gebhart/patrepeval huggingface dataset:
ATF4 Degradation Relies on a Phosphorylation-Dependent Interaction with the SCFβTrCPUbiquitin Ligase (2001)

The ubiquitin-proteasome pathway regulates gene expression through protein degradation. Here we show that the F-box protein betaTrCP, the receptor component of the SCF E3 ubiquitin ligase responsible for IkappaBalpha and beta-catenin degradation, is colocalized in the nucleus with ATF4, a member of the ATF-CREB bZIP family of transcription factors, and controls its stability. Association between the two proteins depends on ATF4 phosphorylation and on ATF4 serine residue 219 present in the context of DSGXXXS, which is similar but not identical to the motif found in other substrates of betaTrCP. ATF4 ubiquitination in HeLa cells is enhanced in the presence of betaTrCP. The F-box-deleted betaTrCP protein behaves as a negative transdominant mutant that inhibits ATF4 ubiquitination and degradation and, subsequently, enhances its activity in cyclic AMP-mediated transcription. ATF4 represents a novel substrate for the SCF(betaTrCP) complex, which is the first mammalian E3 ubiquitin ligase identified so far for the control of the degradation of a bZIP transcription factor.
DNA attachment to optically trapped beads in microstructures monitored by bead displacement (1998)

Reversibly binding silicone cartridges have been developed to form reaction containers in which ‘single molecule chemistry’ can be performed. We use an optical trap to drive 1μm streptavidin-coated beads into a region containing biotinylated DNA until binding of a strand of DNA occurs. A quadrant detector is used in reflective mode to track the lateral position of trapped beads. Relative motion between the bead and the solution causes a viscous drag force which is increased when a single strand of DNA is attached to the bead; DNA-bead attachment is done in minutes with less than a femtomole of DNA. The method allows the study of single molecule digestion.
Treatment of various movement disorders with botulinum A toxin injection: an experience of 900 patients. (1995)

A prospective open study of botulinum toxin A treatment for patients with various movement disorders at Siriraj Hospital, Mahidol University was analysed to evaluate its efficacy. The grand total of 900 patients comprised of a) 592 patients (65.78 per cent) with hemifacial spasm; b) 92 patients (10.22 per cent) with occupational cramp; c) 79 patients (8.78 per cent) with blepharospasm and Meige syndrome; d) 72 patients (8.00 per cent) with spasmodic torticollis; e) 19 patients (2.11 per cent) with hemidystonia and generalised dystonia; f) 11 patients (1.22 per cent) with spasmodic dysphonia; g) 10 patients (1.11 per cent) with spastic hemiparesis; and h) 25 patients (2.78 per cent) with miscellaneous group (i.e. tics, Gilles de la Tourette, facial myokimia, benign fasciculation, etc.). The results of treatment for hemifacial spasm were classified as excellent in 486 patients (82.09 per cent), moderate improvement in 60 patients (10.14 per cent), mild improvement in 39 patients (6.59 per cent) and no improvement or worse in 7 patients (1.18 per cent). There were complications of mild transient facial weakness in 50 patients (8.45 per cent) and mild ptosis in 12 patients (2.02 per cent). The effect of botulinum toxin treatment lasted 3-6 months. In occupational cramp and spasmodic torticollis the good response rate was around two-thirds of all patients, whereas, blephalospasm, spasmodic dysphonia, spastic hemiparesis and tics responsed in 79-88 per cent of the patients. Botulinum toxin A injection is thus a simple, safe, and effective out-patient treatment for patients with various kinds of movement disorders but it is a costly therapy.
Characterization of the Structure and Function of a New Mitogen-activated Protein Kinase (p38β) (1996)

Mitogen-activated protein (MAP) kinase cascades represent one of the major signal systems used by eukaryotic cells to transduce extracellular signals into cellular responses. Four MAP kinase subgroups have been identified in humans: ERK, JNK (SAPK), ERK5 (BMK), and p38. Here we characterize a new MAP kinase, p38beta. p38beta is a 372-amino acid protein most closely related to p38. It contains a TGY dual phosphorylation site, which is required for its kinase activity. Like p38, p38beta is activated by proinflammatory cytokines and environmental stress. A comparison of events associated with the activation of p38beta and p38 revealed differences, most notably in the preferred activation of p38beta by MAP kinase kinase 6 (MKK6), whereas p38 was activated nearly equally by MKK3, MKK4, and MKK6. Moreover, in vitro and in vivo experiments showed a strong substrate preference by p38beta for activating transcription factor 2 (ATF2). Enhancement of ATF2-dependent gene expression by p38beta was approximately20-fold greater than that of p38 and other MAP kinases tested. The data reported here suggest that while closely related, p38beta and p38 may be regulated by differing mechanisms and may exert their actions on separate downstream targets.
Design of Recombinant Antibody Microarrays for Serum Protein Profiling:  Targeting of Complement Proteins (2007)

