gebhart/patrepeval huggingface dataset:
The Complete Amino Acid Sequence of Human Serum Retinol-binding Protein (1987)

The complete amino acid sequence of human serum Retinol-binding protein (RBP) including the distribution of its three disulfide bridges, has been determined. The protein consists of 182 amino acid residues, the order of which was determined following the isolation of five CNBr-fragments. Direct amino acid sequence analysis in an automatic liquid phase sequencer provided almost the entire sequences of the five CNBr-fragments. Several sets of enzymatically derived peptides of RBP were also used to elucidate the primary structure. RBP displays significant homology to bovine beta-lactoglobulin, human alpha 1-microglobulin and rat alpha 1-microglobulin. RBP contains an internal homology. Thus, residues 36 to 83 display statistically significant homology with residues 96 to 141.
Defining a molecular subclass of treatment resistant prostate cancer. (2015)

5004 Background: A subset of advanced prostate cancers can progress from an androgen receptor (AR)-driven state to AR independence, often associated with low or absent AR expression and extensive neuroendocrine differentiation. Once neuroendocrine prostate cancer (NEPC) develops, patients often demonstrate an aggressive clinical course and poor overall survival. Diagnosis is important but remains challenging as the clinical and pathologic features associated with AR independence and NEPC are poorly defined. Methods: We performed whole-exome sequencing of 124 metastatic tumors from 81 patients (35 with morphologic features of NEPC). Serial or synchronous samples were included to characterize heterogeneity and the transition from adenocarcinoma to NEPC. Computational analysis of clonality and allele-specific quantification were performed using CLONET. Quantitative mRNA assessments, including AR signaling genes and DNA methylation, were evaluated in the context of genomic changes. Results: The mutational landscape of NEPC and castration-resistant prostate cancer (CRPC) did not differ significantly by rate of non-synonymous mutations or copy number burden (average > 40% of genome was aberrant), and polyploidy was frequently detected together with common allelic imbalances. Comparative analysis at the DNA and mRNA level identified decreased AR signaling in NEPC and a range of AR signaling in CRPC, enrichment of copy number losses (including RB1 and multiple genes on 16q) in NEPC, and focal high level AR amplification in CRPC in contrast to NEPC (p = 0.0007). DNA allele-specific analysis of multi-sample cases suggested diverse genomic state of key lesions including aberrations in MYCN and CDKN1B. Conclusions: This is largest study to date focused on the molecular landscape of the NEPC resistance phenotype. NEPC is characterized by a molecular profile defined by distinct genomic alterations and decreased AR signaling. A subgroup of CRPC demonstrates lower AR signaling and molecular overlap with NEPC. This study supports clonal evolution of prostate adenocarcinoma to NEPC, provides new insight into NEPC biology and disease heterogeneity, and may aid in the detection of AR independence and emergence of the NEPC subclass of treatment resistance.
Miniature Analytical Methods for Medical Diagnostics (2005)

There is a growing trend to bring medical diagnostics closer to the patient. In his perspective,
 David Walt
 describes how advances in sensors as well as developments in micro and nanotechnologies are enabling the development of miniature diagnostic platforms. These platforms contain all the necessary functions to perform sample processing and analysis. As the systems become simpler and less expensive they will be used closer to the patient and eventually are likely to be used at home for health care and health monitoring.
Assessing daylight & low-dose rate photodynamic therapy efficacy, using biomarkers of photophysical, biochemical and biological damage metrics in situ (2017)

Daylight or artificial light PDT provides an alternative schedule for delivery of drug-light treatment, and this pre-clinical assay demonstrated that in vivo assays of damage could be used to objectively predict a clinical outcome in this altered delivery process.
Parental History of Hypertension Is Associated With Narrower Retinal Arteriolar Caliber in Young Girls (2011)

