gebhart/patrepeval huggingface dataset:
A Phosphorylation‐Induced Turn Defines the Alzheimer’s Disease AT8 Antibody Epitope on the Tau Protein (2015)

Post mortem biochemical staging of Alzheimer's disease is currently based on immunochemical analysis of brain slices with the AT8 antibody. The epitope of AT8 is described around the pSer202/pThr205 region of the hyperphosphorylated form of the neuronal protein tau. In this study, NMR spectroscopy was used to precisely map the AT8 epitope on phosphorylated tau, and derive its defining structural features by a combination of NMR analyses and molecular dynamics. A particular turn conformation is stabilized by a hydrogen bond of the phosphorylated Thr205 residue to the amide proton of Gly207, and is further stabilized by the two Arg residues opposing the pSer202/pThr205.
Crystal Structure of TRAIL-DR5 Complex Identifies a Critical Role of the Unique Frame Insertion in Conferring Recognition Specificity (2000)

TRAIL is a cytokine that induces apoptosis in a wide variety of tumor cells but rarely in normal cells. It contains an extraordinarily elongated loop because of an unique insertion of 12-16 amino acids compared with the other members of tumor necrosis factor family. Biological implication of the frame insertion has not been clarified. We have determined the crystal structure of TRAIL in a complex with the extracellular domain of death receptor DR5 at 2.2 A resolution. The structure reveals extensive contacts between the elongated loop and DR5 in an interaction mode that would not be allowed without the frame insertion. These interactions are missing in the structures of the complex determined by others recently. This observation, along with structure-inspired deletion analysis, identifies the critical role of the frame insertion as a molecular strategy conferring specificity upon the recognition of cognate receptors. The structure also suggests that a built-in flexibility of the tumor necrosis factor receptor family members is likely to play a general and important role in the binding and recognition of tumor necrosis factor family members.
Autonomous Proliferation of Leukemic Cells in Vitro as a Determinant of Prognosis in Adult Acute Myeloid Leukemia (1993)

The capacity of leukemic blasts for autonomous proliferation is associated with highly aggressive acute myeloid leukemia.
A high throughput molecular force assay for protein–DNA interactions (2011)

An accurate and genome-wide characterization of protein-DNA interactions such as transcription factor binding is of utmost importance for modern biology. Powerful screening methods emerged. But the vast majority of these techniques depend on special labels or markers against the ligand of interest and moreover most of them are not suitable for detecting low-affinity binders. In this article a molecular force assay is described based on measuring comparative unbinding forces of biomolecules for the detection of protein-DNA interactions. The measurement of binding or unbinding forces has several unique advantages in biological applications since the interaction between certain molecules and not the mere presence of one of them is detected. No label or marker against the protein is needed and only specifically bound ligands are detected. In addition the force-based assay permits the detection of ligands over a broad range of affinities in a crowded and opaque ambient environment. We demonstrate that the molecular force assay allows highly sensitive and fast detection of protein-DNA interactions. As a proof of principle, binding of the protein EcoRI to its DNA recognition sequence is measured and the corresponding dissociation constant in the sub-nanomolar range is determined. Furthermore, we introduce a new, simplified setup employing FRET pairs on the molecular level and standard epi-fluorescence for readout. Due to these advancements we can now demonstrate that a feature size of a few microns is sufficient for the measurement process. This will open a new paradigm in high-throughput screening with all the advantages of force-based ligand detection.
ADAM7, A Member of the ADAM (A Disintegrin And Metalloprotease) Gene Family Is Specifically Expressed in the Mouse Anterior Pituitary and Epididymis1 (1997)

The maturation of spermatozoa in the epididymis is a complex process that requires the active involvement of the epididymal epithelium. The primary focus toward elucidating the role of the epididymis in the maturation process has been the study of epididymal secretory proteins and their interaction with spermatozoa. To date there is a paucity of information regarding epididymal epithelial cell surface proteins, which may also play important roles in epididymal function. Through a subtractive hybridization approach to identify genes specifically expressed in the caput epididymidis, the mouse homologue of a member of the ADAM (a disintegrin and metalloprotease) family of proteins was identified. This rapidly growing gene family encodes cell surface proteins that possess putative adhesion and protease domains. Northern blot analyses demonstrated that the mouse ADAM gene, termed ADAM7, is expressed in the caput region of the epididymis and in the anterior pituitary gonadotropes with no detectable expression in the twenty-six other tissues examined. Furthermore, in situ hybridization experiments revealed that the ADAM7 messenger RNA (mRNA) exhibited an apical localization within the proximal caput epididymal epithelium that may correlate with an unusual sparsely granulated endoplasmic reticulum uniquely present in the proximal region of the epididymidis and to which no known function has been ascribed. Hormonal, surgical, and genetic strategies demonstrated that ADAM7 gene expression requires, in a region-dependent manner, androgens as well as testicular factors for expression. Interestingly, the apical localization of ADAM7 mRNA is dependent upon an intact testis, because in situ hybridization analyses of the proximal caput epididymidis from a testosterone maintained castrate mouse did not show the apical localization of ADAM7 mRNA. Finally, chromosomal mapping demonstrated that the ADAM7 gene maps to the central region of mouse Chromosome 14, approximately 4-5 cM distal from the fertilin beta locus, which encodes another reproductive-specific ADAM protein.
Three Epitope-Specific Monoclonal Antibodies against the Hapten Penicillin (1985)

