gebhart/patrepeval huggingface dataset:
1,2-Silyl-Migrative Cyclization of Vinylsilanes Bearing a Hydroxy Group:  Stereoselective Synthesis of Multisubstituted Tetrahydropyrans and Tetrahydrofurans1 (2002)

Acid-catalyzed intramolecular addition of a hydroxy group to alpha-alkylated vinylsilanes has been studied. Treatment of (Z)-5-alkyl-5-silyl-4-penten-1-ols 1 (R = alkyl) with 5 mol % TiCl(4) in CHCl(3) gave trans-2-alkyl-3-silyltetrahydropyrans 2 exclusively (trans/cis = >99/1 to 97/3). The cyclization efficiency and rate strongly depended on the geometry of the C-C double bond and the silyl group. The use of (E)-vinylsilanes resulted in lower yields with poor cis-selectivity. In the cyclization of (Z)-1 (R = Bu), the silyl group used, the reaction time, and the yield of 2 were as follows: SiMe(2)Ph, 9.5 h, 75%; SiMe(3), 7.5 h, 66%; SiMePh(2), 24 h, 58%; SiMe(2)-t-Bu, 0.75 h, 85%; SiMe(2)Bn, 1.5 h, 78%. This 1,2-silyl-migrative cyclization could be applied to stereoselective synthesis of trisubstituted tetrahydropyrans. The acid-catalyzed reaction of 1-, 2-, or 3-substituted (Z)-5-silyl-4-nonen-1-ols 8 gave r-2,t-3,c-6-, r-2,t-3,t-5-, or r-2,t-3,c-4-trisubstituted tetrahydropyrans with high diastereoselectivity, respectively. (Z)-4-Alkyl-4-silyl-3-buten-1-ols 5 as well as 1 underwent the 1,2-silyl-migrative cyclization to give 2-alkyl-3-silyltetrahydrofurans 6 with high trans-selectivity. This silicon-directed cyclization was also available for the stereoselective synthesis of tri- and tetrasubstituted tetrahydrofurans.
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server (2013)

Supplementary data are available at Bioinformatics online.
Mixed membership analysis of high-throughput interaction studies: Relational data (2007)

In this paper, we consider the statistical analysis of a protein interaction network. We propose a Bayesian model that uses a hierarchy of probabilistic assumptions about the way proteins interact with one another in order to: (i) identify the number of non-observable functional modules; (ii) estimate the degree of membership of proteins to modules; and (iii) estimate typical interaction patterns among the functional modules themselves. Our model describes large amount of (relational) data using a relatively small set of parameters that we can reliably estimate with an efficient inference algorithm. We apply our methodology to data on protein-to-protein interactions in saccharomyces cerevisiae to reveal proteins' diverse functional roles. The case study provides the basis for an overview of which scientific questions can be addressed using our methods, and for a discussion of technical issues.
Bulk silicon for photonics applications (2005)

This study explores possibilities for integrating silicon light emitters into high-density microelectronic circuits. Silicon-on-insulator (SOI) substrates seem most suitable for this application, due to the optical confinement provided by the buried-oxide layer.
ENZYME-LINKED IMMUNOASSAY FOR ANTI-HLA ANTIBODIES—AN ALTERNATIVE TO PANEL STUDIES BY LYMPHOCYTOTOXICITY (1993)

In order to provide a simple and specific assay for the detection and quantitation of IgG and IgM anti-HLA antibodies in sera, HLA antigens purified from a pool of 240 random donor platelets were used to develop a solid-phase enzyme-linked immunoassay (EIA). The reference values for identifying the presence of IgG or IgM anti-HLA antibodies were determined by assaying sera from 39 healthy individuals without prior HLA alloimmunization. The assay was evaluated by studying sera from 122 patients who had been characterized previously for panel reactive antibodies by the lymphocytotoxicity assay (LCA). A significant linear correlation between two assays was noted (r = 0.8, P = 0.0001). Further analyses of the data demonstrated that the newly developed EIA has 100% specificity and 95.3% sensitivity as compared with the LCA. Additional studies revealed that patients whose PRA increased or decreased over time were in parallel with antibody levels measured by EIA. When the EIA was used to measure anti-HLA antibody titers, it was more sensitive than the LCA. Since the EIA is sensitive, specific, and technically less demanding, it should provide an useful alternative to reduce the number of the more laborious panel studies for monitoring anti-HLA antibody status in candidates for organ transplantation and recipients of blood transfusions.
Studies on organic fluorine compounds. Part 25. Diels–Alder reaction of hexakis(trifluoromethyl)benzvalene (1979)

