gebhart/patrepeval huggingface dataset:
Solution Structure of Oxidized Saccharomyces cerevisiae Iso-1-cytochrome c, (1997)

The solution structure of oxidized Saccharomycescerevisiae Cys102Ser iso-1-cytochromechas been determined using 1361 meaningful NOEs (of 1676 total) after extending the published proton assignment [Gao, Y., et al. (1990) Biochemistry 29, 6994-7003] to 77% of all proton resonances. The NOE patterns indicate that secondary structure elements are maintained upon oxidation in solution with respect to the solid state and solution structures of the reduced species. Constraints derived from the pseudocontact shifts [diamagnetic reference shift values are those of the reduced protein [Baistrocchi, P., et al. (1996) Biochemistry 35, 13788-13796]] were used in the final stages of structure calculations. After restrained energy minimization with constraints from NOEs and pseudocontact shifts, a family of 20 structures with rmsd values of 0.58 +/- 0.08 and 1.05 +/- 0.10 A (relative to the average structure) for the backbone and all heavy atoms, respectively, was obtained. The solution structure is compared with the crystal structure and the structures of related systems. Twenty-six amide protons were detected in the NMR spectrum 6 days after the oxidized lyophilized protein was dissolved in D2O (pH 7.0 and 303 K); in an analogous experiment, 47 protons were observed in the spectrum of the reduced protein. The decrease in the number of nonexchanging amide protons, which mainly are found in the loop regions 14-26 and 75-82, confirms the greater flexibility of the structure of oxidized cytochrome c in solution. Our finding of increased solvent accessibility in these loop regions is consistent with proposals that an early step in unfolding the oxidized protein is the opening of the 70-85 loop coupled with dissociation of the Met80-iron bond.
Solidification microstructure and room-temperature fracture toughness of Al-based cast alloys prepared through eutectic reactions in Al-Mg-Zn ternary system (2022)

This study was set to examine the fundamentals of solidification microstructure and room-temperature fracture toughness of different eutectic aluminum (Al) alloys strengthened by T-Al6Mg11Zn11 and/or β-Al3Mg2 intermetallic phases. The thermodynamic calculations for an Al-Mg-Zn ternary system assessed three alloy compositions of Al-22.5Mg-23.5Zn, Al-35.5Mg-2Zn and Al-34.5Mg-5Zn (mol%) corresponding to α-Al/T, α-Al/β and α-Al/T/β eutectic compositions, respectively. The designed alloys were prepared by different cast process for changing the cooling rate in solidification. The Al-22.5Mg-23.5Zn and Al-35.5Mg-2Zn alloys exhibited a number of fibrous α phase surrounded by of T-phase and β-phase matrix, respectively. The morphologies of eutectic microstructures were refined by high cooling rate in solidification. The three-phase microstructure of α, T and β phases was often observed in slowly solidified Al-34.5Mg-5Zn alloy, whereas only the α/β two-phase eutectic microstructure was observed in the rapidly solidified alloy sample. The indentation fracture method using Vickers indentation test was applied to measure the room-temperature fracture toughness of the experimental alloys prepared by mold-casting. The α/β twophase eutectic alloys exhibited a low fracture toughness of 1.1 MPa·m 0.5 in comparison with the α/T two-phase eutectic alloy. The lower fracture toughness would be responsible for the brittleness of β-phase matrix in the α/β twophase eutectic alloys.
Stereo depth map fusion for robot navigation (2011)

We present a method to reconstruct indoor environments from stereo image pairs, suitable for the navigation of robots. To enable a robot to navigate solely using visual cues it receives from a stereo camera, the depth information needs to be extracted from the image pairs and combined into a common representation. The initially determined raw depthmaps are fused into a two level heightmap representation which contains a floor and a ceiling height level. To reduce the noise in the height maps we employ a total variation regularized energy functional.With this 2.5D representation of the scene the computational complexity of the energy optimization is reduced by one dimension in contrast to other fusion techniques that work on the full 3D space such as volumetric fusion. While we show only results for indoor environments the approach can be extended to generate heightmaps for outdoor environments.
Diastereo- and Enantiodifferentiation in Indium-Promoted Allylations of 2,3-Azetidinediones in Water. Definition of Long-Range Stereocontrol Elements on π-Facial Selectivity for β-Lactam Synthesis (1998)

