gebhart/patrepeval huggingface dataset:
Faculty Opinions recommendation of Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors. (2013)

Read the full review for this Faculty Opinions recommended article: Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors.
Strong off-target antibody reactivity to malarial antigens induced by RTS,S/AS01E vaccination is associated with protection (2022)

The RTS,S/AS01E vaccine targets the circumsporozoite protein (CSP) of the Plasmodium falciparum (P. falciparum) parasite. Protein microarrays were used to measure levels of IgG against 1000 P. falciparum antigens in 2138 infants (age 6-12 weeks) and children (age 5-17 months) from 6 African sites of the phase III trial, sampled before and at 4 longitudinal visits after vaccination. One month postvaccination, IgG responses to 17% of all probed antigens showed differences between RTS,S/AS01E and comparator vaccination groups, whereas no prevaccination differences were found. A small subset of antigens presented IgG levels reaching 4- to 8-fold increases in the RTS,S/AS01E group, comparable in magnitude to anti-CSP IgG levels (~11-fold increase). They were strongly cross-correlated and correlated with anti-CSP levels, waning similarly over time and reincreasing with the booster dose. Such an intriguing phenomenon may be due to cross-reactivity of anti-CSP antibodies with these antigens. RTS,S/AS01E vaccinees with strong off-target IgG responses had an estimated lower clinical malaria incidence after adjusting for age group, site, and postvaccination anti-CSP levels. RTS,S/AS01E-induced IgG may bind strongly not only to CSP, but also to unrelated malaria antigens, and this seems to either confer, or at least be a marker of, increased protection from clinical malaria.
Learning Program Representations for Food Images and Cooking Recipes (2022)

In this paper, we are interested in modeling a how-to instructional procedure, such as a cooking recipe, with a meaningful and rich high-level representation. Specifically, we propose to represent cooking recipes and food images as cooking programs. Programs provide a structured representation of the task, capturing cooking semantics and sequential relationships of actions in the form of a graph. This allows them to be easily manipulated by users and executed by agents. To this end, we build a model that is trained to learn a joint embedding between recipes and food images via self-supervision and jointly generate a program from this embedding as a sequence. To validate our idea, we crowdsource programs for cooking recipes and show that: (a) projecting the image-recipe embeddings into programs leads to better cross-modal retrieval results; (b) generating programs from images leads to better recognition results compared to predicting raw cooking instructions; and (c) we can generate food images by manipulating programs via optimizing the latent code of a GAN. Code, data, and models are available online.
Import into Isolated Yeast Mitochondria of Radiolabeled Proteins Synthesized In Vitro (2003)

Much of our current understanding of the mechanisms of cellular protein targeting and membrane translocation of proteins derives from studies on mitochondria. The mitochondrial import process has been studied both in whole cells (including extensive use of mutants, particularly in yeast) and in isolated mitochondria. This chapter will discuss the technical details of in vitro import studies using isolated yeast mitochondria.
Prognostic factors and outcome of adult allogeneic hematopoietic stem cell transplantation patients admitted to intensive care unit during transplant hospitalization (2019)

Patients undergoing allogeneic hematopoietic stem cell transplantation have a high morbidity and mortality, especially after admission to intensive care unit (ICU) during peri-transplant period. The objective of this study was to identify new clinical and biological parameters and validate prognostic scores associated with ICU, short-and long-term survival. Significant differences between ICU survivors and ICU non-survivors for the clinical parameters invasive mechanical ventilation, urine output, heart rate, mean arterial pressure, and amount of vasopressors have been measured. Among prognostic scores (SOFA, SAPSII, PICAT, APACHE II, APACHE IV) assessing severity of disease and predicting outcome of critically ill patients on ICU, the APACHE II score has shown most significant difference (p = 0.002) and the highest discriminative power (area under the ROC curve (AUC) 0.74). An elevated level of lactate at day of admission was associated with poor survival on ICU and the most significant independent parameter (p < 0.001). In our cohort kidney damage with low urine output has a highly relevant impact on ICU, short- and long-term overall survival. The APACHE II score was superior predicting ICU mortality compared to all other tested prognostic scores for patients on ICU during peri-transplant period.
Zona pellucida drilling with cw mid-infrared radiation: basics and applications (1996)

