiple nonoverlapping pathways while eliciting synergistic outcomes and minimizing systemic toxicities. Nanoliposomal irinotecan is approved by the FDA for gemcitabine-refractory metastatic pancreatic cancer. However, the full potential of irinotecan treatment is hindered by several cancer cell survival mechanisms, including ATP-binding cassette G2 (ABCG2) transporter-mediated irinotecan efflux from cells. Here, we demonstrate that benzoporphyrin derivative-based photodynamic therapy (PDT), a photochemical cytotoxic modality that activates the apoptotic pathway, reduced ABCG2 expression to increase intracellular irinotecan levels in pancreatic cancer. Moreover, we show that PDT inhibited survivin expression. Although PDT potentiated irinotecan treatment, we also demonstrate that irinotecan reduced the tumoral expression of monocarboxylate transporter 4, which was upregulated by PDT. Notably, using orthotopic xenograft models, we demonstrate that combination of single low-dose PDT and a subclinical dose of nanoliposomal irinotecan synergistically inhibited tumor growth by 70% for 3 weeks compared with 25% reduction after either monotherapies. Our findings offer new opportunities for the clinical translation of PDT and irinotecan combination therapy for effective pancreatic cancer treatment. Cancer Res; 76(5); 1066–77. ©2015 AACR.
Intrinsic Spin Hall Effect in Platinum: First-Principles Calculations (2008)

Spin Hall effect (SHE) is studied with first-principles relativistic band calculations for platinum, which is one of the most important materials for metallic SHE and spintronics. We find that intrinsic spin Hall conductivity (SHC) is as large as approximately 2000(variant Planck's over 2 pi/e)(Omega cm)(-1) at low temperature and decreases down to approximately 200(variant Planck's over 2 pi/e)(Omega cm)(-1) at room temperature. It is due to the resonant contribution from the spin-orbit splitting of the doubly degenerated d bands at high-symmetry L and X points near the Fermi level. By modeling these near degeneracies by an effective Hamiltonian, we show that SHC has a peak near the Fermi energy and that the vertex correction due to impurity scattering vanishes. We therefore argue that the large SHE observed experimentally in platinum is of intrinsic nature.
Vitamin B12 Level may be Related to the Efficacy of Single Ketamine Infusion in Bipolar Depression (2013)

The single infusion of ketamine, an N-methyl-d-aspartic acid (NMDA) glutamate receptor antagonist, exerts a therapeutic effect in both unipolar and bipolar depression. Homocysteine (HCY) acts agonistically on the NMDA receptor, hyperhomocysteinemia is related to depression, and folic acid and vitamin B12 are associated with HCY system. We estimated the serum levels of these substances in 20 bipolar depressed patients before ketamine infusion. 10 patients responded favorably to this procedure, as their score on the Hamilton depression rating scale, compared to baseline, was reduced by more than 50%, after 7 days. The vitamin B12 level was significantly higher in "responders" compared to the remaining patients. No differences between the 2 groups were found with regard to HCY, folic acid levels and such clinical factors as age, duration of illness and duration of current episode. These preliminary data suggest that the vitamin B12 level may be connected with the efficacy of ketamine infusion in bipolar depression.
The Opposing Transcriptional Activities of the Two Isoforms of the Human Progesterone Receptor Are Due to Differential Cofactor Binding (2000)

