gebhart/patrepeval huggingface dataset:
Polarity as a criterion in protein design (1989)

Hypothetical proteins can be tested computationally by determining whether or not the designed sequence-structure pair has the characteristics of a typical globular protein. We have developed such a test by deriving quantities with approximately constant value for all globular proteins, based on empirical analysis of the exposed and buried surfaces of 128 structurally known proteins. The characteristic quantities that best appear to segregate badly designed or deliberately misfolded proteins from their properly folded natural relatives are the polar fraction of side chains on the protein surface and, independently, in the protein interior. Three of the seven hypothetical structures tested here can be rejected as having too many polar side-chain groups in the interior or too few on the protein surface. In addition, a recently designed nutritional protein is identified as being very much unlike globular proteins. These database-derived characteristic quantities are useful in screening designed proteins prior to experiment and may be useful in screening experimentally determined (X-ray, NMR) protein structures for possible errors.
A ram epididymal secretory protein shares common antigenic determinants with rat epididymal proteins and human seminal plasma proteins (1988)

64 kD molecular weight which runs in the prealbumin region on non-denaturing gels. The protein, synthesized by the epididymis under testosterone stimulation, binds to the plasma membrane covering the acrosome of immature testicular ram spermatozoa and is still present after ejaculation. This protein could thus be involved in sperm-egg interaction at fertilization (Fournier-Delpech et al., 1981 ; Jones, Fournier-Delpech and Willadsen, 1982; Fournier-Delpech et al., 1988).
The Catalytic Effect of Anions upon the Rate of Dissolution of Hydrous Alumina by Acids (1938)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Catalytic Effect of Anions upon the Rate of Dissolution of Hydrous Alumina by AcidsJohn P. Clay and Arthur W. ThomasCite this: J. Am. Chem. Soc. 1938, 60, 10, 2384–2390Publication Date (Print):October 1, 1938Publication History Published online1 May 2002Published inissue 1 October 1938https://pubs.acs.org/doi/10.1021/ja01277a027https://doi.org/10.1021/ja01277a027research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations7LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fibronectin in the tendon‐synovial complex: Quantitation In vivo and In vitro by elisa and relative mRNA levels by polymerase chain reaction and northern blot (1994)

An enzyme-linked immunosorbent assay was used to quantitate fibronectin (Fn) levels in the outer synovia (epitenon) and internal fibrous portion (endotenon) of chicken flexor tendon and sheath. Primary cell cultures from these tissues and their secretions also were assayed for Fn levels. The polymerase chain reaction (PCR) was used to determine relative steady-state levels of Fn mRNA in primary cultures of synovial and internal fibroblasts from chicken tendon, and Northern blot analysis was performed to verify relative levels of the Fn message. The epitenon contained 3.8-fold more Fn than did the endotenon, and the sheath synovium contained 21-fold more Fn than did the internal fibrous portion of sheath. Cells cultured from the epitenon produced 9.3 and 13-fold more cell-associated and secreted Fn, respectively, than did cultured endotenon fibroblasts. Sheath synovial cells produced 17 and 3.2-fold more cell-associated and secreted Fn, respectively, than did sheath internal fibroblasts. Levels of Fn mRNA, as measured by PCR and Northern blot, were 1.6 and 1.8-fold greater, respectively, in tendon synovial cells compared with tendon internal fibroblasts. The biologic reason for increased Fn in tendon synovium is not known. We theorize that Fn may stabilize tendon synovium to shear stress and may play a role in the modulation of synovial rheology in the normal tendon. In the injured tendon, Fn may be involved in the organization of collagen deposition or may act through association with growth factors to aid healing.
A Novel Carrier-Based PWM Scheme for Matrix Converters that is Easy to Implement (2006)

Since the inception of matrix converter concept, various modulation schemes have been proposed for its control. But the explanation of matrix converter operation is complex, and so is the control methodology of it. In this paper a 3-phase to 3-phase matrix converter is explained from the point of view of multi-level inverter topology, and a novel modulation scheme is proposed where the need for sector information and corresponding look-up tables is avoided
Fluorescent Nanorods and Nanospheres for Real‐Time In Vivo Probing of Nanoparticle Shape‐Dependent Tumor Penetration (2011)

