gebhart/patrepeval huggingface dataset:
Polyethyleneglycol crosslinked N -(2-hydroxyethyl)-polyethylenimine nanoparticles as efficient non-viral vectors for DNA and siRNA delivery in vitro and in vivo (2013)

A series of electrostatically crosslinked nanoparticles, N-(2-hydroxyethyl)-polyethylenimine-PEG600 (HePP), was prepared by allowing N-(2-hydroxyethyl)-polyethylenimine (HeP) to interact with polyethyleneglycol (600) dicarboxylic acid (HOOC-PEG600-COOH, PEG600dc), they were then evaluated for their capability to transfect cells in vitro and in vivo. DLS studies revealed the size of the HePP nanoparticles in the range 106-170 nm, which efficiently condensed nucleic acids and provided sufficient protection against nuclease degradation. HePP-pDNA complexes exhibited a considerably higher transfection efficiency and cell viability in various mammalian cell lines, with HePP-3-pDNA displaying the highest gene expression, which outperformed HeP and the commercially available transfection reagent, Lipofectamine™. Also, HePP-3 mediated sequential delivery of GFP specific siRNA resulted in ∼76% suppression of the target gene. Intravenous administration of HePP-3-pDNA complex to mice, followed by monitoring of the reporter gene analysis post 7d, revealed the highest gene expression occurred in the spleen. Together, these results advocate the potential of HePP nanoparticles as efficient vectors for gene delivery in vitro and in vivo.
Dynamic Active Search for quick object detection with pan-tilt-zoom camera (2002)

This paper proposes a search method for detecting known objects quickly in 3D environments with a pan-tilt-zoom camera. In our previous work, we proposed an algorithm named Active Search that greatly reduces the number of calculations required to obtain a match between a reference object and an input image using color histograms. We describe two improvements we have made to Active Search for such practical applications as robots and surveillance. First, we increased the robustness as regards the color histogram changes that result from different lighting conditions and camera angles by using multiple reference images and a pixel color vector quantization. Second, we reduced the number of camera operations (pan, tilt and zoom) by using a best-direction-first and upper bound pruning strategies. We call this camera control Dynamic Active Search. Experiments show an improvement in object detection accuracy and a 78% reduction in detection time.
Comprehensive genome profiling by next generation sequencing of circulating tumor DNA in solid tumors: a single academic institution experience (2022)

Although additional studies are needed to better select patients and setting, NGS F1LA is a useful, noninvasive, and repeatable assay to guide therapeutic choice in oncology. It provides a snapshot of cancer heterogeneity profile that could be incorporated in routinely clinical practice.
A Practical Solution to a Cargo Loading Problem at Bethlehem Steel (1994)

The optimum assignment of structural steel shapes to rail cars is an important logistical problem in the steel industry. In this paper, we discuss an application at Bethlehem Steel that not only involves weight and dimensional constraints, but also customer unloading constraints. The formulation is a generalized bin packing problem which is solved by modifying and extending the first fit decreasing algorithm. The solution algorithm, SOLID (for Structural Optimal Loading IDentification), has been used extensively for one of Bethlehem's high tonnage customers providing very good practical (implementable) results that achieve the desired goals. Bethlehem has enhanced this approach for use with other customers.
Network Pruning via Transformable Architecture Search (2019)

Network pruning reduces the computation costs of an over-parameterized network without performance damage. Prevailing pruning algorithms pre-define the width and depth of the pruned networks, and then transfer parameters from the unpruned network to pruned networks. To break the structure limitation of the pruned networks, we propose to apply neural architecture search to search directly for a network with flexible channel and layer sizes. The number of the channels/layers is learned by minimizing the loss of the pruned networks. The feature map of the pruned network is an aggregation of K feature map fragments (generated by K networks of different sizes), which are sampled based on the probability distribution.The loss can be back-propagated not only to the network weights, but also to the parameterized distribution to explicitly tune the size of the channels/layers. Specifically, we apply channel-wise interpolation to keep the feature map with different channel sizes aligned in the aggregation procedure. The maximum probability for the size in each distribution serves as the width and depth of the pruned network, whose parameters are learned by knowledge transfer, e.g., knowledge distillation, from the original networks. Experiments on CIFAR-10, CIFAR-100 and ImageNet demonstrate the effectiveness of our new perspective of network pruning compared to traditional network pruning algorithms. Various searching and knowledge transfer approaches are conducted to show the effectiveness of the two components. Code is at: https://github.com/D-X-Y/NAS-Projects.
Artificial intelligence for prostate MRI: open datasets, available applications, and grand challenges (2022)

