gebhart/patrepeval huggingface dataset:
Exploiting Spherical Projections To Generate Human-Like Wrist Pointing Movements (2021)

The mechanism behind the generation of human movements is of great interest in many fields (e.g. robotics and neuroscience) to improve therapies and technologies. Optimal Feedback Control (OFC) and Passive Motion Paradigm (PMP) are currently two leading theories capable of effectively producing human-like motions, but they require solving nonlinear inverse problems to find a solution. The main benefit of using PMP is the possibility of generating path-independent movements consistent with the stereotypical behaviour observed in humans, while the equivalent OFC formulation is path-dependent. Our results demonstrate how the path-independent behaviour observed for the wrist pointing task can be explained by spherical projections of the planar tasks. The combination of the projections with the fractal impedance controller eliminates the nonlinear inverse problem, which reduces the computational cost compared to previous methodologies. The motion exploits a recently proposed PMP architecture that replaces the nonlinear inverse optimisation with a nonlinear anisotropic stiffness impedance profile generated by the Fractal Impedance Controller, reducing the computational cost and not requiring a task-dependent optimisation.
The Music Retrieval System Based on the Frequently-Used Rules of Chinese Text (2014)

The conventional music retrieval system is mostly based on accurate matching of keywords, and it is difficult to satisfy the demand of intelligent retrieval. This paper presents a system of music retrieval based on the frequently-used rules of Chinese text. The system not only retains the conventional retrieval, but also is added the frequently-used rules of Chinese text that is “the attribute of the entity” (such as “the singer of the song”) into it. Firstly, the system segments the words of user’s query requests and checks that whether the user’s inputs comply with the rule of “the attribute of the entity”, and then it decides to adopt what kind of retrieval that is retrieval of text rules or conventional retrieval. The experiment proves that the system is better to satisfy the demand of user’s query requests than conventional music retrieval system while coping with the text rule of “the attribute of the entity”.
Determination of optimal dose and treatment schedule of the immunotherapeutic vaccine, DPX-Survivac, for combination immunotherapy treatment of ovarian, fallopian tube or peritoneal cancer (OC): A phase Ib study. (2016)

e14577 Background: Survivin is an important protein that regulates apoptosis, proliferation, and angiogenesis of tumors. Increased expression of survivin in various tumors correlates with progression and drug resistance. DPX-Survivac vaccine contains a mix of survivin HLA class I peptides contained in a novel formulation designed to evoke a cytotoxic T cell response against survivin. A phase 1 study (Berinstein et al, Oncoimmunology, 2015) has demonstrated the immunogenicity of DPX-Survivac in combination with metronomic low dose oral cyclophosphamide (mCPA). This study was designed to explore additional dosing schedules that maintain immunogenicity while limiting local injection site reactions in OC. Methods: Stage IIc-IV OC patients with a complete or partial response after first (adjuvant) or second line chemotherapy and with minimal disease were enrolled. Various vaccination schedules as well as boosting without the oil component of DPX-Survivac were tested. Adverse events and dose limiting toxicities were defined by CTCAE v4.03. Vaccine-induced T cell immunity (ELISpot; tetramer analysis) was assessed in purified PBMC. Clinical response was assessed by CT and CA125 using standard RECIST criteria. Results: 36 patients have been treated with different doses and schedules DPX-Survivac vaccination together with mCPA. Several modifications of the dose and schedule resulted in sustained immune responses of varying magnitude and duration. DPX-Survivac was well tolerated. Conclusions: DPX-Survivac in combination with mCPA results in sustained immune responses. This study will allow us to balance the immune response and site of injection profile for different indications including early prevention of recurrence or treatment of small volume active disease. Clinical trial information: NCT01416038.Cohort Pts (n) Priming DPX Boost DPX/Aq Skin ul ceration Grade (n) Immune ELISpot Re sponse 256 to >4000 SFU/ 106 PBMC n (%) Dose (mL) n Freq wks Vol (mL) n Freq wks 1 6 0.25 2 3 0.1 DPX 4 8 2 (2), 3 (1) 6 (100) 2 9 0.25 2 3 0.1 DPX 4 8 3 (1) 4 (44) 3 6 0.25 3 8 N/A 0 0 1 (1) 5 (83) 4 7 0.25 2 6 0.25 DPX 3 6 TBD TBD 5 8 0.25 2 4 0.5 Aq 4 4 TBD TBD
Mitochondrial deficits in human iPSC-derived neurons from patients with 22q11.2 deletion syndrome and schizophrenia (2019)