Summary form only given. A mid-infrared radiation device has been developed to assist in vitro fertilization procedures. The system is used to generate openings of controlled size in the zona pellucida (ZP), a protein layer that surrounds and protects the oocyte. ZP drilling is intended for assisted fertilization and hatching. The device takes advantage of the typically high numerical aperture of microscope objectives to confine the interaction volume and thus reduce at maximum the extent of lateral damage, which is of prime importance, when performing surgical intervention at the cellular level. As the drilling procedure has to be done within the culture medium in order to preserve the fragile egg, a quasi-cw operation mode has to be preferred to avoid possible laser-induced mechanical effects, such as shock waves or cavitation bubbles. The selected mid-infrared radiation device incorporates an InGaAsP laser diode at 1.48 /spl mu/m, which penetrates deep enough the culture medium. The collimated laser beam is injected into the optical path of an inverted microscope and is focused by the microscope objective. With a 45 X objective, which has a field of view well adapted to the oocyte size, an and 8 /spl mu/m-diameter spot size is obtained at the object plane. Power levels at the focus of 50 to 70 mW and irradiation times of 5 to 60 ms are sufficient to drill apertures of appropriate size in mouse and human oocytes.
Receiver Front-End Architectures – Analysis and Evaluation (2010)

In this chapter we have presented a review of the mostly known receiver architectures, wherein the main advantages and relevant disadvantages of each configuration were identified. We also have analyzed several possible enhancements to the receiver architectures presented, which include Hartley and Weaver configurations, as well as new receiver architectures based in discrete-time analogue circuits. Moreover, the main interference issues that receiver front-end architectures could experience were shown and analyzed in depth. Furthermore, some PAPR reduction techniques that may be applied in these receiver front-ends were also shown. In the final section, two interesting applications of the described theme were presented. As was said, the development of such multi-norm, multi-standard radios is one of the most important points in the actual scientific area. Also, this fact is very important to the telecommunications industry that is expecting for such a thing. Actually, this is what is being searched for in the SDR field where the motivation is to construct a wideband adaptable radio front-end, in which not only the high flexibility to adapt the front end to simultaneously operate with any modulation, channel bandwidth, or carrier frequency, but also the possible cost savings that using a system based exclusively on digital technology could yield. It is expected that this chapter becomes a good start for RF engineers that wants to learn something about receivers and its impairments.
Spirocyclopropane formation and rearrangement in the thermal and photochemical decomposition of photochemical decomposition of 1-pyrazolines from 9-diazofluorene and bicyclic/2.2.1/olefins. (1968)

Spirocyclopropane formation and rearrangement in thermal and photochemical decomposition of 1-pyrazolines from 9-diazofluorene and bicyclic/2.2.1/olefins
Genetics of Type 2 diabetes (2005)

Type 2 diabetes (T2D) has become a health-care problem worldwide, with the rise in disease prevalence being all the more worrying as it not only affects the developed world but also developing nations with fewer resources to cope with yet another major disease burden. Furthermore, the problem is no longer restricted to the ageing population, as young adults and children are also being diagnosed with T2D. In recent years, there has been a surge in the number of genetic studies of T2D in attempts to identify some of the underlying risk factors. In this review, I highlight the main genes known to cause uncommon monogenic forms of diabetes (e.g. maturity-onset diabetes of the young--MODY--and insulin resistance syndromes), as well as describe some of the main approaches used to identify genes involved in the more common forms of T2D that result from the interaction between environmental risk factors and predisposing genotypes. Linkage and candidate gene studies have been highly successful in the identification of genes that cause the monogenic variants of diabetes and, although progress in the more common forms of T2D has been slow, a number of genes have now been reproducibly associated with T2D risk in multiple studies. These are discussed, as well as the main implications that the diabetes gene discoveries will have in diabetes treatment and prevention.
Design considerations for acousto-optic devices (1981)