Three monoclonal antibodies (Pen 4, Pen 7 and Pen 9) were raised against the benzylpenicilloyl group and used to investigate the antigenicity of this group. The binding of Pen 4 to carrier-bound penicillin derivatives was shown in an ELISA to be dependent on the structure of the side chain in the derivative. Hence Pen 4 recognizes this side chain. From the difference in binding to carrier-bound penicillin derivatives in a competitive enzyme immunoassay it was concluded that Pen 7 mainly recognizes the new antigenic determinant which emerges from the binding of the penicillin derivative to a carrier. The binding of Pen 9 to carrier-bound penicillin derivatives was not influenced by the nature of the side chain. Neither was the bound or free nature of the derivative of influence on the binding. Therefore it is concluded that Pen 9 mainly recognizes the thiazolidine ring of penicillin. This study thus shows that in the benzylpenicilloyl group at least three epitopes can be recognized.
Oparin's Reactions Revisited: Enzymic Synthesis of Poly(adenylic acid) in Micelles and Self-Reproducing Vesicles (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOparin's Reactions Revisited: Enzymic Synthesis of Poly(adenylic acid) in Micelles and Self-Reproducing VesiclesPeter Walde, Ayako Goto, Pierre-Alain Monnard, Michaela Wessicken, and Pier Luigi LuisiCite this: J. Am. Chem. Soc. 1994, 116, 17, 7541–7547Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/ja00096a010https://doi.org/10.1021/ja00096a010research-articleACS PublicationsRequest reuse permissionsArticle Views819Altmetric-Citations203LEARN 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
Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies (2000)

Random mutagenesis and selection using phage or cell surface display provides an efficient method for affinity maturation of single chain Fv (scFv) antibodies, thereby improving function in various applications. To investigate the effects of mutation frequency on affinity maturation, error-prone PCR was used to generate libraries containing an average (m) of between 1.7 and 22.5 base substitutions per gene in a high affinity scFv antibody that binds to the cardiac glycoside digoxigenin. The scFv antibody libraries were displayed on Escherichia coli, and mutant populations were analyzed by flow cytometry. At low to moderate mutation frequencies with an average mutation rate of m </= 8, the fraction of clones exhibiting binding to a fluorescently labeled conjugate of digoxigenin decreased exponentially (r(2) = 0.99), but the most highly mutated library (m = 22.5) had significantly more active clones than expected relative to this trend. A library with a low error rate (m = 1.7), one with moderate error rate (m = 3.8), and the one with high error rate (m = 22.5) were screened for high affinity clones under conditions of identical stringency using fluorescence-activated cell sorting. After several rounds of enrichment, each of the three libraries yielded clones with improved affinity for the hapten. The moderate and high error rate libraries gave rise to clones exhibiting the greatest affinity improvement. Taken together, our results indicate that (i) functional clones occur at an unexpectedly high frequency in hypermutated libraries, (ii) gain-of-function mutants are well represented in such libraries, and (iii) the majority of the scFv mutations leading to higher affinity correspond to residues distant from the binding site.
Measurement of Atherosclerotic Carotid Plaque Size In Vivo Using High Resolution Magnetic Resonance Imaging (1998)

MRI is highly accurate for in vivo measurement of artery WA in atherosclerotic carotid lesions. This imaging technique has potential application monitoring lesion size in studies examining plaque progression and/or regression.
Study of Prediagnostic Selenium Level in Toenails and the Risk of Advanced Prostate Cancer (1998)

Our results support earlier findings that higher selenium intakes may reduce the risk of prostate cancer. Further prospective studies and randomized trials of this relationship should be conducted.
Enhancement of laser cancer treatment by a chitosan-derived immunoadjuvant (2004)