Diels–Alder reactions of hexakis(trifluoromethyl)benzvalene (1) with cyclic and acyclic dienes have been examined. The Diels–Alder reaction of cyclic dienes gave only the exo-isomer of two possible stereoisomers. Cyclohexa-1,3-diene gave the dihydro-compound of (1), rather than a Diels–Alder adduct, by an ene-reaction or [π2s+σ2s+σ2s] process.
Silicon diffractive optical element with piecewise continuous profile to focus high-power terahertz radiation into a square area (2021)

A technique of high-frequency laser ablation using a 2D beam scanner has been designed and applied to creation of a silicon diffractive optical element (DOE) with a continuous profile to focus a terahertz Gaussian beam into a square region. The microrelief of the resulting silicon DOE has been analyzed with a white-light interferometer and a scanning electron microscope. The distribution of radiation behind the DOE illuminated by a high-power beam of the Novosibirsk free-electron laser at a wavelength of 130 µm, recorded with a pyroelectric camera, has been demonstrated. The measured diffraction efficiency of the DOE is equal to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>97</mml:mn> </mml:mrow> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mo>±</mml:mo> </mml:mrow> </mml:mrow> <mml:mspace width="thickmathspace"/> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mrow class="MJX-TeXAtom-ORD"> <mml:mn>2</mml:mn> </mml:mrow> </mml:mrow> <mml:mi mathvariant="normal">%</mml:mi> </mml:math> .
A Factor That Regulates the Class II Major Histocompatibility Complex Gene DPA Is a Member of a Subfamily of Zinc Finger Proteins That Includes a Drosophila Developmental Control Protein (1994)

A novel DNA sequence element termed the J element involved in the regulated expression of class II major histocompatibility complex genes was recently described. To study this element and its role in class II gene regulation further, a cDNA library was screened with oligonucleotide probes containing both the S element and the nearby J element of the human DPA gene. Several DNA clones were obtained by this procedure, one of which, clone 18, is reported and characterized here. It encodes a protein predicted to contain 688 amino acid residues, including 11 zinc finger motifs of the C2H2 type in the C-terminal region, that are Krüppel-like in the conservation of the H/C link sequence connecting them. The 160 N-terminal amino acids in the nonfinger region of clone 18 are highly homologous with similar regions of several other human, mouse, and Drosophila sequences, defining a subfamily of Krüppel-like zinc finger proteins termed TAB (tramtrack [ttk]-associated box) here. One of the Drosophila sequences, ttk, is a developmental control gene, while a second does not contain a zinc finger region but encodes a structure important in oocyte development. An acidic activation domain is located between the N-terminal conserved region of clone 18 and its zinc fingers. This protein appears to require both the S and J elements, which are separated by 10 bp for optimal binding. Antisense cDNA to clone 18 inhibited the expression of a reporter construct containing the DPA promoter, indicating its functional importance in the expression of this class II gene.
The Porn Ultimatum: The Dehumanising Effects of Smut (2011)

In a New York times article in 1914 William T Sedgwick, a professor of biology and public health at the Massachusetts institute of technology, warned 'the militant suffragettes' that, were they to succeed in their goal of female liberation, they would 'find that the knightliness and chivalry of gentlemen have vanished, and in their stead will arise a rough male power that will place women where it chooses'. Towards women only 'brutal appetites' would remain: 'naked', 'unfettered' and 'unashamed'. Sedgwick thought this ugly fate unlikely, however, predicting that men would soon lose patience with the feminist endeavour 'and, putting the women back in their homes, say, 'That is where you belong. Now stay there.''
Generalized LRS Estimator for Min-entropy Estimation (2021)