We aimed to assess the associations between parental history of hypertension and indicators of cardiovascular risk (retinal vessel diameter, presence of obesity, and elevated blood pressure) in prepubertal children. There were 1739 (77.7% of those eligible) 6-year-old students (863 girls and 876 boys) who were examined from a random cluster sample of 34 Sydney schools. Parents completed questionnaires about their medical conditions, including whether they have/had hypertension. Retinal images were taken with a digital fundus camera, and retinal vessel caliber was quantified using computer software. Anthropometric (height, weight, percentage of body fat, and body mass index) and blood pressure measures were collected. There were 160 children (9.2%) with a positive parental history of hypertension (either biological mother and/or father). Children with a positive versus negative parental history of hypertension had significantly higher body mass index (16.8 versus 16.5 kg/m(2); P=0.04) and systolic blood pressure (101.3 versus 99.8 mm Hg; P=0.01). Girls with positive versus negative parental history of hypertension had significantly higher diastolic blood pressure (≈3.1 mm Hg; P=0.01) and narrower retinal arteriolar caliber (≈4.3 μm; P=0.0004). Positive parental history of hypertension was not associated with mean retinal vascular caliber among boys. We show that a positive parental history of hypertension in healthy prepubertal girls, but not boys, is associated with narrower retinal arteriolar vessels, likely conveying a predisposition to develop hypertension later in life. These findings may indicate the need for cardiovascular disease prevention measures starting early in life among offspring of hypertensive parents.
Solid‐phase synthesis of C‐terminally modified peptides (2006)

In this paper, a straightforward and generic protocol is presented to label the C-terminus of a peptide with any desired moiety that is functionalized with a primary amine. Amine-functional molecules included are polymers (useful for hybrid polymers), long alkyl chains (used in peptide amphiphiles and stabilization of peptides), propargyl amine and azido propyl-amine (desirable for 'click' chemistry), dansyl amine (fluorescent labeling of peptides) and crown ethers (peptide switches/hybrids). In the first part of the procedure, the primary amine is attached to an aldehyde-functional resin via reductive amination. To the secondary amine that is produced, an amino acid sequence is coupled via a standard solid-phase peptide synthesis protocol. Since one procedure can be applied for any given amine-functional moiety, a robust method for C-terminal peptide labeling is obtained.
A High Isolation and High Selectivity Ladder-Lattice BAW-SMR Filter (2006)

Thispaperpresents aBAW-SMR filter using a combined ladder-lattice topology forapplication inW-CDMA reception front-ends (2.11 -2.17GHz).Thecombined topology allies theadvantages ofbothnetworktypes, having verysteep responses andhighisolation atundesired bands. Thedesign of filter wassimulated using acombined 2DEM-acoustical analysis procedure, itpresents: 1.6dBofinsertion loss, -10dBofreturn lossandisolation higher than-48dB atTX band(1.92 - 1.98 GHz). IndexTerms - BAW filter, SMR,ladder, lattice.
Suprascapular neuropathy. Variability in the diagnosis, treatment, and outcome. (2001)

The functional outcome of operative and nonoperative treatment of suprascapular neuropathy was compared to determine the preferred method of treatment for each etiology of nerve injury. The predictive value of preoperative electromyography also was studied. Fifty-three patients were evaluated at least 1 year (average, 28 months) from the time of operative (n = 36) or nonoperative (n = 17) treatment. A modified American Shoulder and Elbow Surgeons self-assessment score was obtained at presentation and at final followup. Electromyography data were obtained at initial presentation. Minimal electromyographic changes associated with denervation were associated with a limited response to treatment, especially in patients with nerve compression secondary to spinoglenoid notch cysts. Pretreatment electromyographic findings, therefore, were predictive of treatment response. Overall, operative and nonoperative treatment of these suprascapular nerve injuries resulted in significant functional improvement, but the results varied depending on the etiology of the injury. Spinoglenoid notch cysts responded significantly better to operative treatment, with the results for open surgery being the same as the results for arthroscopic decompression. In addition, compressive lesions attributable to suprascapular notch entrapment had the best improvement with surgical decompression. Traumatic lesions, including traction and direct closed injuries, had an equal response to operative and nonoperative treatment. Overuse injuries did not improve with operative treatment. Viral neuritis improved with nonoperative treatment and never was treated with surgery. Overall, traumatic injuries resulted in significantly worse final outcomes than any other etiologic processes. In the nonoperative group, neuropathy secondary to spinoglenoid cysts resulted in significantly worse function. The outcome of treatment is dependent on the severity and etiology of the nerve injury, and the method of treatment.
Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions (2020)