A chitosan derivative, glycated chitosan (GC), has been used as an immunostimulant for cancer treatment in laser immunotherapy. The function of GC is to enhance the host immune response after direct cancer cell destruction by a selective laser photothermal interaction. To further test its effects, laser immunotherapy was extended to include several different adjuvants for immunological stimulation and to include photodynamic therapy (PDT) as a different tumor-destruction mechanism. Complete Freund (CF) adjuvant, incomplete Freund (IF) adjuvant and Corynebacterium parvum (CP) were selected for treatment of metastatic mammary tumors in rats, in combination with a selective photothermal interaction. The solution of the immunoadjuvants admixed with indocyanine green (ICG), a light-absorbing dye, was injected directly into the tumors, followed by noninvasive irradiation of an 805 nm laser. Combined with PDT, in the treatment of tumors in mice, GC was administered peritumorally immediately after laser irradiation. The survivals of treated animals were compared with untreated control animals. In the treatment of rat tumors, CF, IF and CP raised the cure rates from 0% to 18%, 7% and 9%, respectively. In comparison, GC resulted in a 29% long-term survival. In the treatment of EMT6 mammary sarcoma in mice, GC of 0.5% and 1.5% concentrations increased the cure rates of Photofrin-based PDT treatment from 38% to 63% and 75%, respectively. In the treatment of Line 1 lung adenocarcinoma in mice, a 1.67% GC solution enabled a noncurative meso-substituted tetra(meta-hydroxy-phenyl)chlorin-based PDT to cure 37% of the tumor-bearing mice. The experimental results of this study confirmed our previous studies, showing that immunoadjuvants played an active role in laser-related cancer treatment and that GC significantly enhanced the efficacy of laser cancer treatment.
Chronic continuous PTH infusion results in hypertension in normal subjects. (1986)

The factors responsible for the frequent occurrence of hypertension in patients with primary hyperparathyroidism have not been elucidated. Suggested mediators have included hypercalcemia, renal insufficiency, and increased plasma renin activity. However, experimental results have not been reported in any species that test the hypothesis that sustained hypertension in this clinical syndrome is due to consequences of parathyroid hormone (PTH) excess versus unrelated factors (e.g., primary hypersecretion of other hormones, NaCl sensitivity, genetic factors). Moreover, no systematic evaluation of the renin or adrenal cortical responses to chronic PTH excess has been reported in any species. Accordingly, the present studies assessed the effects of chronic (12 days) continuous intravenous b-(1-34) PTH infusion in normal human subjects (n = 4). PTH infusion resulted in persistent hypercalcemia and hypertension, reversible during a 4-8-day recovery period. Transient but significant increases in urinary tetrahydroaldosterone excretion and plasma cortisol concentration were observed as hypercalcemia and hypertension developed. No significant changes in plasma potassium concentration or plasma renin activity were observed, suggesting that hypercalcemia-induced transient hypersecretion of ACTH was responsible for both cortisol and aldosterone responses. The present results suggest that hypertension associated with clinical primary hyperparathyroidism results from either direct or indirect effects of PTH excess, per se, and requires neither the long-term consequences/complications of the clinical disorder (e.g., severe nephrocalcinosis, renal insufficiency) nor primary hypersecretion of additional hormones. These results are consistent with the hypothesis that hypercalcemia alone or in combination with at least permissive levels of PTH can generate short-term, but persistent (12 days) hypertension in human subjects and thus may be the initiating mechanism for hypertension in clinical primary hyperparathyroidism.
Patterned Arrays of Ordered Peptide Nanostructures (2009)

Methods for the deposition of ordered nanostructures on various substrates are a key factor in nanotechnological devices. There is a special interest in the development of methods for the organization of organic nanostructures that are not compatible with some of the conventional fabrication methods. The unique chemical and physical properties of the peptide nanotubes make them excellent component in various devices and the useful application were already demonstrated in the case of biosensors. Here we demonstrate the ability to deposited aromatic dipeptide nanotubes using electron beam treatment of surfaces to control their wettability. The use of a low energy electron irradiation results in the formation of pre-defined surfaces with controlled level of wettability. This treatment allows the precise patterning of the organic tubular assemblies at high resolution. The differential wettability of the surface resulted in organization of the peptide assemblies according to the properties of the different areas of the surface. In the current work, we describe the use of wettability patterned surfaces for the control patterning of horizontal peptide nanotubes and nanospheres. Furthermore, lift-off lithography is used to make patterned arrays of peptide nano-forests, vertically aligned peptide nanotubes. In summary, the novel patterning techniques together with the unique properties of the peptide nanostructures represent an important step in the integration of these assemblies into functional nanosystems and devices.
MEMS based hair flow-sensors as model systems for acoustic perception studies (2006)