Antibody-based microarrays is a novel technology with great promise for high-throughput proteomics. The process of designing high-performing arrays has, however, turned out to be challenging. Here, we have designed the next generation of a human recombinant scFv antibody microarray platform for protein expression profiling of nonfractionated biotinylated human plasma and serum proteomes. The setup, based on black polymer Maxisorb slides interfaced with a fluorescent-based read-out system, was found to provide specific, sensitive (subpicomolar (pM) range) and reproducible means for protein profiling. Further, a chip-to-chip normalization protocol critical for comparing data generated on different chips was devised. Finally, the microarray data were found to correlate well with clinical laboratory data obtained using conventional methods, as demonstrated for a set of medium abundant (micromolar (microM) to nanomolar (nM) range) protein analytes in serum and plasma samples derived from healthy and complement-deficient individuals.
3-Amino-5-phenoxythiophenes:  Syntheses and Structure−Function Studies of a Novel Class of Inhibitors of Cellularl-Triiodothyronine Uptake (1999)

A series of substituted 3-amino-5-phenoxythiophenes was synthesized starting from malodinitrile and carbon disulfide. The resulting dicyanoketenedithiolate reacts via Thorpe-Dieckmann cyclization with halogen methanes bearing electron-withdrawing groups to give thiophene-2-thiolates, which can be transformed into 3-amino-5-(methylsulfonyl)thiophene-4-carbonitriles. Replacement of the methylsulfonyl groups by substituted phenolates provides the substituted 3-amino-5-phenoxythiophenes. Some of the derivatives show a considerable inhibitory potency for the L-T3 uptake in inhibition studies on human HepG2 hepatoma cells with maximum values of about 60% at a dose of 10(-5) M for the most potent 2-benzoyl derivatives. The structure of the phenoxythiophenes fits well into a general concept derived for other classes of L-T3 uptake inhibitors, which postulates an angular and perpendicular orientation of the ring systems in these compounds as a prerequisite for an inhibitory potency. Docking studies for the phenoxythiophenes with transthyretin as a receptor model show their preferred attack at the L-T4/L-T3 binding channel.
Ductile Thin Foils of Ni3Al (2001)

Ni3Al thin foils with 315 to 357 μm thickness were successfully fabricated by cold rolling. X-ray pole figures showed the formation of {110} rolling textures with various rolling directions in the foils cold rolled over 83% reduction. The deformation microstructure consists of fine slip traces and coarse and wavy shear bands. Banded deformation structure was observed in some foils. In the foils cold rolled to 83% reduction, the Vickers hardness number reached over 600 and the ultimate tensile strength over 1.7 GPa, irrespective of rolling texture and deformation microstructure. The cold rolled foils showed no tensile elongation, but it was possible to bend the foils. The foils recrystallized at temperatures over 1273 K had some tensile ductility (3.0 to 14.6%), though the polycrystalline Ni3Al is known to be brittle due to severe grain boundary fracture. Electron backscatter diffraction measurements revealed that the large amount of total grain boundary area consists of low angle (LAB) and ∑3 coincidence lattice boundaries. This large fraction is probably a chief cause of the observed ductility.
Overview of results of peptide receptor radionuclide therapy with 3 radiolabeled somatostatin analogs. (2005)

