gebhart/patrepeval huggingface dataset:
CaspR: a web server for automated molecular replacement using homology modelling (2004)

Molecular replacement (MR) is the method of choice for X-ray crystallography structure determination when structural homologues are available in the Protein Data Bank (PDB). Although the success rate of MR decreases sharply when the sequence similarity between template and target proteins drops below 35% identical residues, it has been found that screening for MR solutions with a large number of different homology models may still produce a suitable solution where the original template failed. Here we present the web tool CaspR, implementing such a strategy in an automated manner. On input of experimental diffraction data, of the corresponding target sequence and of one or several potential templates, CaspR executes an optimized molecular replacement procedure using a combination of well-established stand-alone software tools. The protocol of model building and screening begins with the generation of multiple structure-sequence alignments produced with T-COFFEE, followed by homology model building using MODELLER, molecular replacement with AMoRe and model refinement based on CNS. As a result, CaspR provides a progress report in the form of hierarchically organized summary sheets that describe the different stages of the computation with an increasing level of detail. For the 10 highest-scoring potential solutions, pre-refined structures are made available for download in PDB format. Results already obtained with CaspR and reported on the web server suggest that such a strategy significantly increases the fraction of protein structures which may be solved by MR. Moreover, even in situations where standard MR yields a solution, pre-refined homology models produced by CaspR significantly reduce the time-consuming refinement process. We expect this automated procedure to have a significant impact on the throughput of large-scale structural genomics projects. CaspR is freely available at http://igs-server.cnrs-mrs.fr/Caspr/.
The I-Abm12 mutation, which confers resistance to experimental myasthenia gravis, drastically affects the epitope repertoire of murine CD4+ cells sensitized to nicotinic acetylcholine receptor (1991)

Susceptibility to experimental autoimmune myasthenia gravis (EAMG), which is induced in mice by injection of purified Torpedo nicotinic acetylcholine receptor (TAChR), is influenced by the I-A locus products, which restrict presentation of AChR Th epitopes. The bm12 mutation of the I-Ab molecule in the C57BL/6 strain, which is highly susceptible to EAMG, yields the EAMG resistant mutant B6.C-H-2bm12 (bm12). We investigated here the consequences of the bm 12 mutation on the CD4+ response to the TAChR alpha subunit. Upon immunization with TAChR, CD4+ cells became sensitized to TAChR and anti-AChR antibodies were produced in both bm12 and C57BL/6 strains. Overlapping synthetic peptides, corresponding to the complete sequence of TAChR alpha subunit, were used to identify Th epitopes. CD4+ cells from C57BL/6 mice recognized peptides T alpha 150-169, T alpha 181-200, and T alpha 360-378. CD4+ cells from bm12 mice did not respond to any synthetic sequence. Upon injection of the three C57BL/6 Th epitope peptides, either individually or as a pool, CD4+ cells from C57BL/6 mice recognized each peptide and TAChR. Therefore they recognized epitopes similar or identical to those originated from TAChR processing. CD4+ cells from bm12 mice injected with the same peptides responded to T alpha 360-378 strongly, to a lesser extent to T alpha 181-200, never to peptide T alpha 150-169. Only CD4+ cells sensitized against the T epitope peptide T alpha 181-200 responded to TAChR. We tested if lack of response to T alpha 150-169, and the low response to T alpha 181-200, was due to inability of the I-Abm12 molecule to present the T epitope peptides. bm12 and C57BL/6 APC were used to present the T epitope peptides to specifically sensitized CD4+ cells from C57BL/6 mice. All T epitope peptides were presented by bm12 APC, although T alpha 150-169 was presented less efficiently than by C57BL/6 APC. Resistance to EAMG induced by the bm12 mutation may be due to the change in the epitope repertoire of AChR-specific Th cells, and lack of recognition of otherwise immunodominant Th epitopes. For at least one epitope this might be due to absence of potentially reactive, specific CD4+ clones.
Further thermal characterization of an aspartate aminotransferase from a halophilic organism (1994)