The design and fabrication of wide-band bulk acousto-optic modulators (temporal modulation) and beam deflectors (spatial modulation) are described. Optimized device parameters can be obtained systematically for given specifications of the desired modulation bandwidth, throughput efficiency and number of resolvable elements. As the device operating frequency goes beyond a few hundred megahertz, the acoustic transducer response becomes sensitive to the intermediate metal layers between the piezoelectric transducer and the acoustooptic interaction medium. Transducer bandwidth and impedance matching can be optimized using computer modeling programs. Criteria for material selection based on performance requirements and propagation loss are presented. Practical considerations for the fabrication of high performance devices and specific device parameters are discussed.
Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase (2016)

Oxalate decarboxylase (OxDC) catalyzes the conversion of oxalate into formate and carbon dioxide in a remarkable reaction that requires manganese and dioxygen. Previous studies have shown that replacing an active-site loop segment Ser(161)-Glu(162)-Asn(163)-Ser(164) in the N-terminal domain of OxDC with the cognate residues Asp(161)-Ala(162)-Ser-(163)-Asn(164) of an evolutionarily related, Mn-dependent oxalate oxidase gives a chimeric variant (DASN) that exhibits significantly increased oxidase activity. The mechanistic basis for this change in activity has now been investigated using membrane inlet mass spectrometry (MIMS) and isotope effect (IE) measurements. Quantitative analysis of the reaction stoichiometry as a function of oxalate concentration, as determined by MIMS, suggests that the increased oxidase activity of the DASN OxDC variant is associated with only a small fraction of the enzyme molecules in solution. In addition, IE measurements show that C-C bond cleavage in the DASN OxDC variant proceeds via the same mechanism as in the wild-type enzyme, even though the Glu(162) side chain is absent. Thus, replacement of the loop residues does not modulate the chemistry of the enzyme-bound Mn(II) ion. Taken together, these results raise the possibility that the observed oxidase activity of the DASN OxDC variant arises from an increased level of access of the solvent to the active site during catalysis, implying that the functional role of Glu(162) is to control loop conformation. A 2.6 Å resolution X-ray crystal structure of a complex between oxalate and the Co(II)-substituted ΔE162 OxDC variant, in which Glu(162) has been deleted from the active site loop, reveals the likely mode by which the substrate coordinates the catalytically active Mn ion prior to C-C bond cleavage. The "end-on" conformation of oxalate observed in the structure is consistent with the previously published V/K IE data and provides an empty coordination site for the dioxygen ligand that is thought to mediate the formation of Mn(III) for catalysis upon substrate binding.
Automated Continuous Process Control (2002)

Preface. Introduction. Process Characteristics. Feedback Controllers. Cascade Control. Ratio, Override, and Selective Control. Block Diagrams and Stability. Feedforward Control. Dead-Time Compensation. Multivariable Process Control. Appendix A: Case Studies. Appendix B: Processes for Design Practice. Index.
Heat Shock Protein and Heat Shock Factor Expression in Sperm: Relation to Oligozoospermia and Varicocele (2010)

To our knowledge we describe for the first time the expression of different heat shock proteins and heat shock factors in ejaculated sperm. While some of these proteins are up-regulated in men with oligozoospermia and varicocele, HSFY is up-regulated only in the presence of varicocele and especially in men with normozoospermia. This suggests that it may be a molecular marker of an adequate or inadequate response to the damaging effect of varicocele on spermatogenesis.
Cellular Ras and Cyclin D1 Are Required during Different Cell Cycle Periods in Cycling NIH 3T3 Cells (1999)

