gebhart/patrepeval huggingface dataset:
Supplementary Figure 4 from Therapeutic and Prophylactic Antitumor Activity of an Oral Inhibitor of Fucosylation in Spontaneous Mammary Cancers (2023)

&lt;p&gt;Effect of 2FF-treatment on (A) Mean {plus minus} SEM tumor cell binding of antibody from TgMMTV-neu mice as detected by FACS analysis using (A) untreated (circle) and 2FF-treated (square) purified serum IgG, or untreated (triangle) and 2FF-treated (inverted triangle) serum (n=5 each), (B) geometric mean of untreated (black, MMC; dark gray, M6) or 2FF-treated (unshaded, MMC; light gray, M6) cell surface fucose using LCA, AAL, and AOL lectins, and (C) in vitro growth of untreated cells (circle, MMC; triangle, M6) or cells pretreated with 2FF (&gt;7 days, square, MMC; inverted triangle, M6) and continuously treated with 2FF during the growth analysis (Mean {plus minus} SEM, n=3 each).&lt;/p&gt;
Human safety and genetically modified plants: a review of antibiotic resistance markers and future transformation selection technologies (2005)

... The first generation of genetically modified plants suitable for agriculture was largely produced using antibiotic resistance markers (ARMs) for the preparation of plant transformation vectors or for the plant transformation process itself. In some instances, the ARM gene remains in the finished commercial plant product. Theoretical concerns regarding the risks posed by such markers have resulted in a demand for the production of commercial plants free of ARMs. This, in turn, has resulted in the development of technologies which avoid the use of ARMs or which allow for the efficient excision of such markers following the initial transformation process, but in advance of the selection of commercial plant lines. We review the current status of ARM safety information relevant to existing genetically modified crops as well as reviewing in some detail the available alternatives to ARM use, the utility of these technologies for commercial production, and the issues that might pertain to the use of these alternative technologies for the production of commercial genetically modified crops. Many of the alternative techniques have the potential to be commercially viable, and one or more will necessarily be used for the future production of genetically modified plants free of ARMs. Nonetheless, existing ARM‐containing products will remain in the market for the foreseeable future, and the safety of these products therefore remains a relevant issue. Further, the ease of use, cost, availability, safety profile, regulatory status, and utility of alternative techniques should be kept in proper perspective relative to the long history of safe use of ARMs in plant biotechnology.
A Stab‐and‐Roll Biopsy Technique to Maintain Gingival Epithelium for Desquamative Gingivitis (2014)

A diagnostic biopsy was obtained from the gingiva of patients with DG using the stab-and-roll technique. The gingival epithelium was well maintained, and the relationship with the underlying connective tissue was diagnostic. In the future, this stab-and-roll biopsy technique may facilitate early diagnosis and treatment of diseases causing DG.
Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread (2020)

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12<sup>th</sup> known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.
PRO-FIBROTIC ROLE OF MYOSTATIN IN PEYRONIE'S DISEASE (2008)

You have accessJournal of Urology1 Apr 2008PRO-FIBROTIC ROLE OF MYOSTATIN IN PEYRONIE'S DISEASE Monica G Ferrini, Liliana P Cantini, Dolores Vernet, Thomas R Magee, Ansha Qian, Robert A Gelfand, Jacob Rajfer, and Nestor F Gonzalez-Cadavid Monica G FerriniMonica G Ferrini More articles by this author , Liliana P CantiniLiliana P Cantini More articles by this author , Dolores VernetDolores Vernet More articles by this author , Thomas R MageeThomas R Magee More articles by this author , Ansha QianAnsha Qian More articles by this author , Robert A GelfandRobert A Gelfand More articles by this author , Jacob RajferJacob Rajfer More articles by this author , and Nestor F Gonzalez-CadavidNestor F Gonzalez-Cadavid More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(08)60747-8AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "PRO-FIBROTIC ROLE OF MYOSTATIN IN PEYRONIE'S DISEASE." The Journal of Urology, 179(4S), p. 258 © 2008 by American Urological AssociationFiguresReferencesRelatedDetails Volume 179Issue 4SApril 2008Page: 258 Advertisement Copyright & Permissions© 2008 by American Urological AssociationMetricsAuthor Information Monica G Ferrini More articles by this author Liliana P Cantini More articles by this author Dolores Vernet More articles by this author Thomas R Magee More articles by this author Ansha Qian More articles by this author Robert A Gelfand More articles by this author Jacob Rajfer More articles by this author Nestor F Gonzalez-Cadavid More articles by this author Expand All Advertisement PDF downloadLoading ...
Explainable DRC Hotspot Prediction with Random Forest and SHAP Tree Explainer (2020)

