gebhart/patrepeval huggingface dataset:
Method for nucleic acid hybridization using single-stranded DNA binding protein (2023)

Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.
Assessing Energetic Contributions to Binding from a Disordered Region in a Protein−Protein Interaction, (2010)

Many functional proteins are at least partially disordered prior to binding. Although the structural transitions upon binding of disordered protein regions can influence the affinity and specificity of protein complexes, their precise energetic contributions to binding are unknown. Here, we use a model protein-protein interaction system in which a locally disordered region has been modified by directed evolution to quantitatively assess the thermodynamic and structural contributions to binding of disorder-to-order transitions. Through X-ray structure determination of the protein binding partners before and after complex formation and isothermal titration calorimetry of the interactions, we observe a correlation between protein ordering and binding affinity for complexes along this affinity maturation pathway. Additionally, we show that discrepancies between observed and calculated heat capacities based on buried surface area changes in the protein complexes can be explained largely by heat capacity changes that would result solely from folding the locally disordered region. Previously developed algorithms for predicting binding energies of protein-protein interactions, however, are unable to correctly model the energetic contributions of the structural transitions in our model system. While this highlights the shortcomings of current computational methods in modeling conformational flexibility, it suggests that the experimental methods used here could provide training sets of molecular interactions for improving these algorithms and further rationalizing molecular recognition in protein-protein interactions.
Electronic Pre-Distortion Operating at 1 Sample/symbol with Accurate Bias Control for CD Compensation (2010)

Electronic pre-distortion operating at 1 Sa/sym with anti-aliasing filter and accurate bias control is proposed. This approach guarantees Q penalty within 0.7 dB for 112 Gb/s DP-QPSK coherent system with dispersion up to 25,000 ps/nm.
Post-functionalization and Mechanical Properties of Poly(lactide-cyclohexadiene oxide) Block Copolymers (2023)

A series of lactide (LA) and cyclohexadiene oxide (CHDO) multiblock copolymers was synthesized using a redox switchable complex, (salfen)Zr(OiPr)2 (salfen = N,N’-bis(2,4-di-tert-butylphenoxy)-1,1’-ferrocenediimine), with LA being polymerized by the reduced state, while CHDO was polymerized by the oxidized state of the catalyst. Diblock (PCHDO-PLA) and triblock (PLA-PCHDO-PLA and PCHDO-PLA-PCHDO) copolymers were prepared, and all the copolymers were post-functionalized using a thiol-ene click reaction. Dynamic mechanical analysis showed that both triblock copolymers have a better elasticity than the diblock copolymer, and all the functionalized copolymers have a better elasticity than the corresponding non-functionalized copolymers.
The Eighth Central European Conference “Chemistry towards Biology”: Snapshot (2016)

The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on August 28-September 1, 2016 to bring together experts in biology, chemistry and design of bioactive compounds; promote the exchange of scientific results, methods and ideas; and encourage cooperation between researchers from all over the world. The topics of the conference covered "Chemistry towards Biology", meaning that the event welcomed chemists working on biology-related problems, biologists using chemical methods, and students and other researchers of the respective areas that fall within the common scope of chemistry and biology. The authors of this manuscript are plenary speakers and other participants of the symposium and members of their research teams. The following summary highlights the major points/topics of the meeting.
Linearization of Concurrent Tri-Band Transmitters Using 3-D Phase-Aligned Pruned Volterra Model (2013)

This paper reports a novel digital predistortion (DPD) scheme for concurrent tri-band power amplifiers (PAs). The proposed tri-band DPD is based on a pruned Volterra model that takes into account the impact of the phase distortion observed in multi-band PAs as well as the compound amplitude distortion. By taking into account the phase variation effects across a wide frequency band, the proposed 3-D phase-aligned Volterra DPD can effectively compensate for the crosstalk effects between the fundamental frequencies, their harmonics, and intermodulation products due to the nonlinearity the tri-band PA exhibited. The performance of the proposed DPD is validated using a broadband Class-AB PA driven concurrently by three independent carrier-aggregated long-term evolution signals at separation frequencies around 100 MHz. The measurement results validate the accurate performance of the proposed 3-D phase-aligned pruned Volterra DPD in suppressing the in-band and cross-band intermodulation effects, and shows improvement over a basic 3-D tri-band DPD model that neglects phase variation effects across frequency.
Room-Temperature Midwavelength Infrared InAsSb Nanowire Photodetector Arrays with Al2O3 Passivation (2019)