The stereochemical course of the reactions of N-benzyl-2,3-azetidinedione with six differently functionalized allylic bromides, as promoted by indium metal in 1:1 H2O−THF, were initially examined. Three of the examples that proved to be usefully stereoselective were subsequently reevaluated in azetidinediones which now carried (S)-α-methylbenzyl and (R)-α-(1-naphthyl)ethyl residues bonded to nitrogen. These enantiomerically pure building blocks afforded products that differed in the facial sense of organometallic addition to the ketonic carbonyl. Interestingly, the diastereofacial selectivity is directly linked to the R or S configuration of the exocyclic N-amido substituent. Stereochemical assignments to many of the products were based on X-ray crystallographic measurements. In other cases, spectral correlations were used. The global results clearly show that fundamental, yet previously unappreciated, long-range nonbonded steric interactions do control the extent to which competing cyclic transition states operate.
CD4 T Cells Play Major Effector Role and CD8 T Cells Initiating Role in Spontaneous Autoimmune Myocarditis of HLA-DQ8 Transgenic IAb Knockout Nonobese Diabetic Mice (2006)

In humans, spontaneous autoimmune attack against cardiomyocytes often leads to idiopathic dilated cardiomyopathy (IDCM) and life-threatening heart failure. HLA-DQ8 transgenic IAb knockout NOD mice (NOD.DQ8/Ab(0); DQA1*0301, DQB1*0302) develop spontaneous anticardiomyocyte autoimmunity with pathology very similar to human IDCM, but why the heart is targeted is unknown. In the present study, we first investigated whether NOD/Ab(0) mice transgenic for a different DQ allele, DQ6, (DQA1*0102, DQB1*0602) would also develop myocarditis. NOD.DQ6/Ab(0) animals showed no cardiac pathology, implying that DQ8 is specifically required for the myocarditis phenotype. To further characterize the cellular immune mechanisms, we established crosses of our NOD.DQ8/Ab(0) animals with Rag1 knockout (Rag1(0)), Ig H chain knockout (IgH(0)), and beta(2)-microglobulin knockout (beta(2)m(0)) lines. Adoptive transfer of purified CD4 T cells from NOD.DQ8/Ab(0) mice with complete heart block (an indication of advanced myocarditis) into younger NOD.DQ8/Ab(0) Rag1(0) animals induced cardiac pathology in all recipients, whereas adoptive transfer of purified CD8 T cells or B lymphocytes had no effect. Despite the absence of B lymphocytes, NOD.DQ8/Ab(0)IgH(0) animals still developed complete heart block, whereas NOD.DQ8/Ab(0)beta(2)m(0) mice (which lack CD8 T cells) failed to develop any cardiac pathology. CD8 T cells (and possibly NK cells) seem to be necessary to initiate disease, whereas once initiated, CD4 T cells alone can orchestrate the cardiac pathology, likely through their capacity to recruit and activate macrophages. Understanding the cellular immune mechanisms causing spontaneous myocarditis/IDCM in this relevant animal model will facilitate the development and testing of new therapies for this devastating disease.
Polymeric Fiber Sorbents Embedded with Porous Organic Cages (2021)

