gebhart/patrepeval huggingface dataset:
Brainmap taxonomy of experimental design: Description and evaluation (2005)

Coordinate-based, voxel-wise meta-analysis is an exciting recent addition to the human functional brain mapping literature. In view of the critical importance of selection criteria for any valid meta-analysis, a taxonomy of experimental design should be an important tool for aiding in the design of rigorous meta-analyses. The coding scheme of experimental designs developed for and implemented within the BrainMap database provides a candidate taxonomy. In this study, the BrainMap experimental-design taxonomy is described and evaluated by comparing taxonomy fields to data-filtering choices made by subject-matter experts carrying out meta-analyses of the functional imaging literature. Fifteen publications reporting a total of 46 voxel-wise meta-analyses were included in this assessment. Collectively these 46 meta-analyses pooled data from 351 publications, selected for experimental similarity within each meta-analysis. Filter implementations within BrainMap were graded by ease-of-use (A-C) and by stage-of-use (1-3). Quality filters and content filters were tabulated separately. Quality filters required for data entry into BrainMap were classed as mandatory (five filters), being above the use grading system. All authors spontaneously adopted the five mandatory filters in constructing their meta-analysis, indicating excellent agreement on data quality among authors and between authors and the BrainMap development team. Two non-mandatory quality filters (group size and imaging modality) were applied by all authors; both were Stage 1, Grade A filters. Field-of-view filters were the least-accessible quality filters (Stage 3, Grade C); two field-of-view filters were applied by six and four authors, respectively. Authors made a total of 115 content-filter choices. Of these, 78 (68%) were Stage 1, Grade A filters; 16 (14%) were Stage 2, Grade A; and 21 (18%) were Stage 2, Grade C. No author-applied filter was absent from the taxonomy.
Six-port-based active source-pull measurement technique (1998)

The proposed active source-pull measurement technique allows the creation of variable source impedances having true unitary complex reflection coefficients (total reflection at any desired phase). Based on the use of a reverse six-port reflectometer, frequency-independent source impedances can be synthesized and the power available from the source can also be calculated. The technique is found to be suitable for multi-tone characterization of microwave devices, for use as mixers or broadband power amplifiers. Experimental validations show that the linear measurement accuracy of the proposed technique is about for the reflection coefficients measurements and dB for the transducer gain evaluation while the accuracy for the nonlinear measurements is and dB.
Mucus production, host-microbiome interactions, hormone sensitivity, and innate immune responses modeled in human cervix chips (2023)

ABSTRACT Modulation of mucus production by the human endo– and ecto-cervical epithelium by steroid hormones and associated interactions with commensal microbiome play a central role in the physiology and pathophysiology of the female reproductive tract. However, most of our knowledge about these interactions is based on results from animal studies or in vitro models that fail to faithfully mimic the mucosal environment of the human cervix. Here we describe microfluidic organ-on-a-chip (Organ Chip) models of the human cervical mucosa that recreate the cervical epithelial-stromal interface with a functional epithelial barrier and produce abundant mucus that has compositional, biophysical, and hormone-responsive properties similar to the living cervix. Application of continuous fluid flow to chips lined with primary human cervical epithelial cells from a commercial source that contained a mixture of primary human ecto– and endo-cervical epithelial cells promoted preferential expression of the ecto-cervical phenotype, whereas use of periodic flow including periods of stasis induced endo-cervical specialization. When the periodic flow Cervix Chips were co-cultured with living Lactobacillus crispatus and Gardnerella vaginalis bacterial communities to respectively mimic the effects of human host interactions with optimal (healthy) or non-optimal (dysbiotic) microbiome associated with an ascending infection in the female reproductive tract, significant differences in tissue innate immune responses, barrier function, cell viability and protein profile, and mucus composition were detected reminiscent of those observed in vivo . Thus, these Organ Chip models of human cervix provide a physiologically relevant experimental in vitro model to study cervical mucus physiology and its role in human host-microbiome interactions as well as a potential preclinical testbed for development of therapeutic interventions to enhance women’s health.
Evaluation of probabilistic occupancy map people detection for surveillance systems (2009)