Developing uncooled photodetectors at midwavelength infrared (MWIR) is critical for various applications including remote sensing, heat seeking, spectroscopy, and more. In this study, we demonstrate room-temperature operation of nanowire-based photodetectors at MWIR composed of vertical selective-area InAsSb nanowire photoabsorber arrays on large bandgap InP substrate with nanoscale plasmonic gratings. We accomplish this by significantly suppressing the nonradiative recombination at the InAsSb nanowire surfaces by introducing ex situ conformal Al<sub>2</sub>O<sub>3</sub> passivation shells. Transient simulations estimate an extremely low surface recombination velocity on the order of 10<sup>3</sup> cm/s. We further achieve room-temperature photoluminescence emission from InAsSb nanowires, spanning the entire MWIR regime from 3 to 5 μm. A dry-etching process is developed to expose only the top nanowire facets for metal contacts, with the sidewalls conformally covered by Al<sub>2</sub>O<sub>3</sub> shells, allowing for a higher internal quantum efficiency. Based on these techniques, we fabricate nanowire photodetectors with an optimized pitch and diameter and demonstrate room-temperature spectral response with MWIR detection signatures up to 3.4 μm. The results of this work indicate that uncooled focal plane arrays at MWIR on low-cost InP substrates can be designed with nanostructured absorbers for highly compact and fully integrated detection platforms.
Ultra-Thin Fatigue-Free Bi4Ti3O12 Films for Nonvolatile Ferroelectric Memories (1996)

We have developed a new low temperature growth technique for Bi 4 Ti 3 O 12 thin films using a MOCVD method in which an ultra-thin double buffer layer (5-nm thick Bi 4 Ti 3 O 12 /5-nm thick TiO 2 ) is used to control the crystallization and fine grain structure. The 100-nm thick Bi 4 Ti 3 O 12 thin films fabricated at 400°C showed an extremely smooth surface morphology and good electrical properties, namely, a large remanent polarization of P r =11 µC/cm 2 , a coercive field of E c =90 kV/cm and a low leakage current I L =7×10 -9 A/cm 2 at 3 V. Moreover, we successfully fabricated 50-nm ultra thin Bi 4 Ti 3 O 12 films with P r =9 µC/cm 2 and E c =120 kV/cm at 3 V. For the first time, the fatigue free property, which is very important for nonvolatile ferroelectric memory (NVFRAM) applications, was confirmed up to 1×10 12 switching cycles.
Implicit Behavioral Cloning (2021)

We find that across a wide range of robot policy learning scenarios, treating supervised policy learning with an implicit model generally performs better, on average, than commonly used explicit models. We present extensive experiments on this finding, and we provide both intuitive insight and theoretical arguments distinguishing the properties of implicit models compared to their explicit counterparts, particularly with respect to approximating complex, potentially discontinuous and multi-valued (set-valued) functions. On robotic policy learning tasks we show that implicit behavioral cloning policies with energy-based models (EBM) often outperform common explicit (Mean Square Error, or Mixture Density) behavioral cloning policies, including on tasks with high-dimensional action spaces and visual image inputs. We find these policies provide competitive results or outperform state-of-the-art offline reinforcement learning methods on the challenging human-expert tasks from the D4RL benchmark suite, despite using no reward information. In the real world, robots with implicit policies can learn complex and remarkably subtle behaviors on contact-rich tasks from human demonstrations, including tasks with high combinatorial complexity and tasks requiring 1mm precision.
Caiipa (2014)