Artificial intelligence (AI) for prostate magnetic resonance imaging (MRI) is starting to play a clinical role for prostate cancer (PCa) patients. AI-assisted reading is feasible, allowing workflow reduction. A total of 3,369 multi-vendor prostate MRI cases are available in open datasets, acquired from 2003 to 2021 in Europe or USA at 3 T (n = 3,018; 89.6%) or 1.5 T (n = 296; 8.8%), 346 cases scanned with endorectal coil (10.3%), 3,023 (89.7%) with phased-array surface coils; 412 collected for anatomical segmentation tasks, 3,096 for PCa detection/classification; for 2,240 cases lesions delineation is available and 56 cases have matching histopathologic images; for 2,620 cases the PSA level is provided; the total size of all open datasets amounts to approximately 253 GB. Of note, quality of annotations provided per dataset highly differ and attention must be paid when using these datasets (e.g., data overlap). Seven grand challenges and commercial applications from eleven vendors are here considered. Few small studies provided prospective validation. More work is needed, in particular validation on large-scale multi-institutional, well-curated public datasets to test general applicability. Moreover, AI needs to be explored for clinical stages other than detection/characterization (e.g., follow-up, prognosis, interventions, and focal treatment).
MFT-MAC: A Duty-Cycle MAC Protocol Using Multiframe Transmission for Wireless Sensor Networks (2013)

In many sensor network applications, energy efficiency and latency are major design criteria because battery-operated sensor nodes limit network lifetime. In this paper, we propose a new contention-based duty-cycle MAC protocol using a synchronized approach for use in wireless sensor networks. In the proposed MFT-MAC protocol, we use a control frame that considers the number of DATA frames to be transmitted to the next node in order to improve the energy efficiency and reduce the end-to-end delay. During the SLEEP period, each node transmits multiple DATA frames to the next node through the use of the control frame. The performance of the proposed MAC protocol is confirmed through the use of NS-2 simulator.
Isolation from Klebsiella and Characterization of Two rcs Genes That Activate Colanic Acid Capsular Biosynthesis in Escherichia coli (1987)

Two genes, designated rcsA (regulation of capsule synthesis) and rcsB, that had been cloned from the chromosome of Klebsiella aerogenes (K. pneumoniae) capsular serotype K21 were capable of activating expression of colanic acid capsular polysaccharide in Escherichia coli K12. The Klebsiella rcsA gene encoded a polypeptide of 23 kDa that was required for the induction of a mucoid phenotype at less than or equal to 30 degrees C but not at greater than or equal to 37 C. The Klebsiella rcsB locus encoded no apparent polypeptides and was not capable by itself of causing the overproduction of colanic acid. However, when present in the same cell with rcsA, either in cis or in trans, rcsB caused expression of mucoidy in E. coli at all growth temperatures. These findings are best explained if the Klebsiella rcsA gene product acts as a positive regulator of colanic acid biosynthesis in E. coli and that activity of this protein is in turn subject to regulation by Lon protease. The Klebsiella rcsB locus may exert its effect by preferentially binding a negative regulator of capsular biosynthesis, possibly Lon itself. DNA sequences homologous to the Klebsiella K21b rcsA and rcsB genes were found in the genomes of all other capsular serotypes of klebsiellae examined, including K2, K12, K36 and K43. However, there was no homology between such genes and the chromosome of E. coli. The ability of these rcs genes to induce a mucoid phenotype explains the apparent conjugative transfer from klebsiellae to E. coli of the ability to produce K21 or other Klebsiella capsular polysaccharides that are structurally and antigenically related to colanic acid.
Supplementary Table 1 from Pharmacological Landscape of FDA-Approved Anticancer Drugs Reveals Sensitivities to Ixabepilone, Romidepsin, Omacetaxine, and Carfilzomib in Aggressive Meningiomas (2023)

&lt;p&gt;Drug Screening Data&lt;/p&gt;
Aging and epigenetic drift: a vicious cycle (2014)