Arrays of MEMS fabricated flow sensors inspired by the acoustic flow-sensitive hairs found on the cerci of crickets have been designed, fabricated and characterized. The hairs consist of up to 1 mm long SU-8 structures mounted on suspended membranes with normal translational and rotational degrees of freedom. Electrodes on the membrane and on the substrate form variable capacitors, allowing for capacitive read-out. Capacitance versus voltage, frequency dependence and directional sensitivity measurements have been successfully carried out on fabricated sensor arrays, showing the viability of the concept. The sensors form a model system allowing for investigations on sensory acoustics by their arrayed nature, their adaptivity via electrostatic interaction (frequency tuning and parametric amplification) and their susceptibility to noise (stochastic resonance).
Germanium MOS capacitors incorporating ultrathin high-/spl kappa/ gate dielectric (2002)

For the first time, we have successfully demonstrated the feasibility of integrating a high-permittivity (/spl kappa/) gate dielectric material zirconium oxide into the MOS capacitors fabricated on pure germanium substrates. The entire fabrication process was essentially performed at room temperature with the exception of a 410/spl deg/C forming gas anneal. After processing steps intended to remove the germanium native oxide interlayer between the zirconium oxide dielectric and germanium substrate, an excellent capacitance-based equivalent SiO/sub 2/ thickness (EOT) on the order of 5-8 /spl Aring/ and capacitance-voltage (C-V) characteristics with hysteresis of 16 mV have been achieved. Additionally, excellent device yield and uniformity were possible using this low thermal budget process.
Intelligent vehicle localization using GPS, compass, and machine vision (2009)

Intelligent vehicles require accurate localization relative to a map to ensure safe travel. GPS sensors are among the most useful sensors for outdoor localization, but they still suffer from noise due to weather conditions, tree cover, and surrounding buildings or other structures. In this paper, to improve localization accuracy when GPS fails, we propose a sequential state estimation method that fuses data from a GPS device, an electronic compass, a video camera, and wheel encoders using a particle filter. We process images from the camera using a color histogram-based method to identify the road and non-road regions in the field of view in front of the vehicle. In two experiments, in simulation and on a real vehicle, we demonstrate that, compared to a standard extended Kalman filter not using image data, our method significantly improves lateral localization error during periods of GPS inaccuracy.
The Future of Cancer Therapy: Selecting Patients Likely to Respond to PD1/L1 Blockade (2014)

It is conceivable that, in the near future, an assay that defines the likelihood of a patient with advanced cancer to respond to immunotherapy based on PD1/L1 blockade will be the initial decision point to select the treatment of patients with any cancer type.
Sharing Memory Optimally (1983)

Efficient design of service facilities, such as data or computer networks that meet random demands, often leads to the sharing of resources among users. Contention for the use of a resource results in queueing. The waiting room is a part of any such service facility. The number of accepted service requests per unit of time (throughput), or the fraction of the time the servers are busy (utilization), are often used as performance measures to compare designs. Most common models in queueing theory consider the design of the waiting rooms with the assumption that, although individual requests may differ from one another, they are statistically indistinguishable. However, there are several instances where available information allows us to classify the requests for service into different types. In such cases the design of the service facility not only involves the determination of an optimum size for the waiting room but also the rules of sharing it among the different types. Even with a fixed set of resources, the rules of sharing them can influence performance. In data networks (or computer networks) the "waiting room" consists of memory of one kind or another. Messages (jobs) destined for different locations (processors) sharing common storage is an important example of shared use of memory. Recently, Kleinrock and Kamoun have modeled such use of memory and computed the performance of various policies for managing the allocation of memory to several types of users. Decisions to accept or reject a demand for service were based on the number of waiting requests of each type. However, the optimal policy was not determined even in the case where there were only two types of users. We determine the structure of optimal policies for the model considered with three types of users. The optimal policy consists of limiting the number of waiting requests of each type, and reserving a part of the memory to each type.
The 1997 Mathews Radio-Baton and Improvisation Modes (1997)

When the Radio-Baton is powered up or reset, it's processor enters a polling loop looking for commands received at it's MIDI input terminal.Most commands are encoded as MIDI system-exclusive messages which contain only an operation code as a single information character.For most commands the Radio-Baton sends a confirmation message from its MIDI output to the control computer.TEST
Ultra-fine grained medium-carbon steel produced by equal-channel angular pressing process (2008)

Ultrafine grained medium-carbon steel was prepared by heating the steel with martensite microstructure to temperature below A_(c1) and then quickly conducting equal-channel angular pressing.The results show that the ultra-fine grained ferrite with mean grain size smaller than 0.5μm is obtained in the steel with martensite microstructure heated to 923K and held for proper time and then ECAPed quickly.The grain refinement is due to the interactions of dislocations,dynamic recrystallization,and strain-induced phase transformation.The fine carbide particles are uniformly precipitated from the supersaturated ferrite inside grains and at grain boundaries during ECAP.The grain size and quantity of ferrite,the size and distribution of carbide particles can be controlled by changing tempering temperature and time.The experiment indicates that the ultra-fine microstructure of the steel exhibits excellent thermal stability.