In this paper, we evaluate the Probabilistic Occupancy Map (POM) pedestrian detection algorithm on the PETS 2009 benchmark dataset. POM is a multi-camera generative detection method, which estimates ground plane occupancy from multiple background subtraction views. Occupancy probabilities are iteratively estimated by fitting a synthetic model of the background subtraction to the binary foreground motion. Furthermore, we test the integration of this algorithm into a larger framework designed for understanding human activities in real environments. We demonstrate accurate detection and localization on the PETS dataset, despite suboptimal calibration and foreground motion segmentation input. 1
Two-Year Evaluation of the X-STOP Interspinous Spacer in Different Primary Patient Populations With Neurogenic Intermittent Claudication Because of Lumbar Spinal Stenosis (2012)

Overall data are consistent with the randomized pivotal Investigational Device Exemption trial. On the basis of the COS cohort which was subject to several additional years of failed conservative treatment, overall success rates do not improve as greatly in patients with long-standing lumbar spinal stenosis symptoms.
Structural characterization of GABARAP–ligand interactions (2009)

The GABA(A) receptor-associated protein (GABARAP) plays an important role in intracellular trafficking of several proteins. It undergoes a C-terminal lipidation process that enables anchoring in the cytosolic leaflet of cellular membranes. While the three-dimensional structure of GABARAP itself has been determined, structural investigation of complexes with its interaction partners has just commenced. Studies with indole derivatives revealed that GABARAP features two hydrophobic binding sites (hp1 and hp2). These also play an essential role in complex formation with the native ligand calreticulin. Furthermore, a model of hexameric N-ethylmaleimide-sensitive factor (NSF) suggests that binding of GABARAP to this molecular machine may involve a similar site. Since hp1 and hp2 are highly conserved throughout the GABARAP family, the relevance of the structural data presented here is likely to extend to GABARAP homologues.
DP2 (CRTh2) Antagonism Reduces Ocular Inflammation Induced by Allergen Challenge and Respiratory Syncytial Virus (2011)

These results suggest that a topical DP2 antagonist such as AM156 may represent a novel therapeutic for allergic conjunctivitis.
The polymerization behavior of [1]- and [2]ferrocenophanes containing silicon atoms in the bridge: comparison of the molecular structure of the strained, polymerizable cyclic ferrocenylsilane Fe(.eta.-C5H4)2(SiMe2) with that of the cyclic ferrocenyldisilane Fe(.eta.-C5H4)2(SiMe2)2 (1993)

The strained cyclic ferrocenylsilane Fe(η-C<sub>5</sub>H<sub>4</sub>)<sub>2</sub>(SiMe<sub>2</sub>) (1), containing a single silicon atom in the bridge, undergoes thermal ring-opening polymerization at 130 °C to yield the high-molecular-weight poly(ferrocenylsilane)[Fe(η-C<sub>5</sub>H<sub>4</sub>)<sub>2</sub>(SiMe<sub>2</sub>)]<sub>n</sub> (2). In contrast, the analogous cyclic ferrocenyldisilane Fe(η-C<sub>5</sub>H<sub>4</sub>)<sub>2</sub>(SiMe<sub>2</sub>)<sub>2</sub> (3), with two silicon atoms in the bridge structure, is resistant to polymerization under the same conditions. In order to probe the reasons for the dramatic difference in polymerization behavior between 1 and 3, the molecular structures of these species have been determined by single-crystal X-ray diffraction. This has allowed the first structural comparison of [1] - and [2]ferrocenophanes with the same bridging atoms (silicon) and substituents (methyl). The cyclic ferrocenylsilane 1 was found to possess a strained, ringtilted structure with an angle between the planes of the cyclopentadienyl rings of 20.8(5)°. In addition, considerable distortion from planarity was detected for the cyclopentadienyl carbon atom bonded to the bridging silicon moiety. In contrast, the cyclic ferrocenyldisilane 3 possesses a much less distorted structure and the corresponding tilt angle between the cyclopentadienyl ligands is only 4.19(2)°. Crystals of 1 are monoclinic, space group P2<sub>1</sub>/a, with a = 7.438(3) Å, b = 10.322(4) Å, c = 15.575(6) Å, β = 99.04(3)°, V = 1180.9(8) Å<sup>3</sup>, and Z = 4. Crystals of 3 are monoclinic, space group P2<sub>1</sub>/n, with a = 10.433(2) Å, b = 8.703(1) Å, c = 17.243(2) Å, β = 107.32(1)°, V = 1494.6(12) Å<sup>3</sup>, and Z = 4.
Colloidal Woodpile Structure:  Three-Dimensional Photonic Crystal with a Dual Periodicity (2006)