Novel techniques were used to determine when in the cell cycle of proliferating NIH 3T3 cells cellular Ras and cyclin D1 are required. For comparison, in quiescent cells, all four of the inhibitors of cell cycle progression tested (anti-Ras, anti-cyclin D1, serum removal, and cycloheximide) became ineffective at essentially the same point in G1 phase, approximately 4 h prior to the beginning of DNA synthesis. To extend these studies to cycling cells, a time-lapse approach was used to determine the approximate cell cycle position of individual cells in an asynchronous culture at the time of inhibitor treatment and then to determine the effects of the inhibitor upon recipient cells. With this approach, anti-Ras antibody efficiently inhibited entry into S phase only when introduced into cells prior to the preceding mitosis, several hours before the beginning of S phase. Anti-cyclin D1, on the other hand, was an efficient inhibitor when introduced up until just before the initiation of DNA synthesis. Cycloheximide treatment, like anti-cyclin D1 microinjection, was inhibitory throughout G1 phase (which lasts a total of 4 to 5 h in these cells). Finally, serum removal blocked entry into S phase only during the first hour following mitosis. Kinetic analysis and a novel dual-labeling technique were used to confirm the differences in cell cycle requirements for Ras, cyclin D1, and cycloheximide. These studies demonstrate a fundamental difference in mitogenic signal transduction between quiescent and cycling NIH 3T3 cells and reveal a sequence of signaling events required for cell cycle progression in proliferating NIH 3T3 cells.
Fable II: Design of a modular robot for creative learning (2015)

Robotic systems have a high potential for creative learning if they are flexible, accessible and engaging for the user in the experimental process of building and programming robots. In this paper we describe the Fable modular robotic system for creative learning which we develop to enable and motivate anyone to build and program their own robots. The Fable system consists of self-contained modules equipped with sensors and actuators, which users can use to easily assemble a wide range of robots in a matter of seconds. The robots are user-programmable on several levels of abstraction ranging from a simple visual programming language to powerful conventional ones. This paper provides an overview of the design of Fable for different user groups and an evaluation of critical issues when we attempt to integrate the system into an everyday teaching context.
Near-field spectroscopy and microscopy of InAs single quantum dots (2007)

We have reported the high-resolution photoluminescence (PL) spectroscopic and microscopic study of laterally coupled InAs/GaAs self-assembled quantum dots by using a low-temperature near-field scanning optical microscope. We have observed slightly split PL spectra, which are associated with the bonding and antibonding energy states between two coupled quantum dots.
First-generation clinical dual-source photon-counting CT: ultra-low dose quantitative spectral imaging (2021)

Abstract Objective Evaluation of quantification capabilities at ultra-low radiation dose levels of a first-generation dual-source Photon-Counting Computed Tomography (PCCT) compared to a dual-source dual-energy CT (DECT) scanner. Methods A multi-energy CT phantom was imaged with and without extension ring on both scanners over a range of radiation dose levels (CTDI vol 0.4 - 15.0 mGy). Scans were performed in different modes of acquisition for PCCT with 120 kVp and DECT with 70/Sn150 kVp and 100/Sn150 kVp. Various tissue inserts were used to characterize the precision and repeatability of Hounsfield Units (HUs) on virtual mono-energetic images between 40 and 190 keV. Image noise was additionally investigated at ultra-low radiation dose to illustrate PCCT’s ability to remove electronic background noise. Results Our results demonstrate high precision of HU measurements for a wide range of inserts and radiation exposure levels with PCCT. We report high performance for both scanners across a wide range of radiation exposure levels with PCCT outperforming at low exposures compared to DECT. PCCT scans at lowest radiation exposures illustrate significant reduction in electronic background noise, with a mean percent reduction of 74% (p-value ∼10 −8 ) compared to the 70/Sn150 kVp and 60% (p-value ∼10 −6 ) compared to the 100/Sn150 kVp. Conclusions This paper reports first experiences with a clinical dual-source PCCT scanner with Quantum technology. PCCT provides reliable HUs without disruption from electronic background noise for a wide range of dose values. Diagnostic benefits are not only for quantification at ultra-low-dose but also for imaging of obese patients. Key Points PCCT scanners with Quantum technology provide precise and reliable quantitative Hounsfield Units at ultra-low-dose levels. Influence of electronic background noise can be removed at ultra-low dose acquisitions with PCCT. Both spectral platforms have high performance along a wide range of radiation exposure levels with PCCT outperforming at low radiation exposures.
Two-dimensional dielectric collimator design and its experimental verification for microwave beam focusing (2016)