The human progesterone receptor (PR) exists as two functionally distinct isoforms, hPRA and hPRB. hPRB functions as a transcriptional activator in most cell and promoter contexts, while hPRA is transcriptionally inactive and functions as a strong ligand-dependent transdominant repressor of steroid hormone receptor transcriptional activity. Although the precise mechanism of hPRA-mediated transrepression is not fully understood, an inhibitory domain (ID) within human PR, which is necessary for transrepression by hPRA, has been identified. Interestingly, although ID is present within both hPR isoforms, it is functionally active only in the context of hPRA, suggesting that the two receptors adopt distinct conformations within the cell which allow hPRA to interact with a set of cofactors that are different from those recognized by hPRB. In support of this hypothesis, we identified, using phage display technology, hPRA-selective peptides which differentially modulate hPRA and hPRB transcriptional activity. Furthermore, using a combination of in vitro and in vivo methodologies, we demonstrate that the two receptors exhibit different cofactor interactions. Specifically, it was determined that hPRA has a higher affinity for the corepressor SMRT than hPRB and that this interaction is facilitated by ID. Interestingly, inhibition of SMRT activity, by either a dominant negative mutant (C'SMRT) or histone deacetylase inhibitors, reverses hPRA-mediated transrepression but does not convert hPRA to a transcriptional activator. Together, these data indicate that the ability of hPRA to transrepress steroid hormone receptor transcriptional activity and its inability to activate progesterone-responsive promoters occur by distinct mechanisms. To this effect, we observed that hPRA, unlike hPRB, was unable to efficiently recruit the transcriptional coactivators GRIP1 and SRC-1 upon agonist binding. Thus, although both receptors contain sequences within their ligand-binding domains known to be required for coactivator binding, the ability of PR to interact with cofactors in a productive manner is regulated by sequences contained within the amino terminus of the receptors. We propose, therefore, that hPRA is transcriptionally inactive due to its inability to efficiently recruit coactivators. Furthermore, our experiments indicate that hPRA interacts efficiently with the corepressor SMRT and that this activity permits it to function as a transdominant repressor.
A structured test re-use methodology for core-based system chips (2002)

This paper describes a structured test re-use methodology and infrastructure for core-based system chips. The methodology is based on the use of a structured test bus framework that provides access to virtual components in a system chip allowing the test methodologies and test vectors for these components to be re-used. It addresses the test access, isolation, interconnect and shadow logic test problems without requiring modifications to the components, even for cores with more ports than chip pins. The test area overhead required, including test bus routing, to implement this methodology can be less than 1%.
The novel gene fad 104, containing a fibronectin type III domain, has a significant role in adipogenesis (2004)

A novel gene named fad104 (factor for adipocyte differentiation-104), whose expression level quickly increased in the early stage of adipogenesis, was isolated and characterized. The deduced amino acid sequence of fad104 revealed the possible presence of a fibronectin type III domain and transmembrane domain. The expression of fad104 was detected in adipocyte differentiable 3T3-L1 cells but not observed in the non-adipogenic cell line NIH-3T3. Moreover, the ability of 3T3-L1 cells to differentiate declined with the knockdown of fad104 by RNA interference, strongly indicating that fad104 functions as a positive regulator of adipogenesis.
Functional characterization of the human FSH receptor with an inactivating Ala189Val mutation (2002)

An Ala189Val mutation of the human FSH receptor (FSHR) has been found to cause hypergonadotrophic ovarian failure with arrest of follicular maturation in women, and suppressed spermatogenesis in men. We have now characterized the molecular mechanisms of the receptor inactivation. Wild-type and mutant FSHR cDNAs were expressed in monkey kidney (COS-7) cells and murine granulosa tumour (KK-1) cells. Similar steady-state levels of FSHR mRNA were found in COS-7 and KK-1 cells transfected with both types of FSHR cDNA. Conspicuously, immunofluorescence and confocal microscopy studies revealed that whereas the wild-type receptor could be readily detected on the plasma membrane, most of the mutated protein was intracellularly sequestered. Ligand binding studies confirmed the greatly reduced cell surface expression of the mutant FSHR. A low level of mutated receptors were expressed at the cell surface, as shown by ligand binding and cAMP response. The capacity of these receptors to evoke another second messenger response, that of inositol trisphosphate (IP3), was almost totally lost. This finding may be related to the clinical picture of the patients, i.e. blockade of follicular maturation. There is a highly conserved stretch of five amino acids (Ala-Phe-Asn-Gly-Thr) in the region of the mutation in all glycoprotein hormone receptors. We therefore created the same Ala to Val transition in the human LHR and studied its functional consequences. Similar functional alterations, i.e. intracellular sequestration and attenuated signal transduction, were found, as with mutated FSHR. Hence, this particular mutation in the conserved extracellular region of glycoprotein hormone receptors induces a conformational change that suppresses cell membrane targeting of the mutated receptor, probably through altered intracellular folding.
Monoclonal Antibody Targeting of Ovarian Carcinoma (1998)

