gebhart/patrepeval huggingface dataset:
Highly Potent Vitamin D Receptor Antagonists: Design, Synthesis, and Biological Evaluation (2006)

Vitamin D receptor (VDR) antagonists have attracted significant levels of interest because of their potential utility in the treatment of Paget's disease, which is known as the most flagrant example of disordered bone remodeling and the second most common bone disease after osteoporosis in Anglo-Saxons. Recent studies on Paget's disease suggested a specific increase in osteoclasts' sensitivity to the differentiation activity of active vitamin D(3) as the principal mechanism for abnormal bone formation. We set out to conduct a structure-activity relationship study on the first VDR antagonists, TEI-9647 and TEI-9648 (25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone), with the goal of improved VDR antagonistic activity. Given that both potent agonists and antagonists must have high affinity for the VDR, we hoped that our accumulated knowledge in the field of VDR agonists would help us identify potent antagonists. First 2alpha-modified TEI-9647 analogues were synthesized, and then 24-substitution to stabilize the lactone structure under physiological conditions was investigated. Finally, 2alpha-modified 24-methyl-, 24,24-dimethyl-, and 24,24-ethano-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone analogues were synthesized. The synthesis of the 24,24-ethano-TEI lactone was accomplished through Ru-catalyzed intermolecular enyne metathesis of the alkynone CD-ring side chain with ethylene to give a dienone, followed by regioselective cyclopropanation. It was found that 2alpha,24,24-trimethyl-TEI-9647 (39) possessed an antagonistic activity (IC(50)=0.093 nM) approximately 90 times that of the original TEI-9647 (IC(50)=8.3 nM).
Cryogen spray cooling efficiency: Improvement of port wine stain laser therapy through multiple‐intermittent cryogen spurts and laser pulses (2002)

The new proposed definition allows to compute the cooling efficiency of CSC nozzle devices. Computer models have been developed and used to show that the SCS-SLP approach will not provide adequate epidermal protection for darker skin patients (skin types V-VI), even for eta = 100%. In contrast, the MCS-MLP approach may be a viable solution to improve PWS laser therapy for darker skin patients.
Supplementary Figure 3 from T Lymphocytes Redirected against the Chondroitin Sulfate Proteoglycan-4 Control the Growth of Multiple Solid Tumors both <i>In Vitro</i> and <i>In Vivo</i> (2023)

&lt;p&gt;PDF file - 179K, CSPG4 mRNA expression levels in normal tissues. Top panel, CSPG4 expression across normal human tissues represented in the Novartis GeneAtlas dataset (http://biogps.org). Values represented are relative and the average of Affymetrix probe sets 214297_at and 204736_s_at. Highlighted are normal tissues for which corresponding normal adjacent tissue data were available in TCGA datasets. Bottom panel, CSPG4 mRNA expression by TCGA in a variety of solid tumors (featured in main Figure 1D) and normal adjacent tissues (the normal tissues being also represented in GeneAtlas), with the cancers showing higher CSPG4 levels over that of the normal samples. Note shown is log2 scale.&lt;/p&gt;
STUDIES ON THE STRESS AND DEFORMATION OF SHORING MEMBERS DURING EXCAVATION : A Proposition of Calculation Method on Temporaly Earth Supports (1975)

This report deals with the shoring design for excavation. In the customary design of shrut-shorting, struts, which bear the whole load, are assumedly never dislocated and no consideration is given to the work sequence of excavation. In the strut design it is examined whether the axial force exceeds the allowable unit stress of member. However, shoring is designed to prevent soil and structures around the excavated site from moving towards the site. Therefore, the deformation as well as the strength of shoring members should be examined. It requires many assumptions and is rather difficult to calculate the deformation of shoring and the displacement of soil and near-by structures. Measured values of the strut axial force and the bending moment of the shoring walls during excavation are shown in Fig. 4.1. They show that the strut axial force remains constant or decreases somewhat with the progress of excavation. The modified dividing method shown in Fig. 3.8 is based on this performance. This report gives a calculation method of shoring in which the excavation sequence and above-mentioned bending moment change of shoring walls are taken into consideration. According to the new method shown in Fig. 3.3 and Fig. 3.4, basically, not only the unit stress of shoring members but also their strain should be examined. Because the soil pressure distribution and shoring model are considerably simplified, the unit stress of shoring members are easily determined. Measured valves and calculated values of shoring wall deformation and bendingmoment are shown in Fig. 4.1 and Fig. 4.2, and both values are highly consistent each other.
Supplementary Table 6 from FGFR1/3 Tyrosine Kinase Fusions Define a Unique Molecular Subtype of Non–Small Cell Lung Cancer (2023)