Aspartate aminotransferase (AspAT, EC 2.6.1.1) from the halophilic archaebacterium Haloferax mediterranei was purified [Muriana, Alvarez-Ossorio and Relimpio (1991) Biochem. J. 278, 149-154] and further characterization of the effects of temperature on the activity and stability of the halophilic AspAT were carried out. The halophilic transaminase is most active at 65 degrees C and stable at high temperatures, under physiological or nearly physiological conditions (3.5 M KCl, pH 7.8). Thermal inactivation (60-85 degrees C) of the halophilic AspAT followed first-order kinetics, 2-oxoglutarate causing a shift of the thermal inactivation curves to higher temperatures. The salt concentration affected the thermal stability of the halophilic transaminase at 60 degrees C, suggesting that disruption of hydrophobic interactions may play an important role in the decreased thermal stability of the enzyme.
Myc protein is stabilized by suppression of a novel E3 ligase complex in cancer cells (2010)

Rapid Myc protein turnover is critical for maintaining basal levels of Myc activity in normal cells and a prompt response to changing growth signals. We characterize a new Myc-interacting factor, TRPC4AP (transient receptor potential cation channel, subfamily C, member 4-associated protein)/TRUSS (tumor necrosis factor receptor-associated ubiquitous scaffolding and signaling protein), which is the receptor for a DDB1 (damage-specific DNA-binding protein 1)-CUL4 (Cullin 4) E3 ligase complex for selective Myc degradation through the proteasome. TRPC4AP/TRUSS binds specifically to the Myc C terminus and promotes its ubiquitination and destruction through the recognition of evolutionarily conserved domains in the Myc N terminus. TRPC4AP/TRUSS suppresses Myc-mediated transactivation and transformation in a dose-dependent manner. Finally, we found that TRPC4AP/TRUSS expression is strongly down-regulated in most cancer cell lines, leading to Myc protein stabilization. These studies identify a novel pathway targeting Myc degradation that is suppressed in cancer cells.
The isolation, purification, and preliminary crystallographic characterization of udp‐galactose‐4‐epimerase from Escherichia coli (1991)

Uridine diphosphogalactose-4-epimerase from E. coli has been crystallized in a form suitable for a high-resolution X-ray crystallographic structural analysis. The enzyme complexed with a substrate analogue, uridine diphosphobenzene (UDP-benzene), crystallizes readily using polyethylene glycol 8000 as the precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions, a = 76.3 A, b = 83.1 A, and c = 132.1 A. Based on still setting photographs, the crystals diffract to a nominal resolution of 2.3 A and are stable in the X-ray beam. The enzyme used in these experiments was produced by a new expression system and a modified purification scheme.
The Mammalian Circadian Timing System: Synchronization of Peripheral Clocks (2011)

Mammalian physiology has to adapt to daily alternating periods during which animals either forage and feed or sleep and fast. The adaptation of physiology to these oscillations is controlled by a circadian timekeeping system, in which a master pacemaker in the suprachiasmatic nucleus (SCN) synchronizes slave clocks in peripheral organs. Because the temporal coordination of metabolism is a major purpose of clocks in many tissues, it is important that metabolic and circadian cycles are tightly coordinated. Recent studies have revealed a multitude of signaling components that possibly link metabolism to circadian gene expression. Owing to this redundancy, the implication of any single signaling pathway in the synchronization of peripheral oscillators cannot be assessed by determining the steady-state phase, but instead requires the monitoring of phase-shifting kinetics at a high temporal resolution.
Identity and Nostalgia among the Campbellites (2006)

Cook, James Maverick (2006) "Identity and Nostalgia among the Campbellites,"Restoration Quarterly: Vol. 48 : No. 3. This repository hosts selected Restoration Quarterly articles in downloadable PDF format. For the benefit of users who would like to browse the contents of RQ, we have included all issue covers even when full-text articles from that issue are unavailable. All Restoration Quarterly articles are available in full text in the ATLA Religion Database, available through most university and theological libraries or through your local library’s inter-library loan service.
Integration of acoustic and visual speech signals using neural networks (1989)