The ability to effectively define disease status in ovarian cancer after initial therapy or to selectively screen high-risk populations remains a major challenge for in vivo monoclonal antibody (mAb)-targeted approaches. Antitumour murine mAbs (HMFG1, HMFG2, H317, and H17E2) and the reshaped human antibody Hu2PLAP (against placental alkaline phosphatase; PLAP), labelled with indium-111 and iodine-123, were evaluated for their ability to localise ovarian tumours in sequential studies of our group. Thirty patients with ovarian cancer, aged 40-78 years (median 60 years) were studied with HMFG1/G2: 11, and H317/H17E2: 19 murine mAbs. Six patients with ovarian cancer aged between 36 and 65 years (median 49 years) were studied with the reshaped human Hu2PLAP mAb (5 patients) or the murine H17E2 mAb (2 patients) labelled with 111In via a new macrocyclic chelating agent (DOTA). One of these was imaged twice, with H17E2- and Hu2PLAP-DOTA-111In, respectively. In 20 out of 22 patients with radiologically measurable ovarian cancer, the presence of tumour was confirmed by the murine mAb scan and correlated well with the findings of conventional radiology diagnostic methods. One of these patients with a negative H17E2 scan and a large abdominal mass at laparotomy was found to have a PLAP-negative tumour on immunohistochemistry. Additionally, the antibody scan revealed the presence of active disease, confirmed at laparotomy/laparoscopy, in 6 out of 8 patients considered to be in clinical complete remission. Best images were obtained at 24 and 48 h after the 123I and 111In mAbs, respectively. Successful imaging with the reshaped human antibody, Hu2PLAP, was seen in 2 patients with PLAP-positive tumours. Antibodies to DOTA developed in 2 patients. In conclusion, immunolocalisation of ovarian tumours is feasible with both murine and reshaped human mAbs. The sensitivity and specificity of the method appear very high in this pilot study, and in view of the absence of toxicity, the diagnostic contribution of this approach should be evaluated prospectively. Given the low number of patients without surgically detectable disease in the present study, future investigations should include more patients with no evidence of disease in order to provide more meaningful estimates of specificity.
Phase Characterization of Partially Stabilized Zirconia by Raman Spectroscopy (1985)

Raman spectroscopy was used to characterize phase transformations and transition temperatures in partially stabilized zirconia containing ≤20 wt% Y 2 O 3 . The completeness of the martensitic transition and its thermal hysteresis was followed in samples with ≤4 wt% Y 2 O 3 . Between 5 and 12 wt% the spectra indicate a tetragonal modification precipitated in a disordered cubic fluorite matrix. Above 15 wt% a “density of states” spectrum prevails that is characteristic of the fully stabilized disordered cubic phase.
Bandgap Engineering through Controlled Oxidation of Polythiophenes (2014)

The use of Rozen's reagent (HOF⋅CH3 CN) to convert polythiophenes to polymers containing thiophene-1,1-dioxide (TDO) is described. The oxidation of polythiophenes can be controlled with this potent, yet orthogonal reagent under mild conditions. The oxidation of poly(3-alkylthiophenes) proceeds at room temperature in a matter of minutes, introducing up to 60 % TDO moieties in the polymer backbone. The resulting polymers have a markedly low-lying lowest unoccupied molecular orbital (LUMO), consequently exhibiting a small bandgap. This approach demonstrates that modulating the backbone electronic structure of well-defined polymers, rather than varying the monomers, is an efficient means of tuning the electronic properties of conjugated polymers.
Microarray‐based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status (2008)