&lt;p&gt;PDF file - 77KB, Clinicopathologic Characteristics of 734 Patients with NSCLC in Survival analysis.&lt;/p&gt;
OC.08.4 ENTEROGLIAL CELLS–BACTERIA INTERACTION MODULATES INTESTINAL EPITHELIAL CELLS DIFFERENTIATION (2014)

Background and aim: Human enteroglial cells (EGCs) express TLRs and are able to recognize healthy and harmful bacteria and to interact with intestinal epithelial cells. The putative effects of mediators released by EGCs on the surrounding cells have not been fully investigated. We aimed to evaluate the effect of soluble factors released by EGCs, upon probiotic and pathogenic bacteria stimulation, on intestinal epithelial cells viability, proliferation and differentiation. Material and methods: Human EGCs were exposed to probiotic (Lactobacillus Paracasei F19, 108 bacteria/mL) and pathogenic (Enteroinvasive Escherichia Coli, 108 bacteria/mL) bacteria. After a 24 h incubation, conditioned media (CM) from these cultures were used to challange CaCo2 cells cultured to confluence. CaCo2 viability, proliferation and differentiation state after 24 h were respectively studied by MTT vitality test, BrdU test and lactase enzyme activity test, respectively. CaCo2 cells with medium alone were used as control. Data are expressed as meanSD of 3 independent experiments. Results: CM from EGCs alone and from EGCs stimulated with both probiotic and pathogenic bacteria did not influence neither CaCo2 cells viability (0.790.26, 0.850.36, 0.890.24 vs 0.890.31 540 -630; p=NS) nor CaCo2 proliferation (0.330.10, 0.350.03, 0.400.04 vs 0.300.09 31 450 -540; p=NS). CM from EGCs alone and from probiotics stimulated EGCs significantly increased lactase (5.250.39 and 5.870.43 fold increase vs control; p<0.05) and sucrase activity (4.700.90 and 4.410.73 vs control; p<0.05), as compared to untreated CaCo2 cells. CM from pathogens stimulated EGCs has no effects on both lactase (1.740.57 fold increase vs control; p=NS) and sucrase activity (1.640.45 fold increase vs control; p=NS). Conclusions: We show that soluble factors released by EGCs are able to induce the differentiation of intestinal epithelial cells. Our data also show that these effects are maintained when EGCs are stimulated with probiotics. Conversely, when EGC are stimulated with pathogens, these effects are not observed. These results confirm the role of EGCs in mediating the host-bacteria interaction and put forward the major contribution of EGCs in the control of epithelial barrier function.
Ultraviolet Resonance Raman Spectroscopic Study of the Average Environment of Tyrosine in Native and Denatured Barnase (1997)

Ultraviolet resonance Raman spectroscopy was used to probe the change in the average environment of the seven tyrosine amino acids in barnase when the polypeptide chain folds from the denatured to the native state. The excitation radiation was continuous wave at a wavelength of 244 nm, and was generated from an intracavity-doubled argon ion laser, a BBO non-linear optical crystal being placed within the laser cavity. The change in the intensity ratio of the tyrosine Fermi-resonance doublet at 830/850 cm-1 was calibrated to provide a spectroscopic indicator of tyrosine hydrogen-bond strength. This was achieved by using p-cresol as a model compound, and measuring the resonance Raman spectra of p-cresol when dissolved in a range of solvents with known hydrogen-bond enthalpies of formation. © 1997 by John Wiley & Sons, Ltd.
The leucine zippers of the HLH-LZ proteins Max and c-Myc preferentially form heterodimers (1995)