Results from a series of experiments that use neural networks to process the visual speech signals of a male talker are presented. In these preliminary experiments, the results are limited to static images of vowels. It is demonstrated that these networks are able to extract speech information from the visual images and that this information can be used to improve automatic vowel recognition. The structure of speech and its corresponding acoustic and visual signals are reviewed. The specific data that was used in the experiments along with the network architectures and algorithms are described. The results of integrating the visual and auditory signals for vowel recognition in the presence of acoustic noise are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The synthesis of micrometer‐ and submicrometer‐size spheres of ordered mesoporous oxide MCM‐41 (1997)

Spherical particles of the mesoporous material MCM‐41 have been synthesized and are reported for the first time. The results of characterization of the samples by X‐ray diffraction, scanning electron microscopy, and nitrogen sorption at 77 K (which provides information about the pore system) is described. It is shown that all the properties of the spherical MCM‐41 particles are essentially the same as those of the MCM‐41 materials synthesized by well‐established methods. Finally, possibilities for future research are outlined.
Proteomics uncovers extreme heterogeneity in the Staphylococcus aureus exoproteome due to genomic plasticity and variant gene regulation (2010)

Sequencing of at least 13 Staphylococcus aureus isolates has shown that genomic plasticity impacts significantly on the repertoire of virulence factors. However, genome sequencing does not reveal which genes are expressed by individual isolates. Here, we have therefore performed a comprehensive survey of the composition and variability of the S. aureus exoproteome. This involved multilocus sequence typing, virulence gene, and prophage profiling by multiplex PCR, and proteomic analyses of secreted proteins using 2-DE. Dissection of the exoproteomes of 25 clinical isolates revealed that only seven out of 63 identified secreted proteins were produced by all isolates, indicating a remarkably high exoproteome heterogeneity within one bacterial species. Most interesting, the observed variations were caused not only by genome plasticity, but also by an unprecedented variation in secretory protein production due to differences in transcriptional and post-transcriptional regulation. Our data imply that genomic studies on virulence gene conservation patterns need to be complemented by analyses of the extracellular protein pattern to assess the full virulence potential of bacterial pathogens like S. aureus. Importantly, the extensive variability of secreted virulence factors in S. aureus also suggests that development of protective vaccines against this pathogen requires a carefully selected combination of invariably produced antigens.
Instant architecture (2003)

This paper presents a new method for the automatic modeling of architecture. Building designs are derived using split grammars, a new type of parametric set grammar based on the concept of shape. The paper also introduces an attribute matching system and a separate control grammar, which offer the flexibility required to model buildings using a large variety of different styles and design ideas. Through the adaptive nature of the design grammar used, the created building designs can either be generic or adhere closely to a specified goal, depending on the amount of data available.
Monoclonal antibodies specific for carcinoembryonic antigen and produced by two hybrid cell lines. (1980)

Spleen cells from mice immunized with purified carcinoembryonic antigen (CEA), an important tumor marker of human carcinomas, were fused with the mouse myeloma cell line P3-NSI/1-Ag4. Out of the 400 hybrids obtained, 2 secreted antibodies reacting specifically with two different antigenic determinants present on CEA molecules. They were cloned and established as permanent hybridoma cell lines. These antibodies, which have relatively high-affinities and can be produced in unlimited amounts, will be useful both for the immunochemical characterization of CEA and as a standard reagent for the identification of this antigen in human tissues and body fluids.
Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides. (1995)