Follicular lymphoma (FL) is characterized by a large number of chromosomal aberrations. However, their exact genomic extension and involved target genes remain to be determined. For this purpose, we used array-based intermediate-high resolution genomic profiling in combination with Affymetrix gene expression analysis. Tumor specimens from 128 FL patients were analyzed for the presence of genomic aberrations and the results were correlated to clinical data sets and mRNA expression levels. In 114 (89%) of the 128 analyzed cases, a total of 688 genomic aberrations (384 gains/amplifications and 304 losses) were detected. Frequent genomic aberrations were: -1p36 (18%), +2p15 (24%), -3q (14%), -6q (25%), +7p (19%), +7q (23%), +8q (14%), -9p (16%), -11q (15%), +12q (20%), -13q (11%), -17p (16%), +18p (18%), and +18q (28%). Critical segments of these imbalances were delineated to genomic fragments with a minimum size down to 0.2 Mb. By comparison of these with mRNA gene expression data, putative candidate genes were identified. Moreover, we found that deletions affecting the tumor suppressor gene CDKN2A/B on 9p21 were detected in nontransformed FL grade I-II. For this aberration as well as for -6q25 and -6q26, an association with inferior survival was observed.
Recombinant Modified Vaccinia Virus Ankara Expressing the Spike Glycoprotein of Severe Acute Respiratory Syndrome Coronavirus Induces Protective Neutralizing Antibodies Primarily Targeting the Receptor Binding Region (2005)

Immunization with a killed or inactivated viral vaccine provides significant protection in animals against challenge with certain corresponding pathogenic coronaviruses (CoVs). However, the promise of this approach in humans is hampered by serious concerns over the risk of leaking live severe acute respiratory syndrome (SARS) viruses. In this study, we generated a SARS vaccine candidate by using the live-attenuated modified vaccinia virus Ankara (MVA) as a vector. The full-length SARS-CoV envelope Spike (S) glycoprotein gene was introduced into the deletion III region of the MVA genome. The newly generated recombinant MVA, ADS-MVA, is replication incompetent in mammalian cells and highly immunogenic in terms of inducing potent neutralizing antibodies in mice, rabbits, and monkeys. After two intramuscular vaccinations with ADS-MVA alone, the 50% inhibitory concentration in serum was achieved with reciprocal sera dilutions of more than 1,000- to 10,000-fold in these animals. Using fragmented S genes as immunogens, we also mapped a neutralizing epitope in the region of N-terminal 400 to 600 amino acids of the S glycoprotein (S400-600), which overlaps with the angiotensin-converting enzyme 2 (ACE2) receptor-binding region (RBR; S318-510). Moreover, using a recombinant soluble RBR-Fc protein, we were able to absorb and remove the majority of the neutralizing antibodies despite observing that the full S protein tends to induce a broader spectrum of neutralizing activities in comparison with fragmented S proteins. Our data suggest that a major mechanism for neutralizing SARS-CoV likely occurs through blocking the interaction between virus and the cellular receptor ACE2. In addition, ADS-MVA induced potent immune responses which very likely protected Chinese rhesus monkeys from pathogenic SARS-CoV challenge.
Advances in Mid-Infrared Spectroscopy for Chemical Analysis (2016)

Infrared spectroscopy in the 3-20 μm spectral window has evolved from a routine laboratory technique into a state-of-the-art spectroscopy and sensing tool by benefitting from recent progress in increasingly sophisticated spectra acquisition techniques and advanced materials for generating, guiding, and detecting mid-infrared (MIR) radiation. Today, MIR spectroscopy provides molecular information with trace to ultratrace sensitivity, fast data acquisition rates, and high spectral resolution catering to demanding applications in bioanalytics, for example, and to improved routine analysis. In addition to advances in miniaturized device technology without sacrificing analytical performance, selected innovative applications for MIR spectroscopy ranging from process analysis to biotechnology and medical diagnostics are highlighted in this review.
Novel chemical method for the preparation of nucleic acids for nonisotopic hybridization (1986)

A novel chemical method was used to prepare biotin-labeled nucleic acids for nonisotopic hybridization. The method involves the transamination of unpaired cytosine residues in polynucleotides with sodium bisulfite and ethylenediamine. Primary amino groups on the cytosine derivatives are then reacted with biotinyl-e-aminocaproic acid N-hydroxysuccinimide ester. Biotinylated probes hybridized with 1 to 2 pg of nitrocellulose filter-bound DNA and were visualized with a colorimetric detection technique. This method is simpler and less expensive than other methods for the preparation of nonisotopic probes. In addition, it is more versatile since the chemically modified bases can potentially react with other "indicator" molecules or proteins such as an enzyme. The specificity for unpaired cytosine residues is another advantage which could allow for the selective labeling of a specific region of a double-stranded nucleic acid. This improved labeling method should lead to the wider application of hybridization techniques in diagnostic microbiology and basic research in infectious diseases.
On the Representation and Estimation of Spatial Uncertainty (1986)

