gebhart/patrepeval huggingface dataset:
1000 MeV Proton beam therapy facility at Petersburg Nuclear Physics Institute Synchrocyclotron (2006)

Since 1975 proton beam of PNPI synchrocyclotron with fixed energy of 1000 MeV is used for the stereotaxic proton therapy of different head brain diseases. 1300 patients have been treated during this time. The advantage of high energy beam (1000 MeV) is low scattering of protons in the irradiated tissue. This factor allows to form the dose field with high edge gradients (20%/mm) that is especially important for the irradiation of the intra-cranium targets placed in immediate proximity to the life critical parts of the brain. Fixation of the 6 0mm diameter proton beam at the isodose centre with accuracy of ±1.0 mm, two-dimensional rotation technique of the irradiation provide a very high ratio of the dose in the irradiation zone to the dose at the object's surface equal to 200:1. The absorbed doses are: 120-150 Gy for normal hypophysis, 100-120 Gy for pituitary adenomas and 40-70 Gy for arterio-venous malformation at the rate of absorbed dose up to 50 Gy/min. In the paper the dynamics and the efficiency of 1000 MeV proton therapy treatment of the brain deceases are given. At present time the feasibility study is in progress with the goal to create a proton therapy on Bragg peak by means of the moderation of 1000 MeV proton beam in the absorber down to 200 MeV, energy required for radiotherapy of deep seated tumors.
Updated results from a phase III trial of nivolumab (NIVO) combined with ipilimumab (IPI) in treatment-naive patients (pts) with advanced melanoma (MEL) (CheckMate 067). (2016)

9505 Background: In CheckMate 067, NIVO (anti-PD-1) plus IPI (anti-CTLA-4) significantly improved progression-free survival (PFS) and objective response rate (ORR) vs IPI alone in pts with MEL (N Engl J Med 2015;373:23). We report updated efficacy and safety results from this study. Methods: Treatment-naïve pts (N=945) were randomized 1:1:1 to NIVO 1 mg/kg Q3W + IPI 3 mg/kg Q3W for 4 doses (followed by NIVO 3 mg/kg Q2W), NIVO 3 mg/kg Q2W + placebo, or IPI 3 mg/kg Q3W for 4 doses + placebo, until progression or unacceptable toxicity. Pts were stratified by PD-L1 status, BRAFmutation status, and M-stage. Co-primary endpoints were PFS and overall survival (data remain immature). Secondary endpoints included efficacy by PD-L1 status and safety. Results: At ≥18 months of follow-up, median PFS continued to be significantly longer for NIVO+IPI and NIVO vs IPI (P<0.001), and was numerically longer for NIVO+IPI vs NIVO alone (Table). Median duration of response in 181/314 (57.6%) NIVO+IPI responders has not been reached, and was 22.3 and 14.4 months in 138/316 (43.7%) NIVO and 60/315 (19.0%) IPI responders, respectively. Median PFS was also numerically longer with NIVO+IPI vs NIVO or IPI regardless of PD-L1 tumor expression (Table). For NIVO+IPI, NIVO, and IPI groups, median PFS was 15.5, 5.6, and 4.0 months in pts with a BRAF mutation and was 11.3, 7.1, and 2.8 months in pts with wild-type BRAF, respectively. The frequency and types of drug-related grade 3/4 AEs were consistent with earlier reports (NIVO+IPI, 56.5%; NIVO, 19.8%; IPI, 27.0%). Conclusions: NIVO+IPI and NIVO alone continue to demonstrate superior clinical activity vs IPI monotherapy. NIVO+IPI appears to have greater efficacy than either agent alone, regardless of PD-L1 expression or BRAF mutation status. Clinical trial information: NCT01844505.Median PFS (95% CI) NIVO+IPI NIVO IPI ITT population 11.5 (8.9–16.7) 6.9 (4.3–9.5) 2.9 (2.8–3.4) HR (95% CI) vs NIVO 0.76 (0.60–0.92)a — — PD-L1 expression ≥5% NR (9.7–NR) 22.0 (8.9–NR) 3.9 (2.8–4.2) HR (95% CI) vs NIVO 0.87 (0.54–1.41)a — — <5% 11.1 (8.0–22.2) 5.3 (2.8–7.1) 2.8 (2.8–3.1) HR (95% CI) vs NIVO 0.74 (0.58–0.96)a — — HR, hazard ratio; NR, not reached. aExploratory endpoint.
Dataset of head-related transfer functions measured with a circular loudspeaker array (2014)