Formabhängig: Bei fluoreszierenden Quantenpunkt-Nanokügelchen und -stäbchen mit identischen hydrodynamischen Größen und Oberflächeneigenschaften, aber unterschiedlichen Aspektverhältnissen zeigen bei der In-vivo-Echtzeitbildgebung von Brustkrebstumoren die Nanostäbchen eine schnellere Verteilung als Nanokügelchen vergleichbarer Plasmahalbwertszeit. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Production of Interferon α by Human Immunodeficiency Virus Type 1 in Human Plasmacytoid Dendritic Cells Is Dependent on Induction of Autophagy (2012)

These findings demonstrate that IFN-α production by pDCs exposed to infectious or noninfectious HIV-1 and ssRNA40 occurs through induction of autophagy following TLR7 signaling.
Brain-wave representation of words by superposition of a few sine waves (2000)

Data from three previous experiments were analyzed to test the hypothesis that brain waves of spoken or written words can be represented by the superposition of a few sine waves. First, we averaged the data over trials and a set of subjects, and, in one case, over experimental conditions as well. Next we applied a Fourier transform to the averaged data and selected those frequencies with high energy, in no case more than nine in number. The superpositions of these selected sine waves were taken as prototypes. The averaged unfiltered data were the test samples. The prototypes were used to classify the test samples according to a least-squares criterion of fit. The results were seven of seven correct classifications for the first experiment using only three frequencies, six of eight for the second experiment using nine frequencies, and eight of eight for the third experiment using five frequencies.
Effect of second-order magnetic anisotropy on nonlinearity of conductance in CoFeB/MgO/CoFeB magnetic tunnel junction for magnetic sensor devices (2019)

Abstract We studied the effect of second-order magnetic anisotropy on the linear conductance output of magnetic tunnel junctions (MTJs) for magnetic-field-sensor applications. Experimentally, CoFeB/MgO/CoFeB-based MTJs were fabricated, and the nonlinearity, NL was evaluated for different thicknesses, t of the CoFeB free layer from the conductance. As increasing t from 1.5 to 2.0 nm, maximum NL, NL max was found to decrease from 1.86 to 0.17% within the dynamic range, H d = 1.0 kOe. For understanding the origin of such NL behavior, a theoretical model based on the Slonczewski model was constructed, wherein the NL was demonstrated to be dependent on both the normalized second-order magnetic anisotropy field of H k2 /| H k eff | and the normalized dynamic range of H d /| H k eff |. Here, H k eff , H k2 , are the effective and second-order magnetic anisotropy field of the free layer in MTJ. Remarkably, experimental NL max plotted as a function of H k2 /| H k eff | and H d /| H k eff |, which were measured from FMR technique coincided with the predictions of our model. Based on these experiment and calculation, we conclude that H k2 is the origin of NL and strongly influences its magnitude. This finding gives us a guideline for understanding NL and pioneers a new prospective for linear-output MTJ sensors to control sensing properties by H k2 .
miRNA profiling in a case: Control study of African American women with uterine serous carcinoma (USC). (2017)