This paper describes a general method for estimating the nominal relationship and expected error (covariance) between coordinate frames representing the relative locations of ob jects. The frames may be known only indirectly through a series of spatial relationships, each with its associated error, arising from diverse causes, including positioning errors, measurement errors, or tolerances in part dimensions. This estimation method can be used to answer such questions as whether a camera attached to a robot is likely to have a particular reference object in its field of view. The calculated estimates agree well with those from an independent Monte Carlo simulation. The method makes it possible to decide in advance whether an uncertain relationship is known accu rately enough for some task and, if not, how much of an improvement in locational knowledge a proposed sensor will provide. The method presented can be generalized to six degrees offreedom and provides a practical means of esti mating the relationships ( position and orientation) among objects, as well as estimating the uncertainty associated with the relationships.
Determination of Collision Cross Sections Using a Fourier Transform Electrostatic Linear Ion Trap Mass Spectrometer (2017)

Collision cross sections (CCSs) were determined from the frequency-domain linewidths in a Fourier transform electrostatic linear ion trap. With use of an ultrahigh-vacuum precision leak valve and nitrogen gas, transients were recorded as the background pressure in the mass analyzer chamber was varied between 4× 10<sup>-8</sup> and 7 × 10<sup>-7</sup> Torr. The energetic hard-sphere ion-neutral collision model, described by Xu and coworkers, was used to relate the recorded image charge to the CCS of the molecule. In lieu of our monoisotopically isolating the mass of interest, the known relative isotopic abundances were programmed into the Lorentzian fitting algorithm such that the linewidth was extracted from a sum of Lorentzians. Although this works only if the isotopic distribution is known a priori, it prevents ion loss, preserves the high signal-to-noise ratio, and minimizes the experimental error on our homebuilt instrument. Six tetraalkylammonium cations were used to correlate the CCS measured in the electrostatic linear ion trap with that measured by drift-tube ion mobility spectrometry, for which there was an excellent correlation (R <sup>2</sup> ≈ 0.9999). Although the absolute CCSs derived with our method differ from those reported, the extracted linear correlation can be used to correct the raw CCS. With use of [angiotensin II]<sup>2+</sup> and reserpine, the corrected CCSs (334.9 ± 2.1 and 250.1 ± 0.5, respectively) were in good agreement with the reported ion mobility spectrometry CCSs (335 and 254.3, respectively). With sufficient signal-to-noise ratio, the CCSs determined are reproducible to within a fraction of a percent, comparable to the uncertainties reported on dedicated ion mobility instruments. Graphical Abstract ᅟ.
Evaluation of the rat embryo culture system as a predictive test for human teratogens (1994)

Ingestion of the anticonvulsant drug valproic acid and of the angiotensin converting enzyme inhibitor captopril during pregnancy has been associated with abnormal fetal outcome in humans. In contrast, the use of the antiinflammatory drug ibuprofen and the antihistamine diphenhydramine has not been documented to be embryotoxic in humans. We evaluated the rat embryo culture system as a predictive model of teratogenesis, using these four drugs as test agents. Valproic acid, ibuprofen, and diphenhydramine were embryotoxic, inducing concentration-dependent decreases in growth and a significant increase in anomalies. Valproic acid caused an increase in neural tube defects, ibuprofen increased the incidence of abnormal maxillary processes, and diphenhydramine increased the number of embryos with distorted body morphology. These abnormalities were induced at concentrations of valproic acid and diphenhydramine that are used clinically, but ibuprofen only induced toxicity at concentrations greatly exceeding the therapeutic range. Captopril was not embryotoxic up to 5 mM, the highest concentration tested. These results suggest that the rat embryo culture system produces both false positive and false negative data on the teratogenic potential of drugs. Although such an in vitro assay may be suitable to determine the mechanism of teratogenesis, it is not a sensitive indicator of potential human teratogens on its own. These data support the view that in vitro systems can only supplement clinical and epidemiological observations in humans, possibly as a method to determine mechanisms of actions of teratogens.