In this paper, we describe a dataset of head-related transfer functions (HRTFs) measured at the Research Institute of Electrical Communications, Tohoku University. The current dataset includes HRTFs for 105 subjects at 72 azimuths × 13 elevations of spherical coordinates. Anthropometric data for 39 subjects are also included. The measurement and postprocessing methods are outlined in this paper. These data will be freely accessible for nonprofit academic purposes via the Internet. Moreover, this dataset will be included in an international joint project to gather several HRTF datasets in a unified data format.
Natural Competence in the Hyperthermophilic ArchaeonPyrococcus furiosusFacilitates Genetic Manipulation: Construction of Markerless Deletions of Genes Encoding the Two Cytoplasmic Hydrogenases (2011)

In attempts to develop a method of introducing DNA into Pyrococcus furiosus, we discovered a variant within the wild-type population that is naturally and efficiently competent for DNA uptake. A pyrF gene deletion mutant was constructed in the genome, and the combined transformation and recombination frequencies of this strain allowed marker replacement by direct selection using linear DNA. We have demonstrated the use of this strain, designated COM1, for genetic manipulation. Using genetic selections and counterselections based on uracil biosynthesis, we generated single- and double-deletion mutants of the two gene clusters that encode the two cytoplasmic hydrogenases. The COM1 strain will provide the basis for the development of more sophisticated genetic tools allowing the study and metabolic engineering of this important hyperthermophile.
Antigenic determinants of the chlamydial major outer membrane protein resolved at a single amino acid level (1991)

Antigenic determinants were identified from seven chlamydial major outer membrane proteins by using overlapping hexapeptides and polyclonal antisera. Sixty-one determinants were detected, and 30 were surface exposed on the native organisms. The two negatively charged residues, aspartic acid and glutamic acid, were found most often in determinants. Thirteen antigenic sites were further characterized by alanine substitution. Differences in fine specificities of these linear determinants were observed in alanine substitution profiles. Five determinants had adjacent critical residues, while eight had critical residues alternated with noncritical residues. Complete replacement analysis of two antigenic determinants provided more detailed information for elucidating the structural basis of the specificity of antigen-antibody interaction and suggested a correlation between sequence conservation and tolerance to amino acid substitution for antigenic sites subject to intense immune selection pressure.
UCST Wetting Transitions of Polyzwitterionic Brushes Driven by Self‐Association (2006)

A sweeping success: The surface-initiated, atom-transfer radical polymerization of [2-(methacryloyloxy)ethyl]dimethyl(3-sulfopropyl)ammonium hydroxide (MEDSAH) on silicon and gold surfaces leads to homogeneous and patterned brushes of poly-MEDSAH. The association state of the zwitterionic side-groups is determined (see picture; wettability of thin (left) and thick (right) brushes). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z503264_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Sequence-, Tissue-, and Delivery-Specific Targeting of RNA During Post-Transcriptional Gene Silencing (2002)

Transgenic Nicotiana benthamiana plants expressing an untranslatable version of the coat protein (CP) gene from the Tamarillo mosaic virus (TaMV) were either resistant to TaMV infection or recovered from infection. These phenotypes were the result of a post-transcriptional gene silencing (PTGS) mechanism that targeted TaMV-CP sequences for degradation. The TaMV-CP sequences were degraded when present in the wild-type TaMV potyvirus, in transgene mRNA, or in chimeric viral vectors based on White clover mosaic virus. The more efficiently targeted region was mapped to a 134-nt segment. Differences were observed in the efficiency of targeting during cell-to-cell and long-distance movement of the chimeric viruses. However, the TaMV-CP sequences do not appear to be targeted for degradation when delivered by biolistics.
Soluble CD80 Protein Delays Tumor Growth and Promotes Tumor-Infiltrating Lymphocytes (2017)