The challenge of the Human Genome Project is to increase the rate of DNA sequence acquisition by two orders of magnitude to complete sequencing of the human genome by the year 2000. The present work describes a rapid detection method using a two-dimensional optical wave guide that allows measurement of real-time binding or melting of a light-scattering label on a DNA array. A particulate label on the target DNA acts as a light-scattering source when illuminated by the evanescent wave of the wave guide and only the label bound to the surface generates a signal. Imaging/visual examination of the scattered light permits interrogation of the entire array simultaneously. Hybridization specificity is equivalent to that obtained with a conventional system using autoradiography. Wave guide melting curves are consistent with those obtained in the liquid phase and single-base discrimination is facile. Dilution experiments showed an apparent lower limit of detection at 0.4 nM oligonucleotide. This performance is comparable to the best currently known fluorescence-based systems. In addition, wave guide detection allows manipulation of hybridization stringency during detection and thereby reduces DNA chip complexity. It is anticipated that this methodology will provide a powerful tool for diagnostic applications that require rapid cost-effective detection of variations from known sequences.
Encoder Assisted Frame Loss Concealment for MPEG-AAC Decoder (2006)

This paper proposes an efficient method for frame loss concealment within the advanced audio coding (AAC) decoder, which can effectively mitigate the adverse impact of transmission errors on the reconstruction quality. The lost frame information is estimated in the modified discrete cosine transform (MDCT) domain in terms of magnitude and sign of the coefficients. A computationally efficient approach that is capable of providing accurate estimation is employed for the magnitude estimate. Enhanced sign estimation is developed and implemented, which exploits extra information from encoder. Extensive subjective quality evaluation demonstrates that the proposed method achieves substantial quality improvement with minimal encoder assistance.
Visualization of human brain structure-function relationships (2003)

A procedure is described for combining and visualizing complementary structural and functional information from magnetic resonance imaging (MRI) and positron emission tomography (PET). MR and PET images of the human brain were obtained and correlated to form three-dimensional volumes of image data. Using a volumetric imaging technique, a procedure was developed to texture-map brain glucose metabolism onto brain anatomy. Sequences of three-dimensional views were produced and displayed dynamically to indicate the three-dimensional relationship between brain structure and brain function.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Distinct downstream signaling mechanism between erythropoietin receptor and interleukin-2 receptor. (1992)

Erythropoietin receptor (EPOR) and interleukin-2 receptor beta chain (IL-2R beta) belong to the same cytokine receptor superfamily and have highly conserved sequences in their intracellular signaling domain. However, common downstream signaling pathways of these receptors have not been demonstrated. In the present study, we introduced and expressed the murine EPOR in murine IL-2-, IL-3- and IL-5-dependent cell lines and analyzed their growth response to EPO. We found that the expression of EPOR induced EPO dependence in IL-3-dependent BAF-B03 and IL-5-dependent Y16 cells but not in IL-2-dependent CTLL-2 cells, although the EPOR-expressing CTLL-2 cell lines could bind and internalize EPO as efficiently as the BAF-B03-derived cell lines. Additional expression of AIC2B, a common signal transducer for IL-3R, IL-5R and GM-CSFR, made no difference to the EPO responsiveness of the EPOR-expressing CTLL-2 cell lines. These results suggest that the cellular components required for the transduction of EPOR signal and IL-2R signal are at least partially different, and this difference cannot be explained solely by the absence of AIC2B.
Cancer immunotherapy: a brief review of the history, possibilities, and challenges ahead (2017)

The Journal of Cancer Metastasis and Treatment is an open access journal focused on cancer metastasis and treatment, including the occurrence, development, progression, metastasis, and treatment of oncologic disease. It covers basic, translational and clinical research related to cancer cell biology, genomics, precision medicine, oncology internal medicine, radiotherapy and radiology, obstetrics and gynecology, pediatrics, surgery, hematology, neurooncology, etc.
Telomere length in leukocyte subpopulations of patients with aplastic anemia (2001)