e17116 Background: USC is an aggressive subtype of endometrial cancer associated with worse outcomes in African American patients. We evaluated differences in tumor miRNA expression by race, clinical and tumor characteristics, and survival outcomes. Methods: FFPE tumor tissue from hysterectomy specimens was identified for 29 African American cases. Case matching was performed by computer-based random assignment in a 1:1 ratio with Caucasian controls based on age ( &lt; 70 vs. ≥70 years), stage (FIGO I/II vs. III/IV) and histologic subtype (pure vs. mixed). RNA was extracted from 77 specimens with sufficient tumor cellularity (54 tumors and 23 matched normal endometrium). miRNA array profiling was performed by microRNA Hi-Power Labeling (Hy3/Hy5) and hybridization to miRCURY LNA microRNA Array 7 th Gen (Exiqon, Denmark). Analysis was performed with R/Bioconductor using a moderated t-statistic with multiple testing correction. Validation was done using the TCGA dataset. Results: Clinical and treatment characteristics were similar for cases and controls, although use of adjuvant radiation was less common in African Americans (p = 0.03). With a median follow-up of 43 months, 17 patients had recurrent or progressive disease. DFS and OS rates were similar by race (both logrank p &gt; 0.5). Of 968 miRNAs analyzed, 649 were differentially expressed in normal endometrium vs. tumor. When compared by race, histologic subtype, stage or presence of LVI, no differentially expressed miRNAs were identified. In patients with disease recurrence at 3 years, miR-223 was significantly upregulated (fold change 1.5; p = 0.002). In validation using a TCGA dataset of 131 patients with mixed (n = 22) or pure serous (n = 109) histology, increased miR-223 expression ( &gt; median) was associated with worse overall survival (HR 2.47; 95%CI 0.9-6.6). After adjustment for patient age and BMI, upregulation of miR-223 was a significant risk factor for death (adjusted HR 2.94; 95%CI 1.01-8.52). Conclusions: Upregulation of miR-223 was associated with disease recurrence in a cohort of women with uterine serous carcinoma and validated by TCGA data. miRNA profiling did not identify biological differences between African American and Caucasian patients.
Mutation and Expression of the p51 Gene in Human Lung Cancer (1999)

A newly identified gene, p51, is a functional and structural homologue of the p53 gene and thus a Candidate tumor suppressor gene. To elucidate the role of the p51 gene in lung carcinogenesis, we determined the sequences of exon-intron boundaries and the 5'- and 3'-flanking regions of all the 15 coding exons and performed a mutation analysis, as well as detailed analysis for gene expression. A frameshift mutation was detected in 1 of 44 lung cancer cell lines, whereas no mutation was detected in 45 primary lung cancers. Thus, p51 mutation occurs only in a small subset of lung cancer. Expression of the p51 gene was detected in 23 of 43 cell lines by Northern blot analysis and 34 of 44 by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Thus, p51 expression is low or absent in a subset of lung cancer. The deltaN isotype of p51 transcripts was dominantly expressed in several cell lines, particularly in cell lines with high levels of p51 expression. Because the deltaN isotype encodes a protein that transdominantly suppresses the transactivation function of the TA type of p51, it is possible that p51 protein is not functionally active, even in lung cancer cells with p51 mRNA expression, due to expression of dominant-negative p51 protein. These results suggested that the p51 gene is inactive in a considerable proportion of lung cancers. RT-PCR analysis also revealed the presence of a novel type of mRNA transcript, p51delta, which lacks exons 12 and 13 by alternative splicing. The delta isotype was expressed in 18 of 44 lung cancer cell lines and in diverse normal tissues. Further analysis on p51 expression in cancerous as well as noncancerous cells will provide us with valuable information for the understanding of multiple functions of the p53 family proteins in human carcinogenesis.
Vitamin D3 and Vitamin D3 Analogues as an Adjunct to Cancer Chemotherapy and Radiotherapy (2002)

The development of drugs that are highly selective and yet produce minimal toxicity to host tissue remains one of the most difficult challenges in cancer therapeutics. Since the majority of malignancies are treated with drugs in combination rather than single agents, one practical approach to circumvent this problem is to develop new therapeutic agents that will potentiate the effectiveness of current clinical protocols. This strategy would accelerate the acceptance of new drugs as adjunct therapies since these agents could be used at concentrations well below their maximal tolerated doses. Tumor cells derived from a variety of different sources have been shown to express the Vitamin D(3)receptor and to be susceptible to growth arrest and/or cell death in response to Vitamin D(3)and its analogues. The hypercalcemia that generally accompanies the utilization of pharmacological concentrations of Vitamin D(3) has been ameliorated in part through the development of Vitamin D(3) analogues. Studies in cell culture and in animal model systems as well as clinical trials have established the potential utility of Vitamin D(3) and Vitamin D(3) analogues as agents which can enhance the antiproliferative and/or cytotoxic effects of conventional chemotherapeutic drugs as well as ionizing radiation. Consequently, Vitamin D(3) and Vitamin D(3) analogues, utilized at concentrations which produce limited hypercalcemia, are likely to prove effective as adjuncts to conventional chemotherapy and radiotherapy.
Relaxin gene expression in human reproductive tissues by in situ hybridization. (1995)