A new treatment modality for inoperable or metastasized gastroenteropancreatic tumors is the use of radiolabeled somatostatin analogs. Initial studies with high doses of [(111)In-diethylenetriaminepentaacetic acid (DTPA)(0)]octreotide in patients with metastasized neuroendocrine tumors were encouraging, although partial remissions were uncommon. Another radiolabeled somatostatin analog that is used for peptide receptor radionuclide therapy (PRRT) is [(90)Y-1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid (DOTA)(0),Tyr(3)]octreotide. Various phase 1 and phase 2 PRRT trials have been performed with this compound. Despite differences in the protocols used, complete and partial remissions in most of the studies with [(90)Y-DOTA(0),Tyr(3)]octreotide were in the same ranges, 10%-30%; these ranges were higher than those obtained with [(111)In-DTPA(0)]octreotide. Treatment with the newest radiolabeled somatostatin analog, [(177)Lu-DOTA(0),Tyr(3)]octreotate, which has a higher affinity for the subtype 2 somatostatin receptor, resulted in complete or partial remissions in 30% of 76 patients. Tumor regression was positively correlated with a high level of uptake on OctreoScan imaging, a limited hepatic tumor mass, and a high Karnofsky performance score. Treatment with radiolabeled somatostatin analogs is a promising new tool in the management of patients with inoperable or metastasized neuroendocrine tumors. Symptomatic improvement may occur with all (111)In-, (90)Y-, or (177)Lu-labeled somatostatin analogs that have been used for PRRT. The results obtained with [(90)Y-DOTA(0),Tyr(3)]octreotide and [(177)Lu-DOTA(0),Tyr(3)]octreotate are very encouraging in terms of tumor regression. Also, if kidney protective agents are used, the side effects of this therapy are few and mild, and the duration of the therapy response for both radiopharmaceuticals is more than 2 y. These data compare favorably with those for the limited number of alternative treatment approaches.
Cadherin-11 in Synovial Lining Formation and Pathology in Arthritis (2007)

The normal synovium forms a membrane at the edges of joints and provides lubrication and nutrients for the cartilage. In rheumatoid arthritis, the synovium is the site of inflammation, and it participates in an organized tissue response that damages cartilage and bone. We identified cadherin-11 as essential for the development of the synovium. Cadherin-11-deficient mice have a hypoplastic synovial lining, display a disorganized synovial reaction to inflammation, and are resistant to inflammatory arthritis. Cadherin-11 therapeutics prevent and reduce arthritis in mouse models. Thus, synovial cadherin-11 determines the behavior of synovial cells in their proinflammatory and destructive tissue response in inflammatory arthritis.
Localization and quantification of endoplasmic reticulum Ca(2+)-ATPase isoform transcripts (1995)

The Ca(2+)-adenosinetriphosphatase pump of the sarcoplasmic or endoplasmic reticulum (SERCA) plays a critical role in Ca2+ signaling and homeostasis in all cells and is encoded by a family of homologous and alternatively spliced genes. To understand more clearly the role the different isoforms play in cell physiology, we have undertaken a quantitative and qualitative assessment of the tissue distribution of transcripts encoding each SERCA isoform. SERCA1 expression is restricted to fast-twitch striated muscles, SERCA2a to cardiac and slow-twitch striated muscles, whereas SERCA2b is ubiquitously expressed. SERCA3 is expressed most abundantly in large and small intestine, thymus, and cerebellum and at lower levels in spleen, lymph node, and lung. In situ hybridization analyses revealed SERCA3 transcripts in cells of the intestinal crypt, the thymic cortex, and Purkinje cells in cerebellum. In addition, SERCA3 was expressed abundantly in isolated rat spleen lymphocytes, in various murine lymphoid cell lines, and in primary cultured microvascular endothelial cells. This analysis demonstrates that SERCA3 is expressed selectively in cells in which Ca2+ signaling plays a critical and sensitive role in regulating physiological processes.
Tantalum-microcrystalline CeO2 diffusion barrier for copper metallization (1998)

A tantalum diffusion barrier incorporating microcrystalline CeO2 is proposed for Cu metallization and investigated using Auger electron spectroscopy, x-ray diffraction, optical microscopy, transmission electron microscopy, and sheet resistance measurements. The Cu/Ta+CeO2/Si contact system retained its structure up to 800 °C without an increase in resistivity. The cerium dioxide (CeO2) was stuffed along the grain boundaries during the deposition of Ta layer. Because of its heavier atomic weight than O2- or N2-stuffed elements, it inhibited an interdiffusion of Cu and Si through grain boundaries which can act as fast diffusion paths. It also resulted in preventing the outdiffusion of Ta into the overlayer Cu as well as suppressing the formation of Ta silicide up to 800 °C. It appears that the barrier properties of the tantalum incorporating microcrystalline CeO2 are superior to polycrystalline transition metal barriers, polycrystalline nitride barriers, ternary amorphous compound barriers, and N2- and O2-stuffed barriers.
A Practical, Metal-Free Synthesis of 1H-Indazoles (2008)