Scalable and comprehensive testing of mobile apps is extremely challenging. Every test input needs to be run with a variety of contexts, such as: device heterogeneity, wireless network speeds, locations, and unpredictable sensor inputs. The range of values for each context, e.g. location, can be very large. In this paper we present Caiipa, a cloud service for testing apps over an expanded mobile context space in a scalable way. It incorporates key techniques to make app testing more tractable, including a context test space prioritizer to quickly discover failure scenarios for each app. We have implemented Caiipa on a cluster of VMs and real devices that can each emulate various combinations of contexts for tablet and phone apps. We evaluate Caiipa by testing 265 commercially available mobile apps based on a comprehensive library of real-world conditions. Our results show that Caiipa leads to improvements of 11.1x and 8.4x in the number of crashes and performance bugs discovered compared to conventional UI-based automation (i.e., monkey-testing).
Molecular and Functional Characterization of Monoclonal Antibodies (2009)

This chapter contains sections titled: Introduction Molecular Structural Analysis of mAb by Physicochemical Methods Glycosylation and Glycan Analysis Molecular Heterogeneity Functional Analyses of mAb Candidates Summary and Concluding Remarks Acknowledgments References
Health professionals' perceptions of maggot debridement therapy (2021)

Specifically, the 'yuck' factor and the perception of MDT as an 'ancient' modality contributed towards MDT stigma; in addition, lack of outpatient insurance coverage deterred MDT use. These findings provide useful information regarding the perceptual and systemic barriers that prevent greater acceptance of MDT. Ultimately, these barriers must be understood if we are to facilitate MDT implementation and improve MDT usage in the future.
Antibodies to Domains II and III of the IL-1 Receptor Accessory Protein Inhibit IL-1β Activity But Not Binding: Regulation of IL-1 Responses Is Via Type I Receptor, Not the Accessory Protein (1998)

Abstract The IL-1R accessory protein (IL-1RAcP) plays a role in IL-1R signaling by forming a complex with IL-1RI bound to the IL-1 ligand. We identified four hydrophilic peptide regions of the extracellular IL-1RAcP that may be available for complex formation (peptide 1, 71–83 domain I; peptide 2, 204–211 domain II; peptide 3, 282–292 domain III; and peptide 4, 304–314 domain III). These peptides were synthesized, coupled to keyhole limpet hemocyanin, and used to produce rabbit antisera. Each affinity-purified antiserum showed specificity for the respective peptide without cross-reactivity. Anti-peptide 2, 3, and 4 recognized surface expression of IL-1RAcP on the Th2 D10S cells by FACS and inhibited IL-1-driven proliferation. Anti-peptide 4 recognized intact IL-1RAcP and soluble IL-1RAcP. Anti-IL-1RAcP-peptide 4, which targets the terminal segment of domain III, inhibited 80% of IL-1β-driven proliferation of D10S cells. However, these IL-1RAcP Abs had no effect on the activity of human or mouse IL-1α. Whereas IL-1β down-regulated IL-1RI surface expression (p &amp;lt; 0.05), there was no change in the surface expression of IL-1RAcP. Moreover, murine IL-10 increased surface expression of IL-1RI, but did not affect expression of IL-1RAcP or the proliferation of D10S cells. Steady state levels of mRNA for IL-1RAcP and IL-1RI in D10S cells showed a similar pattern to that of surface expression of the respective receptors. We conclude that 1) blocking IL-1RAcP inhibits IL-1 signaling in D10S cells, 2) domains-II and III may be involved in complex formation with IL-1RI, 3) IL-1RAcP is not regulated as is IL-1RI in the same cells, and 4) IL-1 responsiveness is dependent on the expression of IL-1RI, not IL-1RAcP.
Disulfide Linkage of Growth Hormone (GH) Receptors (GHR) Reflects GH-induced GHR Dimerization (1999)