Tumor cells use various immune-suppressive strategies to overcome antitumor immunity. One such method is tumor expression of programmed death ligand-1 (PD-L1), which triggers apoptotic death or anergy upon binding programmed death-1 (PD-1) on T cells. Our previous <i>in vitro</i> cellular studies with human and mouse PD-L1<sup>+</sup> tumor cells demonstrated that a soluble form of the costimulatory molecule CD80 prevented PD-L1-mediated immune suppression and restored T-cell activation by binding PD-L1 and blocking interaction with PD-1. We now report that <i>in vivo</i> treatment of established syngeneic PD-L1<sup>+</sup> CT26 colon carcinoma and B16F10 melanoma tumors with CD80-Fc delays tumor growth and promotes tumor-infiltrating T cells. Studies with PD-1<sup>-/-</sup> and CD28<sup>-/-</sup> mice demonstrate that soluble CD80 acts <i>in vivo</i> by simultaneously neutralizing PD-1 suppression and activating through CD28. We also report that soluble CD80 mediates its effects by activating transcription factors EGR1-4, NF-κB, and MAPK, downstream signaling components of the CD28 and T-cell receptor pathways. Soluble CD80 binds to CTLA-4 on activated human peripheral blood mononuclear cells. However, increasing quantities of CTLA-4 antagonist antibodies do not increase T-cell activation. These results indicate that soluble CD80 does not suppress T-cell function through CTLA-4 and suggest that CTLA-4 acts as a decoy receptor for CD80, rather than functioning as a suppressive signaling receptor. Collectively, these studies demonstrate that soluble CD80 has therapeutic efficacy <i>in vivo</i> in mouse tumor systems and that its effects are due to its ability to inhibit PD-1-mediated suppression while concurrently activating T cells through CD28. <i>Cancer Immunol Res; 6(1); 59-68. ©2017 AACR</i>.
Validation of a Novel Biomarker Panel for the Detection of Ovarian Cancer (2016)

The implications of our study are 2-fold: (i) we have demonstrated the strengths of HE4 alone and in combination with CA125, lending credence to increasing its usage in the clinic; and (ii) we have demonstrated the clinical utility of our integrated -omics approach to identifying novel serum markers with comparable performance to clinical markers. Cancer Epidemiol Biomarkers Prev; 25(9); 1333-40. ©2016 AACR.
Sensitive Detection of Human Telomerase Reverse Transcriptase mRNA in the Serum of Patients with Hepatocellular Carcinoma (2003)

These results suggest that this assay is sensitive enough to detect hTERT mRNA in serum, and that it would be applicable for early detection and diagnosis of HCC or other cancers by a quantitative method.
Neurotrophic factor intervention restores auditory function in deafened animals (2002)

A primary cause of deafness is damage of receptor cells in the inner ear. Clinically, it has been demonstrated that effective functionality can be provided by electrical stimulation of the auditory nerve, thus bypassing damaged receptor cells. However, subsequent to sensory cell loss there is a secondary degeneration of the afferent nerve fibers, resulting in reduced effectiveness of such cochlear prostheses. The effects of neurotrophic factors were tested in a guinea pig cochlear prosthesis model. After chemical deafening to mimic the clinical situation, the neurotrophic factors brain-derived neurotrophic factor and an analogue of ciliary neurotrophic factor were infused directly into the cochlea of the inner ear for 26 days by using an osmotic pump system. An electrode introduced into the cochlea was used to elicit auditory responses just as in patients implanted with cochlear prostheses. Intervention with brain-derived neurotrophic factor and the ciliary neurotrophic factor analogue not only increased the survival of auditory spiral ganglion neurons, but significantly enhanced the functional responsiveness of the auditory system as measured by using electrically evoked auditory brainstem responses. This demonstration that neurotrophin intervention enhances threshold sensitivity within the auditory system will have great clinical importance for the treatment of deaf patients with cochlear prostheses. The findings have direct implications for the enhancement of responsiveness in deafferented peripheral nerves.
Oscillation damped movement of suspended objects (2003)