The term epigenetics refers to stable patterns of gene expression that are seen during differentiation or X chromosome inactivation and are not dependent on dynamic changes in coding DNA. These gene expression states are encoded in the epigenome - a collection of marks on DNA or on histone tails that are established during embryogenesis. Genome-wide studies in aging cells and tissues have uncovered stochastic DNA methylation drift (gradual increases or decreases at specific loci) that reflects imperfect maintenance of epigenetic marks. Drift creates epigenetic mosaicism in aging stem cells that could potentially restrict their plasticity and worsen phenotypes such as stem cell exhaustion and focal proliferative defects that can lead to cancer.
Phosphorylation of glucosamine-6-phosphate synthase is important but not essential for germination and mycelial growth of Candida albicans (2004)

A site-directed mutagenesis of the GFA1 gene encoding Candida albicans glucosamine-6-phosphate (GlcN-6-P) synthase afforded its GFA1S208A version. A product of the modified gene, lacking the putative phosphorylation site for protein kinase A (PKA), exhibited all the basic properties identical to those of the wild-type enzyme but was no longer a substrate for PKA. Comparison of the C. albicans Deltagfa1/GFA1 and Deltagfa1/GFA1S208A cells, grown under conditions stimulating yeast-to-mycelia transformation, revealed that the latter demonstrated lower GlcN-6-P synthase specific activity, decreased chitin content and formed much fewer mycelial forms. All these findings, as well as the observed effects of specific inhibitors of protein kinases, suggest that a loss of the possibility of GlcN-6-P synthase phosphorylation by PKA strongly reduces but not completely eliminates the germinative response of C. albicans cells.
KPI-based Process Operation (2016)

A key performance indicator (KPI) is a metric used to evaluate factors that are crucial to the success of an organization. Usually these factors are represented by normalized numbers (e.g. 0-100%) and maximizing or minimizing them is equivalent to making progress toward operational or strategic goals of the organization. Different KPIs of variable levels of complexity exist, rating factors such as customer and employee satisfaction, compliance, security or economic success. This article focuses on KPIs closely related to process operations like production performance, energy consumption, availability and safety. These KPIs are mainly based on measurable process data.
Directional diffusion and void formation at a Si (001) bonded wafer interface (2002)

Low-temperature hydrophobic bonding is an enabling technology allowing the fabrication of device structures. Current research into improvement of hydrophobic bonding has focused on the elimination of thermally generated voids. It has been observed that a regular grid etched into the bonding interface can eliminate the thermally generated voids. By manipulation of patterns etched into the bond interface, it was possible to ascertain that the diffusion of interfacial gasses that form the thermally generated voids is enhanced along the 〈110〉 directions. This is shown by an analysis of the void density at various locations in relation to the etched trenches at the bonded interface. Void density between trenches is shown to be 12% of the void density near trenches but nto along a 〈110〉 direction.
Suppressor of Cytokine Signalling-6 Promotes Neurite Outgrowth via JAK2/STAT5-Mediated Signalling Pathway, Involving Negative Feedback Inhibition (2011)

The current paradigm for the first time states that SOCS6, a SOCS family member, plays an important role in the process of neuronal differentiation. These findings define a novel molecular mechanism for Jak2/Stat5 mediated SOCS6 signalling.
Supplementary Figure 5 from Chimeric Transcript Generated by cis-Splicing of Adjacent Genes Regulates Prostate Cancer Cell Proliferation (2023)

&lt;p&gt;PDF file - 384K, Structure of wild type SLC45A3 and ELK4 genes and SLC45A3-ELK4 chimeric transcript&lt;/p&gt;
Elevated Cerebrospinal Fluid Substance P-like Immunoreactivity in Patients with Painful Osteoarthritis, but not in Patients with Rhizopatic Pain from a Herniated Lumbar Disc (1997)