With advanced technology nodes, resolving design rule check (DRC) violations has become a cumbersome task, which makes it desirable to make predictions at earlier stages of the design flow. In this paper, we show that the Random Forest (RF) model is quite effective for the DRC hotspot prediction at the global routing stage, and in fact significantly outperforms recent prior works, with only a fraction of the runtime to develop the model. We also propose, for the first time, to adopt a recent explanatory metric-the SHAP value-to make accurate and consistent explanations for individual DRC hotspot predictions from RF. Experiments show that RF is 21%-60% better in predictive performance on average, compared with promising machine learning models used in similar works (e.g. SVM and neural networks) while exhibiting good explainability, which makes it ideal for DRC hotspot prediction.
Pretargeted radioimmunotherapy significantly improves the treatment of non-Hodgkin’s lymphoma in a nude mouse model (2005)

2548 Background: Radioimmunotherapy (RAIT) is an approved treatment of follicular and transformed non-Hodgkin’s lymphoma (NHL) that uses anti-CD20 IgGs radiolabeled with 90Y or 131I. Administered in cases of refractory disease, there are a number of new trials assessing the prospects for expanding the indication for this treatment. Our studies suggest that significant improvements in the therapy of NHL could be obtained by using a bispecific antibody (bsMAb) pretargeting procedure that enhances the therapeutic window for targeted radionuclides compared to directly radiolabeled IgG. Methods: Nude mice bearing 1.0- to 1.5-cm diameter s.c. human Ramos B-cell lymphoma xenografts were administered a bsMAb composed of the Fab’ fragment of a humanized anti-CD20 MAb (hA20) for tumor localization coupled to the Fab’ of a novel anti-hapten (HSG) antibody for binding a 90Y-labeled HSG-peptide. Forty-eight hours later, a treatment of 0.5 or 0.8 mCi of 90Y-HSG-peptide was given. The pretargeting procedure was compared to equitoxic amounts of 90Y-hA20 IgG (e.g., 0.105 and 0.175 mCi, respectively), 0.8 mCi of 90Y-HSG-peptide alone, or to untreated animals. Results: Biodistribution studies showed tumor uptake of the 90Y-anti-CD20 IgG did not exceed the level of radioactivity in the blood until 7 days after injection, whereas tumor/blood ratios for the pretargeting procedure where 3:1 within 3 h and 30:1 within 24 h. Tumors in animals given 0.8 mCi of the 90Y-HSG-peptide alone progressed as rapidly as in the untreated group, while pretargeting was more effective at controlling and even curing animals than the 90Y-hA20 IgG. In several studies with 6 months of observation, the pretargeting procedure has cured ≥50% of the animals compared to ≤ 10% for the 90Y-hA20 IgG. Conclusions: Time to disease progression and survival analyses showed pretargeting to be significantly better (P < 0.005) than the directly radiolabeled antibody treatment. This suggests that a humanized bsMAb pretargeting procedure could be a more effective treatment of NHL than currently available directly radiolabeled antibodies. (Supported in part from DOE grant DE-FG02-95ER62028 and the Thomas & Agnes Carvel Foundation.) Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration IBC Pharmaceuticals, Immunomedics Immunomedics
Investigating the Shear Strength of Concrete Box Culverts (2007)

This paper summarizes the results of a preliminary series of reinforced concrete shear experiments on precast concrete box culverts. The specimens were half-boxes tested under uniform load with a passive tie-bar to allow full determination of the internal moment throughout the testing process. A total of 12 specimens were tested of which 6 failed in shear. The paper includes crack diagrams and a discussion of the experimental results. Existing numerical models based on the Modified Compression Field Theory are shown to model the load-deformation of the tests well in terms of the location of the inflection point in the slab. The test results indicate that the Canadian Highway Bridge Design Code (CHBDC), which has similar sectional shear strength prediction equations as the AASHTO LRFD Bridge Design Specifications, provide conservative estimates of the shear strength of box culverts. The AASHTO LRFD special box culvert shear design rules are conservative for thin slabs but unconservative for very thick slabs, say greater than 16 inches deep, and they provide a less uniform level of safety than the CHBDC provisions. A potential explanation for the conservative results is presented and shown to explain the test results well.
Proteomic Profiling of Mycobacterium tuberculosis Identifies Nutrient-starvation-responsive Toxin–antitoxin Systems (2013)