The min-entropy is a widely used metric to quantify the randomness of generated random numbers, which measures the difficulty of guessing the most likely output. It is difficult to accurately estimate the min-entropy of a non-independent and identically distributed (non-IID) source. Hence, NIST Special Publication (SP) 800-90B adopts ten different min-entropy estimators and then conservatively selects the minimum value among ten min-entropy estimates. Among these estimators, the longest repeated substring (LRS) estimator estimates the collision entropy instead of the min-entropy by counting the number of repeated substrings. Since the collision entropy is an upper bound on the min-entropy, the LRS estimator inherently provides \emph{overestimated} outputs. In this paper, we propose two techniques to estimate the min-entropy of a non-IID source accurately. The first technique resolves the overestimation problem by translating the collision entropy into the min-entropy. Next, we generalize the LRS estimator by adopting the general R{é}nyi entropy instead of the collision entropy (i.e., R{é}nyi entropy of order two). We show that adopting a higher order can reduce the variance of min-entropy estimates. By integrating these techniques, we propose a generalized LRS estimator that effectively resolves the overestimation problem and provides stable min-entropy estimates. Theoretical analysis and empirical results support that the proposed generalized LRS estimator improves the estimation accuracy significantly, which makes it an appealing alternative to the LRS estimator.
Power generation in externally fired air turbine feed by biomass derived syngas (2018)

In a context where the depletion of traditional energy sources together with the emission reduction question reached a dead end, increasing attention is posed towards emerging technologies. Among such technologies, those for which energy is produced locally by residual biomass have gained in the last decades a role of first relevance. Today, different technologies can be successfully applied for distributed energy production from biomass. Gasification is the most promising because offers the possibility to achieve the highest net efficiency. Nevertheless, several questions need to be addressed to get this technology ready to market. The major drawback is related to the presence, in the produced gas, of tars and condensables that still greatly inhibits the application of this technology. The most common configuration for small scale applications is that where the syngas produced in a downdraft gasifier is feed, after its purification, in an internal combustion engine (ICE) for power production. In this work, a new configuration where syngas produced by downdraft gasifier is feed directly in an externally fired air turbine is discussed and numerically analysed. A numerical model of the whole process was built using an in-house code and results were evaluated in terms of first law efficiency. © 2018 AMSE Press. All rights reserved.
Supplementary Figure 1 from Antibody-Drug Conjugates for the Treatment of Non–Hodgkin's Lymphoma: Target and Linker-Drug Selection (2023)

Supplementary Figure 1 from Antibody-Drug Conjugates for the Treatment of Non–Hodgkin's Lymphoma: Target and Linker-Drug Selection
Ambient noise in the Arctic Ocean measured with a drifting vertical line array (2015)

In mid-April 2013, a Distributed Vertical Line Array (DVLA) with 22 hydrophone modules over a 600-m aperture immediately below the subsurface float was moored near the North Pole. The mooring parted just above the anchor shortly after deployment and subsequently drifted slowly south toward Fram Strait until it was recovered in mid-September 2013. The DVLA recorded low-frequency ambient noise (1953.125 samples per second) for 108 minutes six days per week. Previously reported noise levels in the Arctic are highly variable, with periods of low noise when the wind is low and the ice is stable and periods of high noise associated with pressure ridging. The median noise level at 98 m depth during the first two weeks of May not far from the North Pole had a maximum between 10 and 20 Hz of approximately 75 dB re 1 μPa2/Hz. The background noise levels are at times extraordinarily low, with the 10th percentile over a 108-minute period limited by the self-noise of the hydrophones above approximately 100 Hz (35 and 26 dB re 1 μPa2/Hz at 100 and 1000 Hz, respectively). During this time, the median ambient noise levels increased with depth by roughly 3 dB between 100 and 600 m.
Cognitive Behavioral Therapy to Sustain the Antidepressant Effects of Ketamine in Treatment-Resistant Depression: A Randomized Clinical Trial (2021)

This proof-of-concept study provides preliminary data indicating that CBT may sustain the antidepressant effects of ketamine in TRD. Further study and optimization of this treatment approach in well-powered clinical trials is recommended.
Apoptotic Machinery Diversity in Multiple Myeloma Molecular Subtypes (2013)