The expression of the two human relaxin genes termed H1 and H2 in human reproductive tissues ranges from high to very low copy number depending upon the tissue and reproductive state. The aim of this study was to use two approaches to identify total relaxin transcripts (HI and H2) at the cellular level by using a human relaxin H2 riboprobe and a series of six 48-mer synthetic oligoprobes. The results obtained with both methods were similar in all tissues studied; however, a lower background was achieved with the riboprobe. This was especially noticeable after long exposure times, and a better resolution was generally achieved without clustering of the signals. Treatment of the tissues with proteinase-K failed to increase the sensitivity in any tissue with either probe. The relative levels of expression of the total relaxin gene transcripts was estimated from the different exposure times needed to obtain a good hybridization signal. Thus, the order of expression was: corpus luteum of pregnancy > corpus luteum of the cycle > placenta and prostate > decidua parietalis. The results agree well with immunolocalization of the peptide hormone previously performed with both heterologous and homologous relaxin antibodies; the exception was the lack of hybridization signal over the cells of the chorionic cytotrophoblast of the chorion laeve. This suggests that the levels of relaxin gene expression was below the level of detectability with the in situ hybridization technique or that these cells sequester, but do not synthesize, relaxin. Expression in the term placenta varied greatly from tissue to tissue and within any one tissue. A similar variability has been noted for relaxin in this tissue by immunocytochemistry. Methodology for the detection of total relaxin transcripts at the cellular level when expressed in a wide range of copy number will allow the developmental regulation of relaxin gene expression in reproductive and nonreproductive tissues to be visualized.
Carbanionic character of decafluorobenzhydryl bromide. Behaviour towards nucleophiles (1972)

Decafluorobenzhydryl bromide (1) reacts with nucleophiles to give 1,1,2,2-tetrakis(pentafluorophenyl)-ethane (2) as the predominant product; there is no evidence of products derived from initial nucleophilic displacement on the carbon of (1).
Posterior Transvertebral Osteotomy for Adult Thoracolumbar Kyphosis (1994)

Study Design A retrospective case study was performed on the single-stage posterior transvertebral closing-wedge osteotomy for treatment of adult thoracolumbar kyphosis. Summary of Background Data Forty-one consecutive cases in 38 patients available for follow-up, averaging 33 months (range 4–87 months), are included. All patients had severe pain and/or deformity; 51% of cases had previous fractures, and 49% had postlaminectomy failed back syndromes with kyphosis. A preoperative neurologic deficit was present in 34% of the cases including two with cauda equina syndrome. Methods Patient examination and interviews, subjective questionnaire, chart reviews, and radiographic measurements were performed independently. Complications, risks, benefits, results, and biomechanical considerations were evaluated and discussed as compared with other techniques. Results All cases had solid union at follow-up; 93% maintained correction averaging 35° with three requiring revision for failure. Postoperatively, 19.5% of the cases had new neurologic deficits with five (12.2%) temporary or minor and three (7.3%) major, including one with unimproved paraplegia at follow-up. Eight of the 14 preoperative neurologic deficit cases improved postoperatively; 26 additional surgeries were performed on 18 patients most commonly for pain (x11) and additional trauma (x4). The subjective questionnaire results indicated significant patient satisfaction, with 76% stating they would repeat the surgery and 90% recommending it to another. Conclusion This technically demanding high-risk procedure provides an effective and mechanically superior correction for acute angle thoracolumbar kyphosis in selected adult patients, with high subjective satisfaction.
Demodulation of aggregated RF Signal in three Frequencies bands with a Unique Rx Chain (2013)