The synthesis of 1H-indazoles is achieved from o-aminobenzoximes by the selective activation of the oxime in the presence of the amino group. The reaction occurs with a variety of substituted o-aminobenzoximes using a slight excess of methanesulfonyl chloride and triethylamine at 0-23 degrees C and is amenable to scale-up. The synthesis of 1H-indazoles under these conditions is extremely mild compared with previous synthetic approaches and affords the desired compounds in good to excellent yields.
Survey on Roller-type Nanoimprint Lithography (RNIL) Process (2008)

Nanoimprint Lithography has been demonstrated as a high-throughput, high-resolution and low-cost manufacturing method on nano scale pattering since it was first proposed by Dr. S.Y. Chou in 1995. In this article we presented a general literature review on the Roller-type Nanoimprint Lithography (RNIL), a continuous nanoimprint lithography process. Several kinds of typical Roller-type Nanoimprint Lithography process have been briefly introduced and some examples are also introduced to gain a clear general view and perceive.
Structure-Based Design, Synthesis, and Biological Evaluation of a Series of Novel and Reversible Inhibitors for the Severe Acute Respiratory Syndrome−Coronavirus Papain-Like Protease (2009)

We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, nonpeptide inhibitors of SARS-CoV PLpro. Our initial lead compound was identified via high-throughput screening of a diverse chemical library. We subsequently carried out structure-activity relationship studies and optimized the lead structure to potent inhibitors that have shown antiviral activity against SARS-CoV infected Vero E6 cells. Upon the basis of the X-ray crystal structure of inhibitor 24-bound to SARS-CoV PLpro, a drug design template was created. Our structure-based modification led to the design of a more potent inhibitor, 2 (enzyme IC(50) = 0.46 microM; antiviral EC(50) = 6 microM). Interestingly, its methylamine derivative, 49, displayed good enzyme inhibitory potency (IC(50) = 1.3 microM) and the most potent SARS antiviral activity (EC(50) = 5.2 microM) in the series. We have carried out computational docking studies and generated a predictive 3D-QSAR model for SARS-CoV PLpro inhibitors.
Probing serpin reactive-loop conformations by proteolytic cleavage (1996)

Several crystal structures of intact members of the serine proteinase inhibitor (or serpin) superfamily have recently been solved but the relationship of their reactive-loop conformations to those of circulating forms remains unclear. Here we examine reactive-loop conformational changes of anti-trypsin and anti-thrombin by using limited proteolysis and binary complex formation with synthetic homologous reactive-loop peptides. Proteolysis at the P10-P9, P8-P7 and P7-P6 of anti-trypsin was distorted by binary complex formation. The P1'-P2' bond in anti-thrombin was more accessible to proteolysis after binary complex formation, whereas cleavage at the P4-P3 bond was variably altered by synthetic peptide insertion. The proteolytic accessibility of the reactive-site P1-P1' bond of anti-trypsin and anti-thrombin binary complexes was identical with that of the native form and no cleavage was observed in the hinge region (P15-P10) of either protein, whether native or as binary complexes. these results fit with the proposal that the hydrophobic reactive loop of serpins adopts a modified helical conformation in the circulation, with the hinge region being partly incorporated into the A beta-pleated sheet. This loop can be displaced by peptides and induced to adopt a new conformation similar to the three-turn helix of ovalbumin. Both the native and binary complexed forms of anti-thrombin showed a greatly increased proteolytic sensitivity in the presence of heparin, indicating that heparin either induces a conformational change in the local structure of the helical reactive loop or facilitates the approximation of enzyme and inhibitor.
Regulatory T‐Cell‐Associated Cytokines in Systemic Lupus Erythematosus (2011)

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by autoantibody production, complement activation, and immune complex deposition, resulting in tissue and organ damage. An understanding of the mechanisms responsible for homeostatic control of inflammation, which involve both innate and adoptive immune responses, will enable the development of novel therapies for SLE. Regulatory T cells (Treg) play critical roles in the induction of peripheral tolerance to self- and foreign antigens. Naturally occurring CD4+CD25+ Treg, which characteristically express the transcription factor forkhead box protein P3 (Foxp3), have been intensively studied because their deficiency abrogates self-tolerance and causes autoimmune disease. Moreover, regulatory cytokines such as interleukin-10 (IL-10) also play a central role in controlling inflammatory processes. This paper focuses on Tregs and Treg-associated cytokines which might regulate the pathogenesis of SLE and, hence, have clinical applications.
CD59 expressed on a tumor cell surface modulates decay-accelerating factor expression and enhances tumor growth in a rat model of human neuroblastoma. (2000)