Multiple myeloma (MM) is a plasma-cell (PC) malignancy that is heterogeneous in its clinical presentation and prognosis. Monoclonal gammopathy of undetermined significance (MGUS) consistently preceded development of MM. The presence of primary IgH translocations and the universal overexpression of cyclin D genes led to a molecular classification of MM patients into different disease subtypes. Since Bcl-2 family proteins determine cell fate, we analyzed a publicly available Affymetrix gene expression of 44 MGUS and 414 newly diagnosed MM patients to investigate (1) the global change of Bcl-2 family members in MM versus MGUS (2) whether the four major subtypes defined as hyperdiploid, CyclinD1, MAF, and MMSET, display specific apoptotic machineries. We showed that among the main anti-apoptotic members (Bcl-2, Bcl-xL, and Mcl-1), Mcl-1 up-regulation discriminated MM from MGUS, in agreement with the prominent role of Mcl-1 in PC differentiation. Surprisingly, the expression of multi-domain pro-apoptotic Bak and Bax were increased during the progression of MGUS to MM. The combined profile of Bcl-2, Bcl-xL, and Mcl-1 was sufficient to distinguish MM molecular groups. While specific pro-apoptotic members expression was observed for each MM subtypes, CyclinD1 subgroup, was identified as a particular entity characterized by a low expression of BH3-only (Puma, Bik, and Bad) and multi-domain pro-apoptotic members (Bax and Bak). Our analysis supports the notion that MM heterogeneity is extended to the differential expression of the Bcl-2 family content in each MM subgroup. The influence of Bcl-2 family profile in the survival of the different patient groups will be further discussed to establish the potential consequences for therapeutic interventions. Finally, the use of distinct pro-survival members in the different steps of immune responses to antigen raises also the question of whether the different Bcl-2 anti-apoptotic profile could reflect a different origin of MM cells.
Spektren, Struktur, Ligandenaustausch und Reaktionen eines Ether-Wolfram(II)- Komplexes (1998)

Leicht abspalten läßt sich der Etherligand aus dem Komplex 1 und ermöglicht damit einen Zugang zu dem reaktiven Kation [WTp′(CO)(PhC≡CMe)]+ (Tp′=Hydridotris(3,5-dimethylpyrazol-1-ylborat). In Dichlormethan zerfällt 1 in Abwesenheit potentieller Liganden und reagiert mit dem Lösungsmittel zum Metallacyclus 2 [Gl. (a)].
Structure and rheological properties of polymer mixtures (1967)

Abstract Investigations were undertaken of the structure and rheological properties of mixtures consisting of one crystallizing and one amorphous polymers. It was established that mixtures of poly(ethylene adipate) and poly(vinyl acetate); of poly(ethylene adipate) and poly(methyl methacrylate); and of poly(ethylene sebacinate) and poly(methyl methacrylate) can form amorphous solid solutions with one another or can crystallize without any apparent division of the two components. The phase condition of the mixture is determined by the nature of the two polymers, by the ratio between them, and by their molecular weights. The melting point of these mixtures drops in proportion to the content of the amorphous component. The assumption is made on the basis of the results obtained that the amorphous component occupies the defective areas in the crystal grating. The fluidity of the mixtures was measured by means of a capillary viscosimeter. It was established in all cases that there appear deviations from the proportional change of the effective viscosity between the viscosities of the components. These deviations are explained by the change in the energy of activation of the viscous flow of the melts which was also subject to determination.
Photochemistry of Benzotriazole:  An Unprecedented Tautomer-Selective Intermolecular [2+2] Photocycloaddition (2002)

[reaction: see text]. Irradiation of benzotriazole with a variety of maleimide derivatives leads to the stereo- and regioselective formation of aryl [2 + 2] photocycloaddition products. Further studies with 2-alkyl benzotriazole derivatives indicates that in the case of the parent benzotriazole this cycloaddition proceeds selectively via the 2H-tautomer.
Segmentation of random fields via borrowed strength density estimation (1997)

In many applications, spatial observations must be segmented into homogeneous regions and the number, positions, and shapes of the regions are unknown a priori. Information about the underlying probability distributions are often unknown. Furthermore, the anticipated regions of interest may be small with few observations from the individual regions. This paper presents a technique designed to address these difficulties. A simple segmentation procedure can be obtained as a clustering of the disjoint subregions obtained through an initial low-level partitioning procedure. Clustering of these subregions based upon a similarity matrix derived from estimates of their marginal probability density functions yields the resultant segmentation. It is shown that this segmentation is improved through the use of a "borrowed strength" density estimation procedure wherein potential similarities between the density functions for the subregions are exploited. The borrowed strength technique is described and the performance of segmentation based on these estimates is investigated through an example from statistical image analysis.
A COMPONENT-ORIENTED ENVIRONMENT FOR SYSTEMS DEVELOPMENT (2005)