With planar photolithography and self-assembly techniques, multilayer colloidal crystals with a woodpile structure were fabricated. They represent a new kind of photonic crystals, that is, three-dimensional (3D) photonic crystals with a dual periodicity; one comes from the face-centered cubic (fcc) structure within the colloidal crystal strips and the other one results from the periodic arrangement of the colloidal crystal strips.
B107 Results of a phase 1 using CCR5 Deficiency with Zinc Finger Nuclease-modified Autologous CD4 T Cells (SB-728-T) in HIV-infected Subjects (2013)

CCR5 is an important co-receptor for HIV entry and zinc finger nuclease (ZFN)-mediated modification of this receptor in CD4 T cells may render a survival advantage in HIV infection. Methods: We conducted a Phase 1 clinical trial at the University of Pennsylvania evaluating the use of genetically modified CD4 T cells with SB-728-T (a CCR5 directed ZFN). Results: 6 immunologic responders (IR) with CD4≥450 were infused with 1010 genetically modified cells. At week 4, all participants underwent a 12-week HAART treatment interruption (TI). In addition 6 immunological non responders (NIR) were also infused. The mean CD4 and SB-728-T count increased by 1533/µL (range 216 to 3025) and 83/µL, respectively, on D7. Increases in CD4 over time correlated with SB-728-T engraftment (= 0.78, p <0.0001). SB-728-T was detected in the gut mucosa of all subjects biopsied (median 6%). During TI, HIV-RNA dropped ∼0.8 to 2.1 log from their peak levels in 3 subjects. In one CCR5 32 heterozygous subject with a viral set point of 165K copies/mL, viral load peaked at 6247 during week 6 of TI and was undetectable by week 12. HIV proviral DNA was evaluated using a new Digital Droplet qPCR method. The levels of HIV proviral DNA returned quickly to baseline levels after the resumption of ART. SB-728-T infusions were well tolerated with only mild reversible infusion-related adverse events. SB-728-T infusion increases CD4 counts that persist over time both in IR and NIR. SB-728-T expands rapidly and home to the gut. In one subject with the highest level of CCR5 modification, viral load was controlled for 12 weeks. Conclusions: These data suggest that in addition to the previously documented increases in CD4 cell, SB-728-T may also suppress HIV replication.
N-[6-Amino-2-(heteroaryl)pyrimidin-4-yl]acetamides as A2A Receptor Antagonists with Improved Drug Like Properties and in Vivo Efficacy (2009)

In the present article, we report on a strategy to improve the physical properties of a series of small molecule human adenosine 2A (hA2A) antagonists. One of the aromatic rings typical of this series of antagonists is replaced with a series of aliphatic groups, with the aim of disrupting crystal packing of the molecule to lower the melting point and in turn to improve the solubility. Herein, we describe the SAR of a new series of water-soluble 2,4,6-trisubstituted pyrimidines where R1 is an aromatic heterocycle, R2 is a short-chain alkyl amide, and the typical R3 aromatic heterocyclic substituent is replaced with an aliphatic amino substituent. This approach significantly enhanced aqueous solubility and lowered the log P of the system to provide molecules without significant hERG or CYP liabilities and robust in vivo efficacy.
Assessing the Predictive Accuracy of QUICKI as a Surrogate Index for Insulin Sensitivity Using a Calibration Model (2005)