In order to successfully enter the latent stage, Mycobacterium tuberculosis must adapt to conditions such as nutrient limitation and hypoxia. In vitro models that mimic latent infection are valuable tools for describing the changes in metabolism that occur when the bacterium exists in a non-growing form. We used two complementary proteomic approaches, label-free LC-MS/MS analysis and two-dimensional difference gel electrophoresis, to determine the proteome profile of extracellular proteins from M. tuberculosis cultured under nutrient starvation. Through the label-free LC-MS/MS analysis of fractionated samples, 1176 proteins were identified from culture filtrates of log phase and nutrient-starved cultures, and the protein levels of 230 proteins were increased in nutrient-starved culture filtrates, whereas those of 208 proteins were decreased. By means of Gene Ontology clustering analysis, significant differences in the overall metabolism during nutrient starvation were detected. Notably, members of the toxin-antitoxin systems were present in larger quantities in nutrient-starved cultures, supporting a role for these global modules as M. tuberculosis switches its metabolism into dormancy. Decreased abundance of proteins involved in amino acid and protein synthesis was apparent, as well as changes in the lipid metabolism. Further analysis of the dataset identified increased abundance of lipoproteins and decreased abundance of ESAT-6 family proteins. Results from the two-dimensional difference gel electrophoresis proteomics demonstrated overall agreement with the LC-MS/MS data and added complementary insights about protein degradation and modification.
Instability in Primary Total Knee Arthroplasty (2011)

Instability is one of the most common causes of failure of total knee arthroplasty (TKA). The presentation can vary from pain to frank dislocation with the etiologies just as varied. Instability after TKA can be classified by where the instability occurs in the knee's arc of motion as well as the chronicity of the problem. Acute instability is related to intraoperative injuries or excessive release of important coronal stabilizers such as the medial collateral ligament in extension or the posterolateral corner in flexion. Chronic instability in extension is often related to varus/valgus malalignment. Chronic instability in flexion can be related to an undersized femoral component, excessive tibial slope, or excessive elevation of the joint line affecting the isometry of the collateral ligaments in midflexion. Recurvatum instability is a rare complication that often coincides with extensor mechanism dysfunction or neuromuscular disorders. When addressing instability after TKA, it is critical to determine the root cause of the problem as well as evaluate for other causes of pain such as infection or aseptic loosening. When revision surgery is warranted, it should follow the basic principles of restoring a neutral mechanical alignment, setting the appropriate component rotation, balancing the flexion and extension spaces, and restoring the height of the native joint line.
Battery-free, wireless soft sensors for continuous multi-site measurements of pressure and temperature from patients at risk for pressure injuries (2021)

Capabilities for continuous monitoring of pressures and temperatures at critical skin interfaces can help to guide care strategies that minimize the potential for pressure injuries in hospitalized patients or in individuals confined to the bed. This paper introduces a soft, skin-mountable class of sensor system for this purpose. The design includes a pressure-responsive element based on membrane deflection and a battery-free, wireless mode of operation capable of multi-site measurements at strategic locations across the body. Such devices yield continuous, simultaneous readings of pressure and temperature in a sequential readout scheme from a pair of primary antennas mounted under the bedding and connected to a wireless reader and a multiplexer located at the bedside. Experimental evaluation of the sensor and the complete system includes benchtop measurements and numerical simulations of the key features. Clinical trials involving two hemiplegic patients and a tetraplegic patient demonstrate the feasibility, functionality and long-term stability of this technology in operating hospital settings.
Thermal stability of NIMN valve heads (1999)

The antiferromagnet (AFM) has been called the Achilles' heel of the Spin Valve head, since it frequently fails to provide exchange pinning with sufficient strength and stability at elevated operating temperatures (~150C).
Stationarity Region of Mm-Wave Channel Based on Outdoor Microcellular Measurements at 28 GHz (2017)

The stationarity region, i.e., the area in which the statistics of a propagation channel remain constant, is an important measure of the propagation channel, and essential for efficient system design. This paper presents what is to our knowledge the first extensive measurement campaign for measuring the stationarity region of MIMO mm-wave channels. Using a novel 28 GHz phased-array sounder with high phase stability, we present results in an urban microcell LoS, and LOS to NLOS transition region scenario, for the stationarity region of shadowing, power delay profile, and the angular power spectrum. A comparison to results at cm-waves shows considerably reduced stationarity region size, which has an important impact on system design.
Optimization of Acetazolamide-Based Scaffold as Potent Inhibitors of Vancomycin-Resistant Enterococcus (2020)

Vancomycin-resistant enterococci (VRE) are the second leading cause of hospital-acquired infections (HAIs) attributed to a drug-resistant bacterium in the United States, and resistance to the frontline treatments is well documented. To combat VRE, we have repurposed the FDA-approved carbonic anhydrase drug acetazolamide to design potent antienterococcal agents. Through structure-activity relationship optimization we have arrived at two leads possessing improved potency against clinical VRE strains from MIC = 2 μg/mL (acetazolamide) to MIC = 0.007 μg/mL (<b>22</b>) and 1 μg/mL (<b>26</b>). Physicochemical properties were modified to design leads that have either high oral bioavailability to treat systemic infections or low intestinal permeability to treat VRE infections in the gastrointestinal tract. Our data suggest the intracellular targets for the molecules are putative α-carbonic and γ-carbonic anhydrases, and homology modeling and molecular dynamics simulations were performed. Together, this study presents potential anti-VRE therapeutic options to provide alternatives for problematic VRE infections.
Excitatory synapses and gap junctions cooperate to improve Pv neuronal burst firing and cortical social cognition in Shank2-mutant mice (2021)