The synthesis and functionalization of porous organic cages (POCs) for separation have attracted growing interest over the past decade. However, the potential of solid-phase POCs for practical, large-scale separations will require incorporation into appropriate gas-solid or liquid-solid contactors. Contactors with more effective mass transfer properties and lower pressure drops than pelletized systems are preferred. Here, we prepared and characterized fiber sorbents with POCs throughout a cellulose acetate (CA) polymer matrix, which were then deployed in model separations. The POC CC3 was shown to be stable after exposure to spinning solvents, as confirmed by NMR, powder X-ray diffraction, and gas sorption experiments. CC3-CA fibers were spun using the dry-jet wet-quench spinning method. Spun fibers retained the adsorptive properties of CC3 powders, as confirmed by CO<sub>2</sub> and N<sub>2</sub> physisorption and TGA, reaching upward of 60 wt % adsorbent loading, whereas the pelletized CC3 counterparts suffered significant losses in textural properties. The separation capabilities of the CC3-CA fibers are tested with both simulated postcombustion flue gas and with Xe/Kr mixtures. Fixed bed breakthrough experiments performed on fibers samples show that CC3 embedded in polymeric fibers can effectively perform these proof-of-concept gas separations. The development of fiber sorbents embedded with POCs provides an alternative to traditional pelletization for the incorporation of these materials into adsorptive separation systems.
A randomized phase III trial of docetaxel plus cisplatin or paclitaxel plus carboplatin compared with doxorubicin plus cisplatin as adjuvant chemotherapy for endometrial cancer at high risk of recurrence: Japanese Gynecologic Oncology Group study (JGOG2043). (2017)

5503 Background: The superiority of chemotherapy regimens employing a taxane plus a platinum agent over standard therapy with doxorubicin plus cisplatin (AP) was recently demonstrated for advanced or recurrent endometrial cancer. This multicenter phase III trial evaluated the clinical benefit of taxane plus platinum agent regimens as adjuvant chemotherapy compared with AP for endometrial cancer patients at high risk of recurrence after surgery. Methods: Endometrial cancer patients having a high risk of recurrence and postoperative residual disease &lt; 2 cm were randomly assigned (1:1:1) with stratification by FIGO stage and histologic grade to receive 6 cycles of doxorubicin (60 mg/m 2 ) plus cisplatin (50 mg/m 2 ) on day 1 (AP), docetaxel (70 mg/m 2 ) plus cisplatin (60 mg/m 2 ) on day 1 (DP) or paclitaxel (180 mg/m 2 ) plus carboplatin (AUC 6.0 mg/mL x minute) on day 1 (TC) every 3 weeks as adjuvant chemotherapy. The primary endpoint was progression-free survival (PFS). Secondary endpoints were overall survival (OS), adverse events, and tolerability. Results: From November 2006 to January 2011, 788 patients were enrolled from 118 institutions in Japan and were eligible for evaluation. The proportion of patients receiving 6 cycles was 80% for AP, 83% for DP, and 76% for TC, and tolerability of the regimens showed no significant difference. After a median follow-up period of 7.0 years, there was no statistical difference of PFS (P=0.1246) or OS (P=0.6734) among the 3 groups. The 5-year PFS rate was 74.9% for AP, 80.9% for DP, and 74.7% for TC, while the 5-year OS rates were 84.3%, 89.3%, and 88.4%, respectively. Conclusions: There was no significant difference of survival among patients receiving AP, DP, or TC as adjuvant chemotherapy for endometrial cancer. Since each regimen showed adequate tolerability, taxane plus platinum agent regimens may be a reasonable alternative to AP. Clinical trial information: UMIN000000522.
Renal Denervation in a Hypertensive Patient With End‐Stage Renal Disease and Small Arteries: A Direction for Future Research (2012)

Sympathetic overactivity plays a crucial pathogenetic role in the maintenance and aggravation of arterial hypertension in patients with end-stage renal disease (ESRD). Renal denervation has been shown to be effective and safe in reducing blood pressure (BP) in patients with treatment-resistant hypertension; however, there are only case reports in hypertensive patients with ESRD and data are lacking about possibility of renal denervation in small renal arteries. A woman with uncontrolled treatment-resistant hypertension on chronic hemodialysis underwent bilateral native kidney, catheter-based renal denervation. Both native renal arteries were <4 mm. After 6 months without any change of antihypertensive medication or hemodialysis parameters, the authors observed a remarkable BP reduction of 38/30 mm Hg (from baseline 172/100 mm Hg to 134/70 mm Hg) as evaluated by 24-hour ambulatory BP monitoring. The authors report that renal denervation seems to be effective in controlling hypertension in patients with ESRD, even in cases of small renal arteries.
Supplementary Figure 2 from Preclinical Activity of the Type II CD20 Antibody GA101 (Obinutuzumab) Compared with Rituximab and Ofatumumab <i>In Vitro</i> and in Xenograft Models (2023)