Transportation of objects using overhead cranes or manipulators can induce pendulum motion of the object. Residual oscillation from transportation typically must be damped or allowed to decay before the next process can take place. By properly programming the acceleration of the transporting device (e.g. crane) an oscillation damped transport and swing-free stop is obtainable. The authors review the theory associated with oscillation-damped trajectories for simply suspended objects and describe a particular implementation using a CIMCORP XR 6100 gantry robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Complex intracardiac nervous system. (2006)

The heart is an organ with continuous activity, which must satisfy demands of an organism on various conditions. Therefore, heart activity is modulated at many levels, including intrinsic regulatory mechanisms, humoral factors and autonomic nervous system. The regulation of heart activity by sympathetic and parasympathetic nervous system is well known. Accumulated evidence in recent decades indicates that intracardiac neurons can also significantly regulate heart activity. These neurons are concentrated in multiple heart ganglia. Interactions between neurons within intracardiac ganglia together with interconnections between individual ganglia provide anatomical and functional basis of complex nervous network of the heart. This complex intracardiac nervous system together with extracardiac autonomic neurons, innervating heart, provides modulation of heart activity during both physiological and pathological conditions. This review article summarizes recent knowledge about the role of heart neurons in physiological conditions and in etiopathogenesis of selected diseases. Effect of pharmacological and surgical interventions on heart neurons is also discussed (Fig. 2, Ref. 70).
Bactericidal Group IIA Phospholipase A2 in Serum of Patients with Bacterial Infections (2002)

Group IIA phospholipase A2 (PLA2-IIA) is a newly recognized antibacterial acute phase protein. The concentration of PLA2-IIA increases up to 500-fold in the blood plasma of patients with severe acute diseases, compared with healthy persons. Despite numerous studies, the exact roles of this enzyme in human diseases are unknown. This study investigated the antibacterial properties of PLA2-IIA in human acute phase serum. PLA2-IIA in serum samples of patients with bacterial infections was capable of killing 90% of Staphylococcus aureus and 99% of Listeria monocytogenes in vitro after incubation for 2 h. At concentrations found in normal human serum, PLA2-IIA killed 90% of L. monocytogenes but did not kill S. aureus or Escherichia coli. The bactericidal effects of acute phase and normal human serum were abolished after depletion of PLA2-IIA by immunoadsorption.
Glycan arrays lead to the discovery of autoimmunogenic activity of SARS-CoV (2004)

Using carbohydrate microarrays, we characterized the carbohydrate binding activity of SARS-CoV neutralizing antibodies elicited by an inactivated SARS-CoV vaccine. In these antibodies, we detected undesired autoantibody reactivity specific for the carbohydrate moieties of an abundant human serum glycoprotein asialo-orosomucoid (ASOR). This observation provides important clues for the selection of specific immunologic probes to examine whether SARS-CoV expresses antigenic structures that mimic the host glycan. We found that lectin PHA-L (Phaseolus vulgaris L.), which is specific for a defined complex carbohydrate of ASOR, stained the SARS-CoV-infected cells specifically and intensively. Taken together, we present immunologic evidence that a carbohydrate structure of SARS-CoV shares antigenic similarity with host glycan complex carbohydrates. The experimental approaches we applied in this study are likely applicable for the identification of immunologic targets of other viral pathogens.
Boronic acid compounds as potential pharmaceutical agents (2003)