NMDA receptor (NMDAR) and GABA neuronal dysfunctions are observed in animal models of autism spectrum disorders, but how these dysfunctions impair social cognition and behavior remains unclear. We report here that NMDARs in cortical parvalbumin (Pv)-positive interneurons cooperate with gap junctions to promote high-frequency (>80 Hz) Pv neuronal burst firing and social cognition. Shank2<sup>-/-</sup> mice, displaying improved sociability upon NMDAR activation, show impaired cortical social representation and inhibitory neuronal burst firing. Cortical Shank2<sup>-/-</sup> Pv neurons show decreased NMDAR activity, which suppresses the cooperation between NMDARs and gap junctions (GJs) for normal burst firing. Shank2<sup>-/-</sup> Pv neurons show compensatory increases in GJ activity that are not sufficient for social rescue. However, optogenetic boosting of Pv neuronal bursts, requiring GJs, rescues cortical social cognition in Shank2<sup>-/-</sup> mice, similar to the NMDAR-dependent social rescue. Therefore, NMDARs and gap junctions cooperate to promote cortical Pv neuronal bursts and social cognition.
An Anatomical Evaluation of the Mini-Supraorbital Approach and Comparison with Standard Craniotomies (2006)

The mini-SO approach may offer a similar surgical working area compared with that provided by standard craniotomies and constitutes an excellent alternative to the OZ and PT craniotomies in selected patients. Selection should not be based primarily on the area to be exposed, but rather on the working angles that are anticipated to be required. The key point is to use the most adequate technique for a particular patient, rather than using a one-size-fits-all approach for all patients.
Campylobacter jejuni-mediated disease pathogenesis: an update (2007)

Infection by Campylobacter jejuni is considered to be the most prevalent cause of bacterial-mediated diarrhoeal disease worldwide. Both in the developing and the developed world, young children remain most susceptible. Although disease is generally mild and self-limiting, severe post-infectious complications such as Gullain-Barré syndrome may occur. Despite the significant health burden caused by the organism, our current understanding of disease pathogenesis remains in its infancy. Elucidation of the genome sequences of many different C. jejuni strains in recent years has started to accelerate research in Campylobacter genetics, pathogenesis and host immunity in response to infection. Campylobacter jejuni is the first prokaryote shown to code for both O- and N-linked glycosylation systems, a feature that is likely to not only modulate bacterial virulence and survival, but also influence host-pathogen interactions and disease outcome. Here recent developments in C. jejuni research, with a particular focus on disease pathogenesis including early host immune responses, are highlighted.
Resveratrol regulates neuro-inflammation and induces adaptive immunity in Alzheimer’s disease (2017)

ClinicalTrials.gov NCT01504854.
Fluorescent dopamine tracer resolves individual dopaminergic synapses and their activity in the brain (2012)

We recently introduced fluorescent false neurotransmitters (FFNs) as optical tracers that enable the visualization of neurotransmitter release at individual presynaptic terminals. Here, we describe a pH-responsive FFN probe, FFN102, which as a polar dopamine transporter substrate selectively labels dopamine cell bodies and dendrites in ventral midbrain and dopaminergic synaptic terminals in dorsal striatum. FFN102 exhibits greater fluorescence emission in neutral than acidic environments, and thus affords a means to optically measure evoked release of synaptic vesicle content into the extracellular space. Simultaneously, FFN102 allows the measurement of individual synaptic terminal activity by following fluorescence loss upon stimulation. Thus, FFN102 enables not only the identification of dopamine cells and their processes in brain tissue, but also the optical measurement of functional parameters including dopamine transporter activity and dopamine release at the level of individual synapses. As such, the development of FFN102 demonstrates that, by bringing together organic chemistry and neuroscience, molecular entities can be generated that match the endogenous transmitters in selectivity and distribution, allowing for the study of both the microanatomy and functional plasticity of the normal and diseased nervous system.
Generation of Protein Crystals Using a Solution-Stirring Technique (2004)

Crystals of bovine adenosine deaminase (ADA) were grown over a two week period in the presence of an inhibitor, whereas ADA crystals did not form using conventional crystallization methods when the inhibitor was excluded. To obtain ADA crystals in the absence of the inhibitor, a solution-stirring technique was used. The crystals obtained using this technique were found to be of high quality and were shown to have high structural resolution for X-ray diffraction analysis. The results of this study indicate that the stirring technique is a useful method for obtaining crystals of proteins that do not crystallize using conventional techniques.