A collimator is an electromagnetic device that focuses or aligns the direction of wave propagation to achieve a narrow, intense beam. In this study, we propose a two-dimensional dielectric collimator for microwave beam focusing. This is something that is difficult to achieve using theoretical- or intuition-based approaches. We therefore used a systematic design process, which is referred to as the phase field design method, to obtain an optimal topological configuration for the collimator. The phase field parameter determines the optimal configuration of the dielectric material and, as a consequence, it determines the relative permittivity of the component. To verify the design results, we fabricated a prototype via three-dimensional printing and performed an experimental verification using an electric field scanner to measure the near field distributions of the designed collimator positioned parallel to an incident wave. We also performed angle dependent experiments for which the collimator position was offset at various angles. We confirmed that the experimental results are consistent with the simulation results.
Analysis of UGR Values and Results of UGR Calculations in Commercial Lighting Simulation Software (2015)

The Unified Glare Rating (UGR) is an international index presented by the CIE that quantifies discomfort glare and has become of recent important. The UGR can be calculated using commercial lighting simulation software such as Relux 2013, AGi32 v2.04, and Dialux 4.11, but the values vary depending on which software is used. It appears that because the UGR input variables used in the UGR calculations of commercial lighting simulation software differ, there are differences in the calculated UGR values. Therefore, this study modified the UGR calculation modeling and made it possible to calculate UGR values with various calculation conditions of input variables. Then, the UGR values were calculated by changing calculation conditions under the following three input variables: field of view for the calculation of the background luminance (Lb) and for the calculation of luminance of the luminous parts of each luminaire (L) and the position index (P). Among the calculation conditions under these three input variables, the conditions that have an effect on the UGR values have been analyzed, and these UGR values were compared to those from commercial lighting simulation software, from which we could speculate the UGR calculation algorithm in commercial lighting simulation.
vSQL: Verifying Arbitrary SQL Queries over Dynamic Outsourced Databases (2017)

Cloud database systems such as Amazon RDS or Google Cloud SQLenable the outsourcing of a large database to a server who then responds to SQL queries. A natural problem here is to efficiently verify the correctness of responses returned by the (untrusted) server. In this paper we present vSQL, a novel cryptographic protocol for publicly verifiable SQL queries on dynamic databases. At a high level, our construction relies on two extensions of the CMT interactive-proof protocol [Cormode et al., 2012]: (i) supporting outsourced input via the use of a polynomial-delegation protocol with succinct proofs, and (ii) supporting auxiliary input (i.e., non-deterministic computation) efficiently. Compared to previous verifiable-computation systems based on interactive proofs, our construction has verification cost polylogarithmic in the auxiliary input (which for SQL queries can be as large as the database) rather than linear. In order to evaluate the performance and expressiveness of our scheme, we tested it on SQL queries based on the TPC-H benchmark on a database with 6 million rows and 13 columns. The server overhead in our scheme (which is typically the main bottleneck) is up to 120 times lower than previousapproaches based on succinct arguments of knowledge (SNARKs), and moreover we avoid the need for query-dependent pre-processing which is required by optimized SNARK-based schemes. In our construction, the server/client time and the communication cost are comparable to, and sometimessmaller than, those of existing customized solutions which only support specific queries.