Boronic acid compounds have been used, because of their unique structural features, for the development of potent enzyme inhibitors, boron neutron capture agents for cancer therapy, and as antibody mimics that recognize biologically important saccharides. Consequently, there has been a surge of interests in boronic acid compounds. This study reviews the recent development in this area during the last six years.
Single mutations in the transmembrane envelope protein abrogate the immunosuppressive property of HIV-1 (2012)

These findings indicate that the isu domain of gp41 modulates cytokine expression in vitro and suppresses antibody response in vivo and therefore may contribute to the virus induced immunodeficiency.
Integration of DNA Copy Number Alterations and Prognostic Gene Expression Signatures in Breast Cancer Patients (2010)

There is a strong correlation between the different gene expression signatures and underlying genomic changes. These findings help to establish a link between genomic changes and gene expression signatures, enabling a better understanding of the tumor biology that causes poor prognosis.
Mutational analysis of simian virus 40 small-t antigen (1990)

Several point mutations in the simian virus 40 (SV40) small-t antigen have been analyzed for their effects on protein stability, transformation, transactivation, and binding of two cellular proteins. All mutations which affected cysteine residues in two cysteine clusters produced highly unstable small-t antigens. Four point mutations outside these clusters and one in-frame deletion mutant, dl890, produced stable proteins but reduced transformation efficiency. These were able to transactivate the EII promoter and bind the cellular proteins, suggesting that these activities are not sufficient for small-t-mediated enhancement of transformation.
Diphenyldiazomethane (2001)

[883-40-9] C13H10N2 (MW 194.25) InChI = 1S/C13H10N2/c14-15-13(11-7-3-1-4-8-11)12-9-5-2-6-10-12/h1-10H InChIKey = ITLHXEGAYQFOHJ-UHFFFAOYSA-N (alkylating agent for carboxylic acids; reagent for the synthesis of diphenylcyclopropanes from alkenes1) Physical Data: red solid, mp 29–32 °C. Solubility: sol most organic solvents including ether, dichloromethane, petroleum ether, ethanol. Preparative Methods: most commonly prepared by the oxidation of benzophenone hydrazone. The oxidants that are most frequently used are Mercury(II) Oxide2 and Nickel(II) Peroxide,3 though the use of Manganese Dioxide,4 Silver(II) Oxide,5 and Peracetic Acid6 have been reported. Typical reaction conditions involve addition of the oxidant to a solution of the hydrazone in a suitable solvent at rt. The oxidation requires 1–6 h to complete, depending on the conditions employed. Solvents that have been used are petroleum ether, diethyl ether and other ethereal solvents, and dichloromethane. When mercury(II) oxide is used, the addition of a basic ethanol solution speeds up the reaction and allows the oxidation to occur at a lower temperature. The reagent is typically not stored and is synthesized immediately prior to use. If the reagent is to be used for the esterification of a carboxylic acid, then an in situ oxidation can be employed using phenyliodine(III) diacetate ((Diacetoxyiodo)benzene)7 or peracetic acid with a trace of iodine.8 Interestingly, phenyliodine(III) diacetate provides a low yield of diphenyldiazomethane when used in the absence of a carboxylic acid, this has led the authors to suggest that the active alkylating agent is a species other than diphenyldiazomethane. Handling, Storage, and Precautions: diphenyldiazomethane is potentially explosive. For this reason, extreme care must be observed in the synthesis and use of this compound with all operations being conducted behind a blast shield in a fume hood. There are also health related hazards that must be considered. Diazo compounds, as a class, are toxic and irritating and can be sensitizers. For a description of the hazards associated with this class of compounds, see the handling and storage precautions listed for Diazomethane.
Speciation and Domestication in Maize and Its Wild Relatives: Evidence From the Globulin-1 Gene (1998)

The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa-maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged approximately 700, 000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology.
Downlink scheduling in CDMA data networks (2000)

Packet data is expected to dominate third generation wireless networks, unlike current generation voice networks. This opens up new and interesting problems. Physical and link layer issues have been studied extensively, while resource allocation and scheduling issues have not been addressed satisfactorily.