c-Myc and Max are members of a subfamily of the helix-loop-helix transcription-regulating proteins. Their function is mediated by switches in the dimerization partners; c-Myc does not homodimerize in vivo but competes with Mad, another member of the subfamily, to form heterodimers with Max, leading to either activation or repression of transcription. Max is also able to form homodimers. In an attempt to identify which regions of the proteins carry the information to determine specific recognition of the dimerization partner, we have investigated the dimerization properties of synthetic peptides corresponding to the leucine zipper sequence of Max and c-Myc using circular dichroism and nuclear magnetic resonance techniques. We show that the heterodimer is obtained readily by simply mixing the peptides and that at neutral pH it is more stable than the homodimer of the Max leucine zipper. We have shown in a previous paper [Muhle-Goll, C. et al. (1994) Biochemistry 33, 11296-11306] that the leucine zipper of c-Myc does not form stable homodimers under these conditions. Thus, the leucine zipper regions of these two proteins by themselves display the same behavior as the entire proteins. However, even the heterodimer is less stable than dimers of leucine zippers of the basic leucine zipper family such as GCN4 and Fos-Jun. The specificity of the interaction between different monomers can be explained by polar interactions. We investigate the structural role of the polar and charged residues in the hydrophobic interface by molecular-modeling studies.
Real-time human detection using histograms of oriented gradients on a GPU (2009)

Human detection has always been an important part of computer vision but many implementations lack the real-time performance that real world applications require. This paper presents a real-time implementation of human detection in video using the state-of-the-art histograms of oriented gradients method. Each image in the video sequence is tested at multiple scales using a sliding window. Histograms of oriented gradients are created for each window and passed to a support vector machine to classify it as human or not. The histograms of oriented gradients method is implemented on a GPU using the NVIDIA CUDA architecture. The implementation significantly speeds up computation, achieving approximately 38 frames a second on VGA video while testing 11,160 windows per frame. Accuracy remains comparable to the CPU implementation. The flexibility and computational power the GPU affords users is discussed. These discussions should benefit those researchers who are interested in using a GPU for high-performance computing tasks.
Assessment of serum myeloperoxidase in children with bronchial asthma (1999)

Our data indicate that serum MPO - a marker of neutrophil activation - does not contribute to the assessment of the inflammatory process in childhood asthma. In addition, measurement of serum MPO appears not to be useful in assessing the participation of the neutrophil in asthmatic children. However, assessment of MPO may be useful to distinguish between bacterial and viral infection.
Inhibition of glioma growth by microbubble activation in a subcutaneous model using low duty cycle ultrasound without significant heating (2011)

In a subcutaneous C6 glioma model, MB destruction with low-duty cycle 1-MHz ultrasound can be used to markedly inhibit growth, without substantial tumor tissue heating. These results may have a bearing on the development of transcranial high-intensity focused ultrasound treatments for brain tumors that are not amenable to thermal ablation.
Strategies for Human Adipose Tissue Repair and Regeneration (2012)

In plastic and reconstructive surgery there is an increasing demand for malleable implants to repair soft tissue congenital defects, or those resulting from aging, traumatic injury and tumour resection. However, currently available methods present a number of limitations such as volume loss over time and eventual resorption of the graft. Tissue engineering techniques provide promising therapeutic solutions to these inconveniences through development of engineered equivalents that best imitate adipose tissue, both structurally and functionally. Here we review the latest achievements in the human adipose tissue engineering field, with a focus on its regenerative potential for a number of clinical applications.
Rewiring of B cell receptor signaling by Epstein–Barr virus LMP2A (2020)