Metabolic engineering in the post-genomic era is characterised by the development of new methods for metabolomics and fluxomics, supported by the integration of genetic engineering tools and mathematical modelling. Particularly, constraint-based stoichiometric models have been widely studied: (i) flux balance analysis (FBA) (in silico), and (ii) metabolic flux analysis (MFA) (in vivo). Recent studies have enabled the incorporation of thermodynamics and metabolomics data to improve the predictive capabilities of these approaches. However, an in-depth comparison and evaluation of these methods is lacking. This study presents a thorough analysis of two different in silico methods tested against experimental data (metabolomics and 13C-MFA) for the mesophile Escherichia coli. In particular, a modified version of the recently published matTFA toolbox was created, providing a broader range of physicochemical parameters. Validating against experimental data allowed the determination of the best physicochemical parameters to perform the TFA (Thermodynamics-based Flux Analysis). An analysis of flux pattern changes in the central carbon metabolism between 13C-MFA and TFA highlighted the limited capabilities of both approaches for elucidating the anaplerotic fluxes. In addition, a method based on centrality measures was suggested to identify important metabolites that (if quantified) would allow to further constrain the TFA. Finally, this study emphasised the need for standardisation in the fluxomics community: novel approaches are frequently released but a thorough comparison with currently accepted methods is not always performed.
Primary Epithelioid Sarcoma of the Hand and Forearm (1974)

Of eighty-five primary soft-tissue and sixteen primary bone sarcomas involving the hand and forearm, thirteen were epithelioid sarcomas, making this lesion third in frequency after fibrosarcoma and rhabdomyosarcoma in the whole series and first in frequency in the hand. In all thirteen patients the initial diagnosis was misleading; and recurrence, metastasis, or both occurred in all but the one patient who had primary forearm amputation. Primary en bloc excision and midforearm amputation are recommended if the lesion recurs.
Applications of geometry and topology for quadrilateral meshprocessing and verifiable visualization (2010)

Computational geometry, computer graphics, and visualization are closely related ares that have had great synergy over the years. Point-based graphics~\cite{Gross:2007:PBG}, for example, grew out of contributions from all of these different areas. In this talk, we present results that show non-trivial applications of geometric and topological techniques to graphics and visualization.
Peripheral NK Cell Activation and Expansion by Artificial Antigen Presenting Cells, 2D11 (41.25) (2009)

Abstract Natural killer (NK) cells play an important role in early immune defenses against both nonself cells and autologous cells infected with viruses, bacteria, or parasites or in malignant transformation. NK cells mediate direct cytotoxic attack without prior sensitization on their targets through activating receptors, NKG2D, NCR, TRAIL, and inhibitory receptors ("absence of self"), and/or produce cytokines and chemokines that contribute to cytotoxicity and immunoregulation. A number of studies have reported that activation/expansion enhances NK cytotoxicity, but optimal methods for activating and expanding NK cells have not been well defined. Here we demonstrate that artificial APCs (2D11), previously reported and used to expand antigen-specific T cells, also efficiently expand NK cells via NKG2D and 4-1BB signaling mediated by MICA/B and 4-1BBL expression respectively on 2D11 aAPCs. In the presence of exogenous IL15, which is trans-presented by IL-15Rα on 2D11, robust expansion of highly lytic activated NK cells occurs. Compared to resting NK cells, IL15/2D11-activated NK cells upregulated TRAIL and NKp30, 44, 46 expression, and exerted enhanced cytotoxicity against K562, Ewing’s tumor cell lines, including autologous tumors, ALL, as well as NK-resistant Daudi cells. In previous studies, expression of KIR ligands on tumor cells has been put forth as a mechanism of tumor immune escape from NK cell mediated killing. Our preliminary results demonstrate that expression of KIR ligands on tumor targets no longer inhibits killing by NK cells activated with 2D11. Ongoing studies are underway to test the hypothesis that NK cells activated by IL15/2D11 will prove more effective therapeutics due to breaking up of KIR-mediated inhibition of tumor cell killings.
Immunisation against Human c-MYC Elicits a T-Cell Response and Influences Growth of High Grade B-Cell Lymphoma in Mice. (2009)