The growth hormone (GH) receptor (GHR) binds GH in its extracellular domain and transduces activating signals via its cytoplasmic domain. Both GH-induced GHR dimerization and JAK2 tyrosine kinase activation are critical in initiation of GH signaling. We previously described a rapid GH-induced disulfide linkage of GHRs in human IM-9 cells. In this study, three GH-induced phenomena (GHR dimerization, GHR disulfide linkage, and enhanced GHR-JAK2 association) were examined biochemically and immunologically. By using the GH antagonist, G120K, and an antibody recognizing a dimerization-sensitive GHR epitope, we demonstrated that GH-induced GHR disulfide linkage reflects GH-induced GHR dimerization. GH, not G120K, promoted both GHR disulfide linkage and enhanced association with JAK2. Measures that diminished GH-dependent JAK2 and GHR tyrosine phosphorylation diminished neither GH-induced GHR disulfide linkage nor GH-enhanced GHR-JAK2 association. By using both transient and stable expression systems, we determined that cysteine 241 (an unpaired extracellular cysteine) was critical for GH-induced GHR disulfide linkage; however, GH-induced GHR dimerization, GHR-JAK2 interaction, and GHR, JAK2, and STAT5 tyrosine phosphorylation still proceeded when this cysteine residue was mutated. We conclude GH-induced GHR disulfide linkage is not required for GHR dimerization, and activation and GH-enhanced GHR-JAK2 association depends more on GHR dimerization than on GHR and/or JAK2 tyrosine phosphorylation.
Acoustic radiation force to reposition kidney stones (2013)

Our group has introduced transcutaneous ultrasound to move kidney stones in order to expel small stones or relocate an obstructing stone to a nonobstructing location. Human stones and metalized beads (2–8 mm) were implanted ureteroscopically in kidneys of eight domestic swine. Ultrasonic propulsion was performed using a diagnostic imaging transducer and a Verasonics ultrasound platform. Stone propulsion was visualized using fluoroscopy, ultrasound, and the ureteroscope. Successful stone movement was defined as relocating a stone to the renal pelvis, ureteropelvic junction (UPJ), or proximal ureter. Three blinded experts evaluated for histologic injury in control and treatment arms. All stones were moved. 65% (17/26) of stones/beads were moved the entire distance to the renal pelvis (3), UPJ (2), or ureter (12). Average successful procedure per stone required 14±8 min and 23±16 pushes. Each push averaged 0.9 s in duration. Mean interval between pushes was 41±13 s. No gross or histologic kidney damage was identified in six kidneys from exposure to 20 1-s pushes spaced by 33 s. Ultrasonic propulsion is effective with most stones being relocated to the renal pelvis, UPJ, or ureter. The procedure appears safe without evidence of injury. [Work supported by NIH DK43881, DK092197, and NSBRI through NASA NCC 9-58.]
<title>Microendoscopic holography with flexible fiber bundle</title> (1994)

An in situ holographic technique, involving the use of a flexible miniaturized endoscope (diameter less than 1 mm) coupled to a CCD camera, to record the hologram, has been developed for medical applications. The hologram is formed, by reflection, on the tip of a multimode fiber bundle (MMB), sampled, and then treated electronically. The image is reconstructed numerically, providing more flexibility to the holographic process. Reconstructed images show the capability of the microendoscopic system to restore 3D informations of the observed scene. The limitations of the holographic approach with the microendoscope have been evaluated and discussed in terms of the resolution limit. In particular, the low frequency sampling of the hologram through the MMB is not a limiting factor for the range of observation distance investigated (4 - 10 mm). A good accordance between the experimental results and the theoretical predictions was found by comparing the cut-off frequency obtained. Our results show that, for the considered observation distances, objects of a few micrometers can be clearly identified. The different sources of noise are analyzed and their influence on the quality of the reconstructed image have been quantified.
Interaction of cycloSal-Pronucleotides with Cholinesterases from Different Origins. A Structure−Activity Relationship (2004)

A large number of cycloSal-nucleotide triesters 1-49 have been studied concerning their ability to inhibit cholinesterases of different origins as well as to inhibit HIV replication in cell culture. It was shown that none of the triesters showed inhibitory effects against human acetylcholinesterase (AChE; isolated enzyme) as well as against AChE from beef erythrocytes and calf serum. In contrast, inhibition of butyrylcholinesterase (BChE) has been observed for some triesters in human and mouse serum. cycloSal pronucleotides showed strong competitive inhibition with respect to the substrate acetylcholine chloride (K(i)/K(m): approximately 2 x 10(-5)) and acted by time-dependent irreversible inhibition of the human serum BChE. Detailed studies demonstrated that the inhibitory effect against BChE is dependent on the nucleoside analogue, the substitution pattern of the cycloSal-moiety, and particularly on the stereochemistry at the phosphorus atom. Structural requirements to avoid the inhibition of BChE by cycloSal-nucleotide triesters have been elucidated in the reported study.
YSO, LSO, GSO and LGSO. A study of energy resolution and nonproportionality (2000)