Epstein-Barr virus (EBV) infects human B cells and reprograms them to allow virus replication and persistence. One key viral factor in this process is latent membrane protein 2A (LMP2A), which has been described as a B cell receptor (BCR) mimic promoting malignant transformation. However, how LMP2A signaling contributes to tumorigenesis remains elusive. By comparing LMP2A and BCR signaling in primary human B cells using phosphoproteomics and transcriptome profiling, we identified molecular mechanisms through which LMP2A affects B cell biology. Consistent with the literature, we found that LMP2A mimics a subset of BCR signaling events, including tyrosine phosphorylation of the kinase SYK, the calcium initiation complex consisting of BLNK, BTK, and PLCγ2, and its downstream transcription factor NFAT. However, the majority of LMP2A-induced signaling events markedly differed from those induced by BCR stimulation. These included differential phosphorylation of kinases, phosphatases, adaptor proteins, transcription factors such as nuclear factor κB (NF-κB) and TCF3, as well as widespread changes in the transcriptional output of LMP2A-expressing B cells. LMP2A affected apoptosis and cell-cycle checkpoints by dysregulating the expression of apoptosis regulators such as BCl-xL and the tumor suppressor retinoblastoma-associated protein 1 (RB1). LMP2A cooperated with MYC and mutant cyclin D3, two oncogenic drivers of Burkitt lymphoma, to promote proliferation and survival of primary human B cells by counteracting MYC-induced apoptosis and by inhibiting RB1 function, thereby promoting cell-cycle progression. Our results indicate that LMP2A is not a pure BCR mimic but rather rewires intracellular signaling in EBV-infected B cells that optimizes cell survival and proliferation, setting the stage for oncogenic transformation.
Evaluation of Colposcopic Skills in an Obstetrics and Gynecology Residency Training Program (1997)

Residents correctly identified cervical dysplasia in the majority of cases but had difficulty in distinguishing between low-grade and high-grade cervical dysplasia and in differentiating dysplasia from benign cellular changes, such as metaplasia and inflammation. Colposcopic accuracy, sensitivity, and specificity did not seem to improve with increasing experience. Resident colposcopic skills may improve if more structured training is implemented, particularly if emphasis is placed on teaching differences between benign cellular changes and dysplastic lesions.
<title>Optimal method for combining two correlated diagnostic assessments with application to computer-aided diagnosis</title> (2001)

We are developing computer-aided diagnosis (CAD) methods that produce a quantitative diagnostic assessment, such as the likelihood of malignancy of a breast lesion. Radiologists who use this computer aid must combine the computer's quantitative assessment with their own. No theoretical or empirical methods are currently available to help radiologists perform this task. Results of recent observer studies show that while CAD helps radiologists improve performance, radiologists' ad hoc performance tends to be inferior to that of the computer alone, indicating that they are unable to use computer aids optimally. We have developed a general method to combine two correlated diagnostic assessments. We calculate a likelihood ratio based on a bivariate binormal model that describes the joint probability density of the latent decision variables from two diagnostic assessments. To the extent that the bivariate binormal model is valid and that the model's parameters can be estimated reliably, results that we obtain in this way will be optimal because that likelihood ratio is used by the ideal observer in combining the diagnostic assessments. Preliminary results indicate that this method can produce better performance than that achieved by radiologists when they use computer aids in an ad hoc way. This method can potentially help radiologists use quantitative computed diagnostic assessments optimally, thereby surpassing the computer in accuracy.
Postoperative infections following autologous and homologous blood transfusions (1992)

Perioperative homologous blood transfusion has been linked to immune suppression and increased risk of postoperative infection. Autologous blood transfusion may not be associated with increased risk of infection because it presumably is not immunosuppressive. Fifty recipients of preoperatively donated autologous blood were matched to 50 recipients of homologous blood who underwent the same procedure, and the hospital course was reviewed for evidence of postoperative infection in both groups. Postoperative leukocytosis and febrile episodes were more common in homologous blood recipients (17 and 6 vs. 12 and 4, respectively). Sixteen percent of the 50 homologous blood recipients had positive cultures, as compared to 4 percent of the 50 autologous blood recipients (p less than 0.05). This study suggests that the association of blood transfusion with infection may be partially abrogated by the use of autologous blood.
A watchdog for controller performance monitoring (2005)

A method is suggested which automatically recognises when a controller is not performing well and is insensitive to changes in process noise.
Synthèse optique d'ondes hyperfréquences et millimétriques à très bas bruit de phase : résultats préliminaires (2015)