Cerebrospinal fluid (CSF) levels of substance P like immunoreactivity (SPLI) were determined in 11 patients with painful osteoarthritis in hip or knee, 9 patients with rhizopatic pain from a herniated lumbar disc, and in 9 healthy volunteers without pain. The patients with osteoarthritis had increased levels of SPLI in CSF (p < 0.001) compared to the controls. A positive correlation was also seen between the CSF SPLI and the degree of pain. At a second lumbar puncture 5 months after operation, SPLI had decreased, but was still significantly higher than in the controls. No difference in CSF SPLI was seen in the patients with herniated lumbar disc compared to the controls, neither before treatment, nor at follow up CSF postoperatively. The results suggest that nociceptive joint pain is consistent with increased SPLI in CSF. Differences in SPLI in CSF may be useful to differentiate pain from various origin, and may also increase our understanding of different pain mechanisms.
Fibrin D-dimer, Tissue Plasminogen Activator, Plasminogen Activator Inhibitor, and the Risk of Major Ischaemic Heart Disease in the Caerphilly Study (1998)

Plasma levels of fibrin D-dimer, tissue plasminogen activator (tPA) and plasminogen activator inhibitor (PAI) have been associated with ischaemic heart disease (IHD). However their associations with incident IHD in samples of the general population are not established. D-dimer antigen, tPA antigen and PAI activity were measured in stored, fasting plasma samples from 1,998 men aged 45-65 examined between 1984 and 1988, during the first re-examination of the Caerphilly Study cohort. These variables were related to major IHD events (myocardial infarction or IHD death) which occurred in 129 men during a follow-up period which averaged 61 months. Mean fibrin D-dimer was higher in men who developed IHD events (90 vs. 71 ng/ml; age-adjusted logarithmic mean difference 0.21; 95% CI 0.11, 0.30; p <0.0001). This association remained after adjusting for baseline IHD and for other risk factors including fibrinogen: the adjusted relative odds of IHD in the highest fifth of D-dimer were 3.5 (95% CI 1.8, 6.9; p = 0.0003). Mean tPA antigen was also higher in men who developed IHD (12.6 vs. 11.6 ng/ml; mean difference 0.9; 95% CI 0.2, 1.7; p = 0.02); however this difference largely disappeared after adjusting for other risk factors. PAI activity was not associated with risk of IHD.
Device Model for Graphene Spin Valves (2015)

A 1-D drift-diffusion device model for graphene spin valves is presented. The model describes properly the electronic and the spintronic properties, such as electrostatics, charge and spin injection, transport, spin relaxation, spin-current profiles, and bias-dependent magnetoresistance. The model calculations agree qualitatively with relevant experimental results, and provide physical insight.
An extended Jacobian matrix and multirate control for bilateral control between different time resolution systems (2012)

In this paper, a way to obtain bilateral control between different time resolution systems is proposed. Bilateral control enables communication of information regarding our tactile sense. A master (local) robot is manipulated by an operator and a slave (remote) robot tracks the position of the master while the reaction force of the slave is fed back to the master. Conventionally, there have been few studies about the difference of time resolution and feedback gains between master and slave systems. First, an extended Jacobian matrix is proposed to describe the dynamics of bilateral control taking time resolution difference into account. The fast (master) and slow (slave) systems are transformed to other fast and slow systems in modal space, which the dynamics of the position accordance and force regulation are described in. Then, a multirate controller is designed to couple the fast system with high feedback gain and the slow system with low feedback gain. The validity of the proposed method is confirmed by simulations and experiments.
Investigation of Phthalocyanine Catalysts for the Aerobic Synthesis of meso-Substituted Porphyrins (1997)

The aerobic oxidation process for the synthesis of porphyrins, previously performed using 5 mol % p-chloranil (TCQ), 5 mol % iron(II) phthalocyanine ( FePc ) and stoichiometric amounts of O 2 , has been refined using new phthalocyanine catalysts. Four phthalocyanine catalysts have been prepared, characterized by Mössbauer spectroscopy and examined for efficacy in the high concentration (0.1 M) synthesis of tetraphenylporphyrin at room temperature. Each phthalocyanine has been identified to be a μ-oxo dimer. Two catalysts are soluble (the μ-oxo dimers [(t-butyl) 4 FePc ] 2 O and [(n- C 6 H 13 O ) 4 FePc ] 2 O ) and enable homogeneous reactions, while two are insoluble (the μ-oxo(1) and μ-oxo(2) dimers of FePc , ( FePc ) 2 O ) and give heterogeneous reactions. These four phthalocyanine compounds provide efficient catalysis at the 0.3–1 mol % level using only 1 mol % quinone or hydroquinone ( TCQ , DDQ , TCQH 2 or DDQH 2 ), affording ~25% yields of tetraphenylporphyrin in 60 min of oxidation. There are no discernible advantages of the homogeneous versus heterogeneous catalysts. The μ-oxo dimers are active, but FePc is inactive, at the 0.3 mol % level. The activity of the FePc sample at the 5 mol % level is attributed to residual μ-oxo dimer impurity. This aerobic oxidation process is superior to stoichiometric oxidation with TCQ or DDQ , and can be performed in the presence of BF 3 · O ( Et ) 2 , trifluoroacetic acid, or under neutral conditions.
MupB, a New High-Level Mupirocin Resistance Mechanism in Staphylococcus aureus (2012)