Among the concerns of 4th generation wireless communication networks, there is the lack of desired bandwidth in a continuous manner in the frequency spectrum. The recommended solution is to transport the information on a Radio Frequency (RF) signal constituted of discontinuous frequency bands. Nowadays, the receiver architecture is generally constituted of n chains of receiver (Rx), n being the number of aggregated frequency bands. This paper demonstrates theoretically and practically that the demodulation of a RF signal having three discontinuous frequency bands can be made by a single Rx chain. The principle consists in down converting aggregated RF signal by mixing with a local oscillator (LO) signal constituted by n Continuous Wave (CW) signals. Using this technique the transposed signals occupy a narrow frequency band.
Synthesis of silica xerogels with high surface area using acetic acid as catalyst (2007)

The influence of acetic acid on the pore structure and surface area of silica prepared by the sol-gel method was investigated. Experimental conditions of synthesis, such as gelation temperature and solvents, were also studied. N2 adsorption isotherms of the samples were type 1, typical of microporous materials, explaining the high surface area values (BET) observed. The simultaneous addition of acetic and hydrochloric acids as catalysts and of acetone as solvent, together with the use of a gelation temperature of 20 ºC, made it possible to prepare amorphous silica materials with surface area values up to 850 m² g-1. The high surface area value of these samples could be explained by the microporosity and the nanometric size of the particles.
The Enhanced Immunogenicity of Horse Cytochrome C by Light Dinitrophenylation (1974)

Monomeric horse cytochrome C is a weak erratic immunogen in rabbits which can be converted to a consistent immunogen by light dinitrophenylation. Antibody responses to the dinitrophenyl group are more vigorous than to the cytochrome C but the responses are parallel, the strongest responses to both the carrier and the hapten occurring in the same animals.
ChemInform Abstract: SYNTHESES OF 11‐HYDROXY AND 11‐HYDROXY‐11‐METHYL‐14‐METHOXY‐14‐AZADISPIRO(5.1.5.2)PENTADEC‐9‐ENE‐7,15‐DIONES (1985)

Abstract Aus den Spirocyclen (I) Qntstehen bei der Oxidation mit Selendioxid die Oxidationsprodukte (II)‐(V).
MUC5B, telomere length and longitudinal quantitative interstitial lung changes: the MESA Lung Study (2022)

Longitudinal increases in HAAs were associated with the <i>MUC5B</i> risk allele and a higher risk of death and ILD.
18F-FDG PET-CT versus MRI for detection of skeletal metastasis in Ewing sarcoma (2019)

Although no definite conclusions can be drawn from this small retrospective study, it shows that caution is needed when using <sup>18</sup>F-FDG PET-CT for diagnosing skeletal metastases in Ewing sarcoma. Poor contrast between metastases and active hematopoietic bone marrow, chemotherapeutic treatment, and/or small size significantly decrease the diagnostic yield of <sup>18</sup>F-FDG PET-CT, but not of MRI.
Structural Consequences of Target Epitope-directed Functional Alteration of an Antibody (2003)

Decreased affinity of an antibody for a mutated epitope in an antigen can be enhanced and reversed by mutations in certain antibody residues. Here we describe the crystal structures of (a) the complex between a naturally mutated proteinaceous antigen and an antibody that was mutated and selected in vitro, and (b) the complex between the normal antigen and the mutated antibody. The mutated and selected antibody recognizes essentially the same epitope as in the wild-type antibody, indicating successful target site-directed functional alteration of the antibody. In comparing the structure of the mutated antigen-mutant antibody complex with the previously established structure of the wild-type antigen-wild-type antibody complex, we found that the enhanced affinity of the mutated antibody for the mutant antigen originated not from improvements in local complementarity around the mutated sites but from subtle and critical structural changes in nonmutated sites, including an increase in variable domain interactions. Our findings indicate that only a few mutations in the antigen-binding region of an antibody can lead to some structural changes in its paratopes, emphasizing the critical roles of the plasticity of loops in the complementarity-determining region and also the importance of the plasticity of the interaction between the variable regions of immunoglobulin heavy and light chains in determining the specificity of an antibody.