Nous avons conçu et construit un système optique de synthèse d’ondes hyperfréquences, millimétriques et submillimétriques à très bas bruit de phase. Les résultats préliminaires montrent une densité spectrale de bruit de phase à 10 kHz de la porteuse d’une onde à 9 GHz limitée par l’appareil de mesure. Pour les bruits plus près de la porteuse, le bruit de phase est limité par une modulation d’amplitude résiduelle : le système est en cours de modifications.
Query segmentation revisited (2011)

We address the problem of query segmentation: given a keyword query, the task is to group the keywords into phrases, if possible. Previous approaches to the problem achieve reasonable segmentation performance but are tested only against a small corpus of manually segmented queries. In addition, many of the previous approaches are fairly intricate as they use expensive features and are difficult to be reimplemented.
Temporal Sequence Modeling for Video Event Detection (2014)

We present a novel approach for event detection in video by temporal sequence modeling. Exploiting temporal information has lain at the core of many approaches for video analysis (i.e., action, activity and event recognition). Unlike previous works doing temporal modeling at semantic event level, we propose to model temporal dependencies in the data at sub-event level without using event annotations. This frees our model from ground truth and addresses several limitations in previous work on temporal modeling. Based on this idea, we represent a video by a sequence of visual words learnt from the video, and apply the Sequence Memoizer [21] to capture long-range dependencies in a temporal context in the visual sequence. This data-driven temporal model is further integrated with event classification for jointly performing segmentation and classification of events in a video. We demonstrate the efficacy of our approach on two challenging datasets for visual recognition.
A phenomenological rate of injection model for predicting fuel injection with application to mixture formation in light-duty diesel engines (2020)

Fuel injection rate laws are one of the most important pieces of information needed when modeling engine combustion with computational fluid dynamics. In this study, a simple phenomenological model of a common-rail injector was developed and calibrated for the Bosch CRI2.2 platform. The model requires three tunable parameter fits, making it relatively easy to calibrate and suitable for injector modeling when high-fidelity information about the internal injector’s geometry and electrical circuit details are not available. Each injection pulse is modeled as a sequence of up to four stages: an injection needle mechanical opening transient, a full-lift viscous flow inertial transient, a Bernoulli steady-state stage, and a needle descent transient. Parameters for each stage are obtained as polynomial fits from measured injection rate properties. The model enforces total injected mass, and the intermediate stages are only introduced if the injection pulse duration is long enough. Experimental rates of injection from two separate campaigns on the same injector were used to calibrate the model. The model was first validated against measured injection rate laws featuring pilot injections, short partially premixed combustion pulses, and conventional diesel combustion injection strategies. Then, it was employed as an input to engine computational fluid dynamics simulations, which were run to simulate experiments of mixture formation in an optically accessible light-duty diesel engine. It was found that, though simple, this model is capable of predicting both pilot and main injection pulse mass flow rates well: the simulations yielded accurate predictions of in-cylinder equivalence ratio distributions from injection strategies for both partially premixed combustion and pilot injections. Also, once calibrated, the model produced appropriate results for a wide range of injected mass and rail pressure values. Finally, it was observed that usage of such a relatively simple model can be a good choice when high-fidelity injection rate input and highly detailed information of the injector’s geometry and operation are not available, particularly as noticeable discrepancies can be present also among different experimental campaigns on similar hardware.
Diversity and Novelty MasterPrints: Generating Multiple DeepMasterPrints for Increased User Coverage (2022)

This work expands on previous advancements in genetic fingerprint spoofing via the DeepMasterPrints and introduces Diversity and Novelty MasterPrints. This system uses quality diversity evolutionary algorithms to generate dictionaries of artificial prints with a focus on increasing coverage of users from the dataset. The Diversity MasterPrints focus on generating solution prints that match with users not covered by previously found prints, and the Novelty MasterPrints explicitly search for prints with more that are farther in user space than previous prints. Our multi-print search methodologies outperform the singular DeepMasterPrints in both coverage and generalization while maintaining quality of the fingerprint image output.