Schizophrenia (SZ) is a highly heterogeneous disorder in both its symptoms and risk factors. One of the most prevalent genetic risk factors for SZ is the hemizygous microdeletion at chromosome 22q11.2 (22q11DS) that confers a 25-fold increased risk. Six of the genes directly disrupted in 22qDS encode for mitochondrial-localizing proteins. Here, we test the hypothesis that stem cell-derived neurons from subjects with the 22q11DS and SZ have mitochondrial deficits relative to typically developing controls. Human iPSCs from four lines of affected subjects and five lines of controls were differentiated into forebrain-like excitatory neurons. In the patient group, we find significant reductions of ATP levels that appear to be secondary to reduced activity in oxidative phosphorylation complexes I and IV. Protein products of mitochondrial-encoded genes are also reduced. As one of the genes deleted in the 22q11.2 region is MRPL40, a component of the mitochondrial ribosome, we generated a heterozygous mutation of MRPL40 in a healthy control iPSC line. Relative to its isogenic control, this line shows similar deficits in mitochondrial DNA-encoded proteins, ATP level, and complex I and IV activity. These results suggest that in the 22q11DS MRPL40 heterozygosity leads to reduced mitochondria ATP production secondary to altered mitochondrial protein levels. Such defects could have profound effects on neuronal function in vivo.
3D/2D Registration of medical images (2008)

The topic of this doctoral dissertation is registration of 3D medical images to corresponding projective 2D images, referred to as 3D/2D registration. There are numerous possible applications of 3D/2D registration in image-aided diagnosis and treatment. In most of the applications, 3D/2D registration provides the location and orientation of the structures in a preoperative 3D CT or MR image with respect to intraoperative 2D X-ray images. The proposed doctoral dissertation tries to find original solutions for the problem of multi-dimensional 3D/2D medical image registration by proposing three different 3D/2D registration methods. The dissertation also addresses the important problems of validation and comparison of different 3D/2D registration methods. The thesis describes the construction of two different “gold standard” image data sets and the corresponding evaluation methodology for the purpose of evaluation and comparison of proposed 3D/2D registration methods. The experimental results show that the three proposed registration methods are able to register a 3D image to two or more 2D images with accuracy that is sufficient for most orthopedic procedures. The proposed 3D/2D registration methods mostly differ in dependence of registration reliability on the initial registration provided by the user.
Combined transbronchial needle aspiration and positron emission tomography for mediastinal staging of NSCLC (2006)

There are no data available combining transbronchial needle aspiration (TBNA) of mediastinal lymph nodes and positron emission tomography (PET) in the staging of nonsmall cell lung cancer (NSCLC). The aim of the current study was to determine if these two methods can enhance the negative predictive value of the individual modality alone, for a specific lymph node station, and if this integrated approach can reduce the number of mediastinoscopies. A total of 113 patients with enlarged mediastinal lymph nodes (> or = 1 cm), who underwent both TBNA and PET scanning, were included. In 51 patients, histopathology, confirmed by surgical lymph node dissection, was compared with PET results and TBNA. Sensitivity, specificity, positive predictive value, negative predictive value and accuracy to detect malignant lymphadenopathy was 68 (13/19), 89 (119/134), 46 (13/28), 95 (119/125) and 86% (132/152) for PET, respectively; 54% (6/11), 100 (53/53), 100 (6/6), 91 (53/58) and 92% (59/64), respectively for TBNA; and 100 (11/11), 94 (50/53), 79 (11/14), 100 (50/50) and 95 (61/64) for combined TBNA and PET, respectively. Combination of transbronchial needle aspiration and positron emission tomography has the potential to allow adequate mediastinal staging of nonsmall cell lung cancer with enlarged lymph nodes in most patients without the need for mediastinoscopy.
Discovery of Type II (Covalent) Inactivation of S-Adenosyl-l-homocysteine Hydrolase Involving Its “Hydrolytic Activity”:  Synthesis and Evaluation of Dihalohomovinyl Nucleoside Analogues Derived from Adenosine (1998)