It has been hypothesized that complement inhibitors expressed on the surface of tumor cells prevent effective immune-mediated clearance. Whereas there are in vitro data to support this hypothesis, the species-selective activity of complement inhibitors has been a hindrance to investigating the role of membrane-bound complement inhibitors in rodent models of human cancer. The CD59-positive LAN-1 human neuroblastoma cell line was significantly more sensitive to lysis by rat complement than by human complement, illustrating the species selectivity of endogenously expressed complement inhibitors. Transfection of LAN-1 cells with rat CD59, an inhibitor of the terminal cytolytic membrane attack complex, effectively protected the cells from lysis by rat complement in vitro. When LAN-1 cells stably expressing rat CD59 were inoculated into immune-deficient rats, the onset of tumor growth and the rate of tumor growth were significantly enhanced compared with those of control-transfected LAN-1 cells. These data show directly that the expression of a complement inhibitor on a tumor cell promotes tumor growth. Flow cytometric analysis revealed that the endogenous expression of decay-accelerating factor (DAF), an inhibitor of complement activation, was up-regulated on the surface of cells after in vivo growth. Of further interest, higher levels of DAF were present on CD59-transfected cells than on control-transfected cells derived from tumors. Increased DAF expression correlated with decreased complement deposition on the tumor cell surface. These results show that expression of complement inhibitors on a tumor cell has functional consequences with regard to complement deposition in vivo and indicate that CD59 can indirectly effect complement activation and C3 deposition in vivo via a link between CD59 and DAF expression.
Molecular characterization of a locus required for hyaluronic acid capsule production in group A streptococci. (1992)

To characterize the production of hyaluronate capsule by the membrane-associated enzyme hyaluronate synthase (HAS), group A streptococci from a recent outbreak of acute rheumatic fever were mutagenized via Tn916 insertion. Acapsular transconjugants harboring multiple, nontandem copies of the transposon were identified and found to lack HAS activity (less than 1% of wild-type levels). Generalized transduction was then performed to determine which Tn916 insertion was responsible for the HAS- phenotype. These marker exchange experiments resulted in the isolation of two distinct classes of acapsular transductants, designated WF61 and WF62. Both transductants also lacked significant HAS activity, and excision of the transposon from WF62 restored capsular hyaluronate production. Southern analysis of WF61 DNA demonstrated a large deletion of genomic DNA adjacent to the Tn916 insertion. This deletion event is presumably responsible for the observed stability of the acapsular phenotype of WF61. Further analyses of transductant whole-cell DNA indicated that the transposon insertions of WF61 and WF62 were separated by 2.5 kb. These studies define a locus required for hyaluronate capsule production in group A streptococci. Further genetic analysis of this locus has identified a gene required for HAS activity which wasd inactivated by TN916 in WF62 and deleted in WF61.
Co‐ordinate regulation of Salmonella typhimurium invasion genes by environmental and regulatory factors is mediated by control of hilA expression (1996)

During infection of their hosts, salmonellae enter intestinal epithelial cells. It has been proposed that when Salmonella typhimurium is present in the intestinal lumen, several environmental and regulatory conditions modulate the expression of invasion factors required for bacterial entry into host cells. We report here that the expression of six different S. typhimurium invasion genes encoded on SPI1 (Salmonella pathogenicity island 1) is co-ordinately regulated by oxygen, osmolarity, pH, PhoPQ, and HilA. HilA is a transcriptional activator of the OmpR/ToxR family that is also encoded on SPI1. We have found that HilA plays a central role in the co-ordinated regulation of invasion genes by environmental and regulatory conditions. HilA can activate the expression of two invasion gene-lacZY fusions on reporter plasmids in Escherichia coll, suggesting that HilA acts directly at invasion-gene promoters in S. typhimurium. We have found that the regulation of invasion genes by oxygen, osmolarity, pH, and PhoPQ is indirect and is mediated by regulation of hilA expression by these environmental and regulatory factors. We hypothesize that the complex and co-ordinate regulation of Invasion genes by HilA is an important feature of salmonella pathogenesis and allows salmonellae to enter intestinal epithelial cells.