Abstract Abstract 5120 Overexpression of the proto-oncogene c-myc due to chromosomal translocation is the hallmark of Burkitt-lymphoma. The evolving high grade lymphoma is dependent on the overexpression of c-myc, which provides the necessary signal to drive uncontrolled proliferation. Therefore loss of function or recognition of c-myc overexpressing cells by c-MYC specific T-cells should result in killing of the target and a halt to lymphoma progression. C-myc is also expressed in a variety of other human malignancies. Peptide prediction reveals several potential foreign epitopes in the context of murine H2b due to 87% homology between human and mouse c-MYC. In this study we explored whether the human c-myc gene product can be a target for T-cell therapy. Wildtype C57BL/6 mice were immunized with recombinant human c-MYC protein in combination with incomplete Freund′s adjuvans and CpG, and were boosted at various time points thereafter using either c-MYC protein or 40mer peptides encompassing the non homologous regions. Control animals were vaccinated with recombinant GFP or OVA protein. C-MYC vaccinated animals displayed a higher IFNg release upon re-stimulation with c-MYC pulsed dendritic cells compared to control vaccinated animals. In ELISPOT assays we observed a higher number of IFNg positive cells (299±17 vs. 122±8.5 (GFP vaccinated) vs. 66±8.5 (OVA vaccinated)). Vaccination using single peptides revealed that peptides spanning the region from amino acid 87-123, 216-255 and 334-376 produced similar results. In addition, using a human c-MYC specific ELISA we were able to detect c-MYC specific antibodies in serum from immunized mice in a concentration up to 40mg/l. Using established cell lines from l-hu-c-myc transgenic mice, where the human c-myc gene is overexpressed due to the juxtaposition of elements of the immunoglobuline lambda locus as found in t(8;22) of Burkitt's lymphoma, we investigated whether vaccination with human c-MYC protein would influence lymphoma growth in a lymphoma transfer model. Animals were s.c. challenged with 0.1 Mio 291cells overexpressing human c-MYC and were monitored for lymphoma growth. C-MYC vaccinated animals (n=15) displayed a delay in tumor onset and a significantly better disease free survival (28 vs. 22 days, p=0.012) compared to control (OVA) vaccinated animals (n=10). This delayed growth was associated with an increased number of infiltrating CD3+/Perforin+ cells. However, all mice eventually succumbed to lymphoma growth, indicating that the T-cell response was not sufficient to control lymphoma growth in the long term. From these data we conclude that the human c-MYC is a possible target antigen for T-cells, but responses are weak and presumably low in frequency. Disclosures No relevant conflicts of interest to declare.
Di‐genic inheritance of germline POLE and PMS2 pathogenic variants causes a unique condition associated with pediatric cancer predisposition (2021)

Polymerase proofreading-associated polyposis (PPAP) and Lynch syndrome, caused by mutated POLE and mismatch repair (MMR) genes, respectively, are associated with adult-onset cancer. PPAP and MMR-deficient tumors are both hypermutated, and each has a unique mutational signature. We describe a 4.5-year-old boy with multiple café au lait spots who presented with metastatic Sonic Hedgehog-activated medulloblastoma, with partial response to intensive chemotherapy and immunotherapy. The tumor showed microsatellite stability, loss of PMS2 nuclear expression, and an exceptionally high tumor mutational burden of 276 Mut/Mb. Germline molecular analysis revealed an inherited heterozygous pathogenic POLE variant and a de novo heterozygous PMS2 pathogenic variant. The tumor featured the MMR, POLE, and POLE+MMR mutational signatures. This is the first description of a di-genic condition, which we named "POL-LYNCH syndrome," manifested by an aggressive ultra-mutant pediatric medulloblastoma with a unique genomic signature.
Read-disturb Detection Methodology for RRAM-based Computation-in-Memory Architecture (2023)

Resistive random access memory (RRAM) based computation-in-memory (CIM) architectures can meet the unprecedented energy efficiency requirements to execute AI algorithms directly on edge devices. However, the read-disturb problem associated with these architectures can lead to accumulated computational errors. To achieve the necessary level of computational accuracy, after a specific number of read cycles, these devices must undergo a reprogramming process which is a static approach and needs a large counter. This paper proposes a circuit-level RRAM read-disturb detection technique by monitoring real-time conductance drifts of RRAM devices, which initiate the reprogramming when actually it needs. Moreover, an analytic method is presented to determine the minimum conductance detection requirements, and our proposed read-disturb detection technique is tuned for the same to detect it dynamically. SPICE simulation result using TSMC 40 nm shows the correct functionality of our proposed detection technique.
Mathematical model for biomolecular quantification using surface-enhanced Raman spectroscopy based signal intensity distributions (2015)