Mupirocin is a topical antibiotic used for the treatment of skin infections and the eradication of methicillin-resistant Staphylococcus aureus carriage. It inhibits bacterial protein synthesis by interfering with isoleucyl-tRNA synthetase activity. High-level mupirocin resistance (MIC of ≥ 512 μg/ml) is mediated by the expression of mupA (ileS2), which encodes an alternate isoleucyl-tRNA synthetase. In this study, we describe high-level mupirocin resistance mediated by a novel locus, mupB. The mupB gene (3,102 bp) shares 65.5% sequence identity with mupA but only 45.5% identity with ileS. The deduced MupB protein shares 58.1% identity (72.3% similarity) and 25.4% identity (41.8% similarity) with MupA and IleS, respectively. Despite this limited homology, MupB contains conserved motifs found in class I tRNA synthetases. Attempts to transfer high-level mupirocin resistance via conjugation or transformation (using plasmid extracts from an mupB-containing strain) were unsuccessful. However, by cloning the mupB gene into a shuttle vector, it was possible to transfer the resistance phenotype to susceptible S. aureus by electroporation, proving that mupB was responsible for the high-level mupirocin resistance. Further studies need to be done to determine the prevalence of mupB and to understand risk factors and outcomes associated with resistance mediated by this gene.
Steroids, lidocain and ioxaglic acid modify the viscosity of hyaluronic acid: in vitro study and clinical implications (2016)

HA viscosity varies widely in presence of other molecules. These changes are due to both dilution and molecular interactions. This study suggests that addition of other molecules with HA can lead to a major decrease of its viscosity. However, provided to respect a maximum ratio of 1:1, the contrast medium and triamcinolone seem to have no major deleterious effect on the viscosity level, especially on crosslinked HA. The study also suggests a deleterious effect of lidocain on the cross-linked HA. These in vitro data suggest that drugs associations must be avoided when they are not essential. However, clinical trials are needed to determine whether these rheological changes may have a significant impact on the clinical outcome.
Automated Cancer Marker Characterization in Human Plasma Using SUrface PLASMON Resonance in Array combined with Mass Spectrometry (SUPRA-MS) (2012)

International audience
Graves' disease (GD) and Hashimoto's thyroiditis (HT) in monozygotic twins: case study as well as transcriptomic and immunohistological analysis of thyroid tissues (2006)

We report on the rare simultaneous occurrence of GD and HT in monozygotic twins. The pattern of thyroid tissue-derived cDNAs were compared to gain insight into previous and ongoing immune destruction and reconstruction processes using microarrays. The results were confirmed by immunohistology and real-time PCR. In HT destruction of thyroid tissue caused lower levels of thyrocyte-specific cDNAs and cDNAs encoding extracellular matrix components, but higher levels of proteases involved in extracellular matrix degradation as in GD. In HT lymphocytic infiltrates forming ectopic follicles replaced the thyroid tissue almost completely. Thus, lymphocyte specific cDNA were higher expressed compared to GD. The same was true for many chemokines and their receptors which not only enable migration toward the thyroid but also maintain the lymphocytic infiltrate. Higher levels of cDNAs encoding molecules related to apoptosis which take place during thyrocyte destruction but also during maturation of B cell responses were present in HT compared to GD. Surprisingly, the suggested Th1 (IL-2, IFN-g) and Th2 (Il-4, Il-5, Il-10 and Il-13) specific cytokine profiles in HT and GD, respectively, could not be confirmed. In GD cDNAs encoding factors and receptors involved in angiogenesis were higher expressed than in HT. In summary, comparison of gene expression reflects the cellular differences between the two types of autoimmune thyroid disease in twins with identical genetic and similar environmental background.