In most human cells, the average length of telomere repeats at the ends of chromosomes provides indirect information about their mitotic history. To study the turnover of stem cells in patients with bone marrow failure syndromes, the telomere length in peripheral blood granulocytes and lymphocytes from patients with aplastic anemia (AA, n = 56) and hemolytic paroxysmal nocturnal hemoglobinuria (n = 6) was analyzed relative to age-matched controls by means of fluorescence in situ hybridization and flow cytometry. The telomere lengths in granulocytes from patients with AA were found to be significantly shorter than those in age-adjusted controls (P =.001). However, surprisingly, telomere length in granulocytes from AA patients who had recovered after immunosuppressive therapy did not differ significantly from controls, whereas untreated patients and nonresponders with persistent severe pancytopenia showed marked and significant telomere shortening. These results support extensive proliferation of hematopoietic stem cells in subgroups of AA patients. Because normal individuals show significant variation in telomere length, individual measurements in blood cells from AA patients may be of limited value. Whether sequential telomere length measurements can be used as a prognostic tool in this group of disorders remains to be clarified. (Blood. 2001;97:895-900)
ChemInform Abstract: STUDIES ON ORGANOPHOSPHORUS COMPOUNDS. XXI. THE DIMER OF P‐METHOXYPHENYLTHIONOPHOSPHINE SULFIDE AS THIATION REAGENT. A NEW ROUTE TO THIOCARBOXAMIDES (1978)

Abstract Die Carboxamide (I) lassen sich mit dem Reagenz (II) in Hexamethylphosphorsäuretriamid leicht zu den Thiocarboxamiden (III) sulfurieren.
A large-area and contamination-free graphene transistor for liquid-gated sensing applications (2013)

We present a simple, low-cost, large area, and contamination-free monolayer graphene field-effect transistor for liquid-gated sensing applications. The graphene surface does not require any photoresist including the commonly used polymethylmethacrylate, thus avoiding possible contamination and mobility degradation. We also examine the effects of different etching solutions and concentrations on the Dirac point of graphene. With optimal device fabrication recipe, we demonstrate the device's capability to sense different KCl concentrations and pH values under liquid gating configuration. Additionally, using polydimethylsiloxane as substrates holds an advantage of enabling simple integration between microfluidic systems and graphene for chemical and biological sensor applications.
Oncolytic Viruses in Cancer Treatment (2016)

Oncolytic viruses are an active area of clinical research. The ability of these agents to harness antitumor immunity appears to be key for their success. Combinatorial studies with immune checkpoint blockade have started and the results are awaited with great interest.
MCL-1 and BCL-xL-dependent resistance to the BCL-2 inhibitor ABT-199 can be overcome by preventing PI3K/AKT/mTOR activation in lymphoid malignancies (2015)

Overexpression of anti-apoptotic BCL-2 family members is a hallmark of many lymphoid malignancies, including chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL) that can be targeted with small molecule inhibitors. ABT-199 is a rationally designed BCL-2 homology (BH)-3 mimetic that specifically binds to BCL-2, but not to MCL-1 and BCL-xL. Although the thrombocytopenia that occurs with navitoclax treatment has not been a problem with ABT-199, clinical trials in CLL could benefit by lowering the ABT-199 concentration through targeting other survival pathways. In this study, we investigated the mechanisms of resistance that develops to ABT-199 therapy by generating ABT-199-resistant (ABT199-R) cell lines via chronic exposure of NHL cell lines to ABT-199. Acquired resistance resulted in substantial AKT activation and upregulation of MCL-1 and BCL-xL levels that sequestered BIM. ABT199-R cells exhibited increased MCL-1 stability and failed to activate BAX in response to ABT-199. The ABT-199 acquired and inherent resistant cells were sensitized to treatment with ABT-199 by inhibitors of the PI3K, AKT, and mTOR pathways, NVP-BEZ235 and GS-1101. NVP-BEZ235, a dual inhibitor of p-AKT and mTOR, reduced MCL-1 levels causing BIM release from MCL-1 and BCL-xL, thus leading to cell death by BAX activation. The PI3Kδ inhibitor GS-1101 (idelalisib) downregulated MCL-1 and sensitized ABT199-R cells through AKT-mediated BAX activation. A genetic approach, through siRNA-mediated down-regulation of AKT, MCL-1, and BCL-xL, significantly decreased cell survival, demonstrating the importance of these cell survival factors for ABT-199 resistance. Our findings suggest a novel mechanism that modulates the expression and activity of pro-survival proteins to confer treatment resistance that could be exploited by a rational combination therapeutic regimen that could be effective for treating lymphoid malignancies.