This paper presents the development of a novel statistical method for quantifying trace amounts of biomolecules by surface-enhanced Raman spectroscopy (SERS) using a rigorous, single molecule (SM) theory based mathematical derivation. Our quantification framework could be generalized for planar SERS substrates, in which the nanostructured features can be approximated as a closely spaced electromagnetic dimer problem. The potential for SM detection was also shown, which opens up an exciting opportunity in the field of SERS quantification.
Introduction to the best papers of ACM multimedia 2009 (2010)

No abstract available.
Carbon Monoxide and Isocyanide Complexes of Trivalent Uranium Metallocenes (1999)

The [Cp′3U] metallocenes contain substituted cyclopentadienyl ligands and UIII with f3 electron configuration. They are good π donors and bind π-accepting ligands (L) such as carbon monoxide and isocyanides to form the corresponding adducts [Cp′3U(L)] (see scheme). The π-donating capability of the [Cp′3U] fragments appears to be readily modulated by the substituents on the cyclopentadienyl ligand.
Measurement of the underlying event activity at the LHC with $ \sqrt {s} = 7 $ TeV and comparison with $ \sqrt {s} = 0.9 $ TeV (2011)

A measurement of the underlying activity in events with a jet of transverse momentum in the several GeV region is performed in proton-proton collisions at s = 0.9 and 7 TeV, using data collected by the CMS experiment at the LHC. The production of charged particles with pseudorapidity || < 2 and transverse momentum p T > 0.5 GeV/c is studied in the azimuthal region transverse to that of the leading set of charged particles forming a track-jet. A significant growth of the average multiplicity and scalar-p T sum of the particles in the transverse region is observed with increasing p T of the leading trackjet, followed by a much slower rise above a few GeV/c. For track-jet p T larger than a few GeV/c, the activity in the transverse region is approximately doubled with a centreof-mass energy increase from 0.9 to 7 TeV. Predictions of several QCD-inspired models as implemented in pythia are compared to the data.
Surgical approach to functional tricuspid regurgitation (2014)

Despite data demonstrating inferior outcomes in the presence of residual tricuspid regurgitation after cardiac surgery, surgical repair for FTR appears to be underutilized. Increased recognition and correction of tricuspid regurgitation at the time of surgery is increasingly supported by published guidelines, although randomized prospective data are needed to bolster current recommendations.
Seed biology: advances and applications. Proceedings of the Sixth International Workshop on Seeds, Merida, Mexico, 1999. (2000)

The history of seed science is discussed, tracing its development from when limits of knowledge were imposed by descriptive physiology, biochemistry and ecology through the period when the horizons were extended by more analytical approaches, to the present when progress in molecular and cell biology, genetics and biophysics offers opportunities for new progress in all branches of research in seed science.
Characterization of an elastic cylinder and an elastic sphere with the time-reversal operator: application to the sub-resolution limit (2008)

The Décomposition de l'Opérateur de Retournement Temporel method applies to scattering analysis with arrays of transducers. It comprises the study of the time-reversal invariants which correspond to the eigenvectors of the time-reversal operator or to the singular vectors of the array response matrix K. In this paper, the decomposition of the scattered pressure into normal modes of vibrations is used to determine the theoretical time-reversal invariants for a large elastic object such as a cylinder or sphere. For an N transducers one-dimensional array, the time-reversal operator is dimension N. It is shown that the dimension is reduced to 2k0a for a cylinder or a sphere, where a is the scatterer radius and k0 is the wave number in the surrounding fluid. Furthermore, this approach provides analytical expressions of symmetric and anti-symmetric singular values and vectors in the sub-resolution limit, i.e. when the scatterer diameter is smaller than the array resolution cell. These results are verified experimentally and in good agreement with the original point of view: for a small scatterer, one singular value dominates and the associated singular vector focuses isotropically on the scatterer.