The quantitative insulin-sensitivity check index (QUICKI) has an excellent linear correlation with the glucose clamp index of insulin sensitivity (SI(Clamp)) that is better than that of many other surrogate indexes. However, correlation between a surrogate and reference standard may improve as variability between subjects in a cohort increases (i.e., with an increased range of values). Correlation may be excellent even when prediction of reference values by the surrogate is poor. Thus, it is important to evaluate the ability of QUICKI to accurately predict insulin sensitivity as determined by the reference glucose clamp method. In the present study, we used a calibration model to compare the ability of QUICKI and other simple surrogates to predict SI(Clamp). Predictive accuracy was evaluated by both root mean squared error of prediction as well as a more robust leave-one-out cross-validation-type root mean squared error of prediction (CVPE). Based on data from 116 glucose clamps obtained from nonobese, obese, type 2 diabetic, and hypertensive subjects, we found that QUICKI and log (homeostasis model assessment [HOMA]) were both excellent at predicting SI(Clamp) (CVPE = 1.45 and 1.51, respectively) and significantly better than HOMA, 1/HOMA, and fasting insulin (CVPE = 3.17, P < 0.001; 1.67, P < 0.02; and 2.85, P < 0.001, respectively). QUICKI and log(HOMA) also had the narrowest distribution of residuals (measured SI(Clamp) - predicted SI(Clamp)). In a subset of subjects (n = 78) who also underwent a frequently sampled intravenous glucose tolerance test with minimal model analysis, QUICKI was significantly better than the minimal model index of insulin sensitivity (SI(MM)) at predicting SI(Clamp) (CVPE = 1.54 vs. 1.98, P = 0.001). We conclude that QUICKI and log(HOMA) are among the most accurate surrogate indexes for determining insulin sensitivity in humans.
Monitoring the Uptake of Glycosphingolipids In Plasmodium falciparum-Infected Erythrocytes Using Both Fluorescence Microscopy and Capillary Electrophoresis with Laser-Induced Fluorescence Detection (2010)

The metabolism of glycosphingolipids by the malaria-causing parasite Plasmodium falciparum plays an important role in the progression of the disease. We report a new and highly sensitive method to monitor the uptake of glycosphingolipids in infected red blood cells (iRBCs). A tetramethylrhodamine-labeled glycosphingolipid (GM1-TMR) was used as a substrate. Uptake was demonstrated by fluorescence microscopy. The iRBCs were lysed with a 15% solution of saponin and washed with phosphate buffered saline to release intact parasites. The parasites were further lysed and the resulting homogenates were analyzed by capillary electrophoresis with laser-induced fluorescence detection. The lysate from erythrocytes infected at 1% parasitemia generated a signal 20 standard deviations larger than uninfected erythrocytes, which suggests that relatively low infection levels can be studied with this technique.
Differential and Synergistic Effects of Epidermal Growth Factor Receptor Antibodies on Unliganded ErbB Dimers and Oligomers (2011)

Antibodies directed against the epidermal growth factor receptor (EGFR) offer a potentially powerful therapeutic approach against cancers driven by the EGFR pathway. EGFR antibodies are believed to halt cell surface activation by blocking ligand-induced receptor tyrosine kinase activation, i.e., ligand binding, a change in conformation, or the monomer-dimer transition. In this work, we demonstrate that wild-type EGFR and the truncated de2-7-EGFR (tumor-associated mutant) formed unliganded homo-oligomers and examined the effects of two clinically relevant antibodies on the conformation and quaternary state of these ligand-free EGFR oligomers on the surface of cells. The EGFR antibodies were mAb528, a ligand-blocking antibody that binds domain III, and mAb806, a conformationally sensitive antibody that binds near the dimer interface in domain II. We used a model cellular system, BaF/3 cells, with GFP-tagged receptors in the absence of interference from secreted ligands or other erbB receptor members. Different antibody-mediated effects (conformational transition, receptor cross-linking, or receptor dissociation) were distinguished by combining two complementary biophysical techniques: image correlation spectroscopy (submicrometer scale clustering) and homo-Forster resonance energy transfer (association and/or conformation on a 1-10 nm scale). mAb528 cross-linked EGFR into an inactive EGFR dimer of dimers but had no effect when added to de2-7-EGFR oligomers. mAb806 had a minor effect on EGFR dimers as expected from its poor binding to a conformationally shielded epitope on wtEGFR but bound de2-7-EGFR oligomers, causing a conformational change in the intracellular C-terminal GFP-tagged tail. The combination of the two antibodies had synergistic effects, increasing the level of cross-linking of de2-7-EGFR, but did not lead to enhanced cross-linking of EGFR. The results reveal new modes of receptor-antibody interactions for EGFR and de2-7-EGFR.
EXPERIMENTAL CHARACTERIZATION OF A DOUBLE BACK TO BACK PULSATING HEAT PIPE FOR POWER ELECTRONICS (2015)