This paper discusses the development and i m pl em en t a t i o n component - o ri e n t e d environment for systems development, known as the ADVISETM product suite. The ADVISETM product suite is composed of a combination of computer hardware, software, and electrical interfaces intended to support the specification, design, integration, and test of air vehicle systems. of a The ADVISETM system contains a library of system components (pumps, valves, control computers, etc.) which the user treats as building blocks. The user configures the components to represent a system. The user can elect to simulate, emulate, or stimulate any or all these components. The flexibility of the component-oriented approach for systems development provides many advantages for managing complex systems development.
P111: Phase I Trial of Brentuximab Vedotin plus Cyclosporine in Relapsed/Refractory Hodgkin Lymphoma (2022)

Treatment of relapsed/refractory (R/R) Hodgkin lymphoma (HL) following failure of brentuximab vedotin (BV) and PD-1 blockade is a major unmet need. Resistance to BV is associated with multidrug resistance gene 1 (MDR1) overexpression. MDR1 inhibitors cyclosporine (CsA) or verapamil (VRP) can re-sensitize cHL to BV. We previously reported preliminary results of a phase I study of BV combined with CsA in R/R HL. Here we report the final results of the completed study. This is a single center, open-label phase I study. The dose finding portion followed a 3 + 3 design with 4 planned dose levels (DL). BV was given at 1.2 mg/kg (DL1) or 1.8 mg/kg (DL2-4) intravenously every 3 weeks. Planned dose of CsA was 5 mg/kg (DL1-2) or 7.5 mg/kg (DL3-4) orally twice daily on days 1–5. Planned dose of VRP was 120 mg orally four times daily on days 1–5 (DL4). Each cycle was 3 weeks. Once the maximum tolerated dose (MTD) was determined, BV-refractory pts were enrolled in an expansion cohort at the MTD. Primary objective was to determine the MTD and safety of the combination. Secondary objectives were overall response rate (ORR), complete response (CR) rate, response duration (DOR), overall survival (OS), and progression-free survival (PFS). 29 pts (14 dose-finding, 15 dose-expansion) were enrolled. Median age was 36 (20–69) and pts had a median of 5 (3–12) prior lines of therapy. All had prior BV (only 2 BV-sensitive) and 27 had prior PD-1 blockade. Four pts were treated on DL1, 22 on DL2, 3 on DL3. MTD was DL2. DLTs observed were: DL1 10-day CsA (n=1) grade (Gr) 3 hyperbilirubinemia, abdominal pain, and hypertension, DL2 (n=1) Gr3 abdominal pain and Gr3-4 neutropenia, DL3 (n=2) Gr3 bone pain/constipation/Gr4 lymphopenia (n=1) and Gr3 hyperglycemia (n=1). Median duration of treatment was 3 (1–16) cycles. Most frequent adverse events (AEs) were nausea (90%), hypertension (90%), anemia (86%), fatigue (76%), neutropenia (76%), and leukopenia (76%). All pts had Gr3+ AEs with most frequent being neutropenia (62%). Reasons for treatment discontinuation included death (n=4), disease progression (n=10), and toxicity (n=2). Treatment-related death occurred in 3 pts (pneumonitis at DL1, respiratory failure and hypotension at DL2). The ORR/CR was 62%/24%. The median DOR and PFS was 5 months and median OS was not reached. BV + CsA was effective in BV-refractory R/R HL but was also associated with toxicity leading to early study termination.
Utilization of genomic sequence information to develop malaria vaccines (2003)

Recent advances in the fields of genomics, proteomics and molecular immunology offer tremendous opportunities for the development of novel interventions against public health threats, including malaria. However, there is currently no algorithm that can effectively identify the targets of protective T cell or antibody responses from genomic data. Furthermore, the identification of antigens that will stimulate the most effective immunity against the target pathogen is problematic, particularly if the genome is large. Malaria is an attractive model for the development and validation of approaches to translate genomic information to vaccine development because of the critical need for effective anti-malarial interventions and because the Plasmodium parasite is a complex multistage pathogen targeted by multiple immune responses. Sterile protective immunity can be achieved by immunization with radiation-attenuated sporozoites, and anti-disease immunity can be induced in residents in malaria-endemic areas. However, the 23 Mb Plasmodium falciparum genome encodes more than 5,300 proteins, each of which is a potential target of protective immune responses. The current generation of subunit vaccines is based on a single or few antigens and therefore might elicit too narrow a breadth of response. We are working towards the development of a new generation vaccine based on the presumption that duplicating the protection induced by the whole organism may require a vaccine nearly as complex as the organism itself. Here, we present our strategy to exploit the genomic sequence of P. falciparum for malaria vaccine development.