We have studied the nonproportionality and intrinsic energy resolution of cerium doped YSO, GSO, LSO and LGSO crystals. While LSO and YSO have similar light output, GSO and LGSO have ca. 70% and 20% lower light output than LSO, respectively. YSO, a compound containing fairly light elements, was expected to have proportional light output vs. energy, like YAP:Ce. Surprisingly it has almost the same non-proportional as LSO and GSO. The nonproportionality of YSO is followed by large values of intrinsic energy resolution. The comparison of the nonproportionality of YSO-LSO and YAP-LuAP pairs indicates that high proportionality is connected with the structure of the crystal and not with the presence of light elements. To our knowledge, this is the first study of nonproportionality and intrinsic resolution for LGSO.
ChemInform Abstract: Acylation of a Transient Ti(IV)‐enolate by Acyl Halides and Anhydrides. Facile Synthesis of α‐Hydroxy‐β‐ketoesters. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comment on the accuracy of Wertheim’s theory of associating fluids (1995)

The results of recently developed Monte Carlo methods for simulation of strongly associating fluids show an apparent disagreement with Wertheim’s theory of associating fluids. In this comment we show that the disagreement observed arises largely from approximations used for the reference-fluid pair distribution function required by the theory.
Geriatric Depression Scale (GDS-15): A Sensitive and Convenient Instrument for Measuring Depression in Young Anorexic Patients (2001)

Zalsman, Gil M.D.; Weizman, Abraham M.D.; Carel, Cynthia A. M.D.; Aizenberg, Dov M.D. Author Information
Quantized Principal Component Selection Precoding for Spatial Multiplexing with Limited Feedback (2008)

In this paper, for spatial multiplexing with limited feedback, a quantized principal component selection (QPCS) precoding scheme is proposed that achieves comparable capacity to the closed-loop multiple-input multiple-output (MIMO) and furthermore adapts to various fading channel conditions without any additional feedback bits and transmit channel state information (CSI). We propose a systematic design method for a codebook consisting of a finite number of unitary matrices based on a maximizing minimum distance criterion in the one- dimensional angular domain and show that the method outperforms the Grassmannian subspace packing method in various fading channel conditions. The proposed QPCS precoding scheme allows for adjustment of the precoding matrix based on limited feedback information on the principal vectors approximating a MIMO channel in the angular domain according to various channel conditions. Furthermore, for practical implementation of the QPCS precoding scheme, we propose a structured precoder optimization procedure and show that the proposed procedure induces a negligible capacity loss compared with the exhaustive precoder optimization, even with considerably reduced complexity.
Induction of p16/INK4a Gene Expression and Cellular Senescence by Toyocamycin. (2002)

We constructed an assay system of a luciferase reporter with p16/lNK4a gene transcriptional regulatory domain to identify p16-inducing substances, and found toyocamycin to induce gene expression from the screening of culture fluids of Streptomyces. Toyocamycin is a nucleoside analog, and it increased the p16 mRNA level in human normal fibroblasts or synovial cells as assessed by Northern blot hybridization or real time RT-PCR. It also induced cellular senescence in normal human fibroblasts. The transcriptional regulatory regions of human p16 gene that were responsible for the induction were analyzed using deletion mutants of the transcriptional regulatory region of p16 linked to the luciferase gene. The DNA fragment -111 to +1 bp from the cap site was sufficient to drive toyocamycin-activated transcription of p16/luciferase reporter. Nucleotide sequences within this domain contained the Sp1- and Ets-binding sequences. Mutations were introduced into these sequences, and the Sp1 sequence was found to be critical for the induction, and this notion was confirmed from gel-mobility shift assay.