Experimental characterization of a 104-turn pulsating heat pipe (PHP) cooler using R245fa and based on the automotive heat exchanger technology for power electronics thermal management is presented. The effects of fluid filling ratio, orientation, and heat load up to 5.75 kW per PHP were investigated. Thermal resistances as low as 8.5 K/kW were measured at 2000 m3/h air flow. However, a thermal resistance increase of 19% and 25% was measured in horizontal and inverted orientations, respectively. Periodic pressure peaks were measured, but with different amplitudes depending on the orientation. The condenser was found to be subcooled at all fillings and all orientations while the evaporator was very close to the saturation temperature. There was superheating measured at the evaporator manifold only at very low fluid fillings. There was a minimum in thermal resistance located between 40% and 50% fluid filling, for all orientations and heat loads tested. The maximal thermal resistance depended very little on the heat load. For a given set of operating conditions, a high frequency combined with low amplitude pressure peaks yielded better cooling performances.
Filamentous Phage Display in the New Millennium (2006)

Abstract For Abstract see ChemInform Abstract in Full Text.
Complement Analysis in Adult Patients with a History of Bacteremic Pneumococcal Infections or Recurrent Pneumonia (1995)

Complement deficiencies are known to be associated with increased susceptibility to bacterial infections. In the present study we investigated 80 patients with either a history of pneumococcal bacteremic infection, or recurrent pneumonia, or both. Hemolytic screening tests for complement deficiency were performed and serum concentrations of C1q, C1s, C2, C3, C4, C4 isotypes, factor B, factor D, and properdin were determined. Complete deficiencies of single complement proteins were not found. 10 patients (12%) had a C4 isotype deficiency, but the frequency of homozygous C4A and C4B deficiency was not significantly increased. Seven patients (9%) had hypocomplementemia with low concentrations of at least 2 complement proteins. One of these patients had profound depletion of classical pathway components and findings suggesting acquired C1 esterase inhibitor deficiency. 16 patients (20%) had minor complement aberrations. A majority of the patients with hypocomplementemia suffered from other conditions associated with pneumococcal infections. However, impaired complement function could be a significant predisposing factor in some patients with invasive pneumococcal infections or recurrent pneumonia.
InP nanowire lasers epitaxially grown on (001) silicon &#x2018;V-groove&#x2019; templates (2014)

We demonstrate an ultra-low threshold nanowire laser monolithically integrated on a (001) silicon substrate. By using a V-groove template we were able to reduce the laser threshold by one order of magnitude (0.19pJ per pulse) compared with our earlier devices and dramatically increased the yield throughout the wafer.
Recurrent Late-Onset Sepsis in Extremely Low Birth Weight Infants Is Associated with Motor Deficits in Early School Age (2022)

Recurrent sepsis in preterm infants is associated with adverse long-term motor development. However, infants with recurrent infections are also more likely to have preterm-related complications, and reasons for a worse neurodevelopmental outcome remain to be elucidated.
Thermal Gait Dataset for Deep Learning-Oriented Gait Recognition (2023)

This study attempted to construct a thermal dataset of human gait in diverse environments suitable for building and evaluating sophisticated deep learning models (e.g., vision transformers) for gait recognition. Gait is a behavioral biometric to identify a person and requires no cooperation from the person, making it suitable for security and surveillance applications. For security purposes, it is desirable to be able to recognize a person in darkness or other inadequate lighting conditions, in which thermal imagery is advantageous over visible light imagery. Despite the importance of such nighttime person identification, available thermal gait datasets captured in the dark are scarce. This study, therefore, collected a relatively large set of thermal gait data in both indoor and outdoor environments with several walking styles, e.g., walking normally, walking while carrying a bag, and walking fast. This dataset was utilized in multiple gait recognition tasks, such as gender classification and person verification, using legacy convolutional neural networks (CNNs) and modern vision transformers (ViTs). Experiments using this dataset revealed the effective training method for person ver-ification, the effectiveness of ViT on gait recognition, and the robustness of the models against the difference in walking styles; it suggests that the developed dataset enables various studies on gait recognition using state-of-the-art deep learning models.