Treatment of the 5'-carboxaldehyde derived by Moffatt oxidation of 6-N-benzoyl-2',3'-O-isopropylideneadenosine (1) with the "(bromofluoromethylene)triphenylphosphorane" reagent and deprotection gave 9-(6-bromo-5, 6-dideoxy-6-fluoro-beta-d-ribo-hex-5-enofuranosyl)adenine (4). Parallel treatment with a "dibromomethylene Wittig reagent" and deprotection gave 9-(6,6-dibromo-5, 6-dideoxy-beta-d-ribo-hex-5-enofuranosyl)adenine (7), which also was prepared by successive bromination and dehydrobromination of the 6'-bromohomovinyl nucleoside 8. Bromination-dehydrobromination of the 5'-bromohomovinyl analogue 11 and deprotection gave (E)-9-(5, 6-dibromo-5,6-dideoxy-beta-d-ribo-hex-5-enofuranosyl)adenine (15). Compounds 4, 7, and 15 were designed as putative substrates of the "hydrolytic activity" of S-adenosyl-l-homocysteine (AdoHcy) hydrolase. Enzyme-mediated addition of water across the 5,6-double bond could generate electrophilic acyl halide or alpha-halo ketone species that could undergo nucleophilic attack by proximal groups on the enzyme. Such type II (covalent) mechanism-based inactivation is supported by protein labeling with 8-[3H]-4 and concomitant release of bromide and fluoride ions. Incubation of AdoHcy hydrolase with 7 or 15 resulted in irreversible inactivation and release of bromide ion. In contrast with type I mechanism-based inactivation, reduction of enzyme-bound NAD+ to NADH was not observed. Compounds 4, 7, and 15 were not inhibitory to a variety of viruses in cell culture, and weak cytotoxicity was observed only for CEM cells.
Osteoporotic Compression Fractures: Outcomes after Single- versus Multiple-Level Percutaneous Vertebroplasty (2006)

PV performed at a single fracture level and that performed at multiple fracture levels were equally effective in facilitating long-term pain relief, increased activity level, and decreased analgesic use in patients with osteoporotic VCFs.
Assessment of Sleep and Mood Symptoms in Patients with Undetected Obstructive Sleep Apnea and Atrial Fibrillation (2018)

Introduction: Obstructive sleep apnea (OSA) is associated with serious cardiovascular consequences. We aimed to determine: • The percentage of patients in arrhythmia clinics who show symptoms suggestive of insomnia, non-refreshing sleep, excessive daytime sleepiness, fatigue, decreased alertness, and/or depression; • If these symptoms predict the severity or the presence of OSA in these patients. Methods: Non-selected consecutive patients were recruited from outpatient arrhythmia clinics. Patients with previously diagnosed and/or treated OSA were excluded. Validated screening tools were administered. Patients underwent ambulatory sleep testing for the diagnosis of OSA. Correlation and regression analyses were performed to detect the predictors of OSA. Results: 100 participants with atrial fibrillation were recruited (72% Males). The mean age was 64 ± 13 years. Sleep related instruments showed that: • Thirty-seven percent of patients have scores suggestive of excessive daytime sleepiness; • Fifty-four percent have excessive daytime fatigue; • Symptoms of non-restorative sleep are present in 57%; • Twenty-five percent have scores suggestive of depression; • Thirty-eight percent have mild insomnia, 14% moderate insomnia, and 5% severe insomnia; • Six percent show scores suggestive of decreased alertness. Eighty-five percent of patients had previously undetected OSA. Only age and male gender were predictors of OSA (p=0.009, p=0.008 respectively). Conclusion: Eighty-five percent of patients with atrial fibrillation have undetected OSA. Scores suggestive of daytime sleepiness, fatigue, insomnia, depression, and non-refreshing sleep do not predict OSA. Sleep studies may be applied routinely for detection of OSA in these patients.
Development of gradient-based surface methods (2007)

This work is a detailed study concerning the development and investigation of surface electric field gradients to spatially control the magnitude and locale of electrochemical reactions on surfaces. It will be illustrated that the use of surface potential gradients enables the simultaneous driving of both oxidation and reduction reactions on the same electrode surface. We anticipate that these features will have broad impact over a wide range of applications including microscale devices, sensors, analytical testing devices, and biological applications requiring spatial control of electrochemical phenomena. One example which will be presented in this work of such an application is the development of a spatially controllable pH gradient within a microfluidic channel for isoelectric focusing. Spatial control will also be demonstrated for the local control of adsorbates. In particular, surface potential gradients are used for the maskless patterning of polymers for corrosion protection and sensor applications. Further exploration will delve into the spatial control of metal supported phospholipids, a model system for biological membranes. One final application of surface electric fields will consist of the spatial control of metal electrodeposition and spatiotemporal control of passivating metal oxide film growth, important in studies of catalysis. A separate project will also be discussed concerning the fabrication of low precious metal content monolayer coated nanoscale catalysts for applications in fuel cells. This project utilizes recently developed redox replacement reactions to reduce the amount of catalytic platinum used to only a single monolayer.
Multiple Penicillin Binding Protein Profiles in Penicillin Resistant Pneumococci: Evidence for the Clonal Nature of Resistance Among Clinical Isolates (1989)