&lt;p&gt;PDF file - 307K, Whole-blood B-cell depletion mediated by GA101 (black squares), rituximab (open diamonds), and ofatumumab (open triangles) in lepirudin-treated (A, B) and heat-inactivated (HI) (C) whole-blood samples. GA101 mediated superior B-cell depletion in human whole-blood samples in all experimental conditions (A-C). Heat inactivation of human serum revealed that, in contrast to GA101, ofatumumab and rituximab rely more strongly on complement for efficient B-cell depletion (C). The average B-cell depletion and standard deviations were calculated from the triplicates of each experiment.&lt;/p&gt;
Aqueous Humor Dynamics in Ocular Hypertensive Patients (2002)

The increased IOP in ocular hypertensive patients is caused by a reduction in trabecular outflow facility and uveoscleral outflow. Aqueous flow remains normal. When both ocular normotensive and hypertensive groups are combined, aqueous flow and anterior chamber volume decrease slightly with age.
An integrative approach to the facile functional classification of dorsal root ganglion neuronal subclasses (2020)

Somatosensory neurons have historically been classified by a variety of approaches, including structural, anatomical, and genetic markers; electrophysiological properties; pharmacological sensitivities; and more recently, transcriptional profile differentiation. These methodologies, used separately, have yielded inconsistent classification schemes. Here, we describe phenotypic differences in response to pharmacological agents as measured by changes in cytosolic calcium concentration for the rapid classification of neurons in vitro; further analysis with genetic markers, whole-cell recordings, and single-cell transcriptomics validated these findings in a functional context. Using this general approach, which we refer to as tripartite constellation analysis (TCA), we focused on large-diameter dorsal-root ganglion (L-DRG) neurons with myelinated axons. Divergent responses to the K-channel antagonist, κM-conopeptide RIIIJ (RIIIJ), reliably identified six discrete functional cell classes. In two neuronal subclasses (L1 and L2), block with RIIIJ led to an increase in [Ca] <sub><i>i</i></sub> Simultaneous electrophysiology and calcium imaging showed that the RIIIJ-elicited increase in [Ca] <sub><i>i</i></sub> corresponded to different patterns of action potentials (APs), a train of APs in L1 neurons, and sporadic firing in L2 neurons. Genetically labeled mice established that L1 neurons are proprioceptors. The single-cell transcriptomes of L1 and L2 neurons showed that L2 neurons are Aδ-low-threshold mechanoreceptors. RIIIJ effects were replicated by application of the K<sub>v</sub>1.1 selective antagonist, Dendrotoxin-K, in several L-DRG subclasses (L1, L2, L3, and L5), suggesting the presence of functional K<sub>v</sub>1.1/K<sub>v</sub>1.2 heteromeric channels. Using this approach on other neuronal subclasses should ultimately accelerate the comprehensive classification and characterization of individual somatosensory neuronal subclasses within a mixed population.
Caenorhabditis elegans in anthelmintic research – Old model, new perspectives (2020)

For more than four decades, the free-living nematode Caenorhabditis elegans has been extensively used in anthelmintic research. Classic genetic screens and heterologous expression in the C. elegans model enormously contributed to the identification and characterization of molecular targets of all major anthelmintic drug classes. Although these findings provided substantial insights into common anthelmintic mechanisms, a breakthrough in the treatment and control of parasitic nematodes is still not in sight. Instead, we are facing increasing evidence that the enormous diversity within the phylum Nematoda cannot be recapitulated by any single free-living or parasitic species and the development of novel broad-spectrum anthelmintics is not be a simple goal. In the present review, we summarize certain milestones and challenges of the C. elegans model with focus on drug target identification, anthelmintic drug discovery and identification of resistance mechanisms. Furthermore, we present new perspectives and strategies on how current progress in C. elegans research will support future anthelmintic research.
Slotted high-T/sub c/ dc SQUID magnetometers (1999)