Previous studies have shown that penicillin resistance in pneumococci is a multigenic property that involves the accumulation of chromosomal mutations in the structural genes of penicillin binding proteins (PBPs), resulting in the greatly decreased reactivity of these proteins for betalactam antibiotics. We examined the patterns and affinities of PBPs in 160 clinical isolates representing a wide range of MICs (from 0.005–16 μg/ml), serotypes, isolation dates and sites. The vast majority of penicillin-susceptible isolates showed a common, predictable pattern of five PBPs with high affinities for benzylpenicillin in the relative order of 3 > 1A > 2A > IB > 2B. In contrast, the PBP profiles became variable in strains for which MICs were > 0.1 jug/ml and PBPs 1 A, 2A and 2B of these strains showed decreased penicillin affinity parallel to the increasing levels of antibiotic resistance. While resistant strains exhibited a variety of distinct PBP profiles, these were stable for each particular strain and it is suggested that clinical isolates sharing a common PBP profile may represent the progeny of a distinct mutant clone. Penicillin-resistant clinical isolates and genetic transformants showed profoundly altered cell wall stem peptides. Our data suggest that the decreased penicillin affinity of mutationally altered PBPs results in such a distortion of the active sites that these PBPs also become altered in their reactivity toward their normal natural substrates. Successful expression of high level penicillin resistance in pneumococci may require the acquisition of auxiliary mutation(s) that assure a sufficient supply of the chemically unusual wall precursors needed for the synthesis of the cell wall in penicillin-resistant pneumococci.
Precise Targeting of Liver Tumor Using Glycol Chitosan Nanoparticles: Mechanisms, Key Factors, and Their Implications (2016)

Herein, we elucidated the mechanisms and key factors for the tumor-targeting ability of nanoparticles that presented high targeting efficiency for liver tumor. We used several different nanoparticles with sizes of 200-300 nm, including liposome nanoparticles (LNPs), polystyrene nanoparticles (PNPs) and glycol chitosan-5β-cholanic acid nanoparticles (CNPs). Their sizes are suitable for the enhanced permeation and retention (EPR) effect in literature. Different in vitro characteristics, such as the particle structure, stability, and bioinertness, were carefully analyzed with and without serum proteins. Also, pH-dependent tumor cell uptakes of nanoparticles were studied using fluorescence microscopy. Importantly, CNPs had sufficient stability and bioinertness to maintain their nanoparticle structure in the bloodstream, and they also presented prolonged circulation time in the body (blood circulation half-life T<sub>1/2</sub> = about 12.2 h), compared to the control nanoparticles. Finally, employing liver tumor bearing mice, we also observed that CNPs had excellent liver tumor targeting ability in vivo, while LNPs and PNPs demonstrated lower tumor-targeting efficiency due to the nonspecific accumulation in normal liver tissue. Liver tumor models were produced by laparotomy and direct injection of HT29 tumor cells into the left lobe of the liver of athymic nude mice. This study provides valuable information concerning the key factors for the tumor-targeting ability of nanoparticles such as stability, bioinertness, and rapid cellular uptake at targeted tumor tissues.
Rock Physics Constrained Estimation of Shale Anisotropy for Microseismic Processing - From VTI to ORThorhombic (2015)

Summary Shale intrinsically exhibits transverse isotropy because of the alignment and lamination of softer and platy clay mineral and organics. The presence of preferred-aligned fractures usually cause azimuthal anisotropy. If the fractures in shale are orthogonal to fabric alignment, the intrinsic transverse isotropy and additional fracture-induced azimuthal anisotropy combine to form an equivalent orthorhombic model. Rock physics studies provide useful constraints for such orthorhombic velocity model. The fabric anisotropy of shale strongly depends on compliant and platy components of shale, e.g. clay and kerogen, but can be weakened by stiffer and non-platy minerals, e.g. quartz. We use these relationships constrain the optimization of fabric anisotropy of Horn River shales. The optimized VTI model not only improves the time misfit and locations of microseismic events, but is explicable geologicaly and physically. Schoenberg’s theory give us a simple and effective way of including the effect of fractures. Fracture-induced anisotropy is expressed in terms of normal and tangential fracture compliance. Theoretical modeling and measurements show that fracture compliances increase with fracture size and normal to tangential fracture compliances ratio ZN/ZT is less than or slightly larger than 1. The optimized ZN and ZT is consistent with other measurements in crosshole and microseismic scale.
Studies on the synthesis of lopamidol (2011)