Recently, it was observed that the low frequency noise of slotted SQUIDs is not affected when cooling them down in magnetic fields up to 0.05 mT. This behavior is ascribed to the fact that magnetic vortices are expelled out of the narrow strips into the slots. Thus 1/f noise by hopping of vortices in the superconducting structure is eliminated. Here we present a systematic investigation on a series of slotted high-Tc dc SQUIDs. The number of slots varies from zero to eight. A model is developed that provides values for the effective area and inductance of the slotted washers and the current distribution within the slotted SQUIDs. The model can explain the experimentally observed maximum in the effective area for four slots very well. The observed agreement with respect to the modulation depth supports the theoretical values for the inductance. The white noise of the slotted SQUIDs is higher than expected, while the expected rise of low frequency noise for field cooled solid washer SQUIDs was not observed
Radio Resource Management for New Generation Wireless Networks (2010)

In the next future, wireless communication systems will move towards the achievement of high transmission rates for both fixed and mobile users. The main topics of this thesis are the investigation of adaptive radio resource allocation strategies in the presence of a finite number of modulation and coding profiles and the evaluation of their impact on the interference distribution in a multi-user/multi-cellular wireless network based on Orthogonal Frequency Division Multiplexing Access (OFDMA). These kinds of allocation procedures are based on the assumption of having a perfect knowledge of the Channel State Indicator (CSI) and they involve many degrees of freedom (i.e. frequency, time, space, modulation, coding and power). Each allocation algorithm could be based on many different strategies according to the required Quality of Service (QoS), fairness and complexity criteria.
Teach and try: A simple interaction technique for exploratory data modelling by end users (2014)

The modern economy increasingly relies on exploratory data analysis. Much of this is dependent on data scientists - expert statisticians who process data using statistical tools and programming languages. Our goal is to offer some of this analytical power to end-users who have no statistical training through simple interaction techniques and metaphors. We describe a spreadsheet-based interaction technique that can be used to build and apply sophisticated statistical models such as neural networks, decision trees, support vector machines and linear regression. We present the results of an experiment demonstrating that our prototype can be understood and successfully applied by users having no professional training in statistics or computing, and that the experience of interacting with the system leads them to acquire some understanding of the concepts underlying exploratory statistical modelling.
Modeling user behavior and attention in search (2013)

In Web search, query and click log data are easy to collect but they fail to capture user behaviors that do not lead to clicks. As search engines reach the limits inherent in click data and are hungry for more data in a competitive environment, mining cursor movements, hovering, and scrolling becomes important. This dissertation investigates how remotely collecting rich user interaction data in the form of mouse cursor activity can help researchers understand fundamental human behavior and improve the design of search engines. Specifically, mining cursor activity can improve upon state-of-the-art methods for scoring and ranking search results, and estimating where users are looking without eye-tracking. Descriptive analyses of cursor movements show how users move their cursor when they search to provide signals of relevance and explain reasons for abandoning a search. User models can be used to infer visual attention on the page to identify what content users are looking at, as well as compute the relevance and attractiveness of search results to the user. This implicit feedback given to the search engine can then inform the layout and content presented on the pages, or improve the ranking of search results.
This dissertation will demonstrate the following thesis: users' mouse cursor interactions can be collected efficiently on the Web, used to understand users' search behaviors, and can be useful in the design of Web search engines.
C-RAN at Millimeter Wave and Above: Full-Beamspace Radio Access Architecture (2023)

We report progress toward a RF-photonic centralized radio access network (C-RAN) architecture for distributed multi-point transmission over millimeter wave (mmW) spectra. The architecture comprises three components: (1) access points (APs) employing RF-photonic phased arrays capable of multibeam and multiband operation; (2) an RF-photonic beamspace processor unit (BPU) that carries out centralized beamspace processing across multiple APs, and (3) a single-fiber fronthaul capable of full-dimensional beamspace transportation between the BPU and the APs. It is shown that the photonic portion of the AP and the BPU can be extended with minimal alteration to include arrayed waveguide grating (AWG) functionality. The AWG feature allows a direct conversion between RF beams and optical wavelengths at the AP and the BPU, providing a scalable means of transporting the entire beamspace over a fronthaul network employing single-fiber wavelength division multiplexing (WDM).