S-2-Acetoxypropionyl chloride was synthesized from L-lactic acid in two steps with a yield of 55%. 5-Amino-2,4,6-triiodo-1,3-phthalic acid was converted to the acid chloride and was then coupled with S-2-acetoxypropionyl chloride to give 5-[(2S)-2-acetoxypropionylamino]-2,4,6-triiodo-1,3-phthaloylchloride.Further reaction with 2-amino-1,3-propanediol afforded N,N'-bis[2-hydroxy-(1-hydroxymethyl)ethyl]-5-[(2S)-(2-acetoxypropionamido)] -2,4,6-triiodo-1,3-phthalamide.Hydrolysis to remove the acetyl group yielded Iopamidol with an overall yield of 50%for four steps.
The Reaction of Water with Iron‐ and Rutheniuncarbonyl Complexes of Polyolefins: 1,2‐ and 1,4‐hydrogenation of 1,3‐dienes. hydrogenolysis of allylic ethereal bonds and deoxygenation of 7‐oxabicyclo[2.2.1]hept‐2‐enes (1988)

Abstract Under basic conditions, H 2 O reacts with tricarbonyl[(1 R ,2 R ,3 S ,4 S ,5 R ,6 S )‐ C ,5,6, C ‐η‐(2‐ exo ,3‐ exo ‐bis‐(chloromethyl)‐5,6‐dimethylidene‐7‐oxabicyclo[2.2.1]heptane)]iron) (1) , and ‐ruthenium (4), with tricarbonyl‐[(1 R ,2 R ,3 S ,4 S )‐ C ,2,3,C‐η‐(2,3,5,6‐teramethylidene)‐7‐oxabicyclo[2.2.1]heptane)]iron (6) and ‐ruthenium (7) , and with cis ‐η‐[1 S ,2 S ,3 R ,4 S ,5 S ,6 R )‐ C ,2,3,C‐η : C‐η‐(2,3,5,6‐tetramethylidene‐7‐oxabicyclo)[2.2.1]heptane)bis‐(tricarbonyliron) (11) ] to give products of demetallation and 1,2‐ or/and 1,4‐hydrogenation. Reductive demetallation of tricarbonyl[ C ,5,6, C ‐η‐(1‐(dimethoxymethyl)‐5,6‐dimethylidenecylohexa‐1,3‐diene]iron (14) required heating under acidic conditions, giving 2,3‐dimethylbenzaldehyde (16) . H 2 O reacted under neutral conditions with cis ‐heptacarbonyl‐μ‐[(1 RS ,2 SR ,3 RS ,4 SR ,5 RS ,6 SR )‐2,3‐η : C ,5,6, C ‐η‐(1‐(dimethyoxymethyl)‐5,6,‐(dimethylidene‐7‐oxabicyclo[2.2.1]hept‐2‐ene]diiron (17) and with tricaboyl[(1 RS ,2 SR ,3 RS ,4 SR ,5 RS ,6 SR )‐C‐η5,6,C‐η‐(1‐(dimethyoxymethyl)‐5,6‐dimethyldidene‐7‐oxabicyclo[2.2.1]hept‐2‐ene)]iron (18) to give the orthoquinodimethane complex 14 as major product. This reaction was accompanied by hydrogenolysis of the allylic ethereal C(4)O(7) bond in 17 and 18 and gave tricarbonyl[(1 RS ,5 RS ,6 SR )‐ C ,5,6,C‐η‐(1‐(dimethoxymethyl)‐5,6‐dimethylidenecylohex‐2‐en‐1‐ol)]iron (21) as minor product. The latter was not an intermediated of reaction 17 → 14. Reactions with D 2 O allowed one to discuss the possible mechanism of this deoxygenation process. With Trans ‐heptacarbonyl‐μ‐[(1 RS ,2 SR ,3 RS ,4 SR ,5 RS ,6 SR )‐2,3‐η : C ,5,6,C‐η‐(1‐(dimethoxymethyl‐5,6‐dimethylidene‐7‐oxabicyclo[2.2.1]‐hept‐2‐ene)diiron (38) ], the reaction with THF/H 2 O gave 14 nearly quantitatively, with no D‐incorporation in the presence of D 2 O.