gebhart/patrepeval huggingface dataset:
Global analyses of mRNA expression in human sensory neurons reveal eIF5A as a conserved target for inflammatory pain (2022)

Nociceptors are a type of sensory neuron that are integral to most forms of pain. Targeted disruption of nociceptor sensitization affords unique opportunities to prevent pain. An emerging model for nociceptors are sensory neurons derived from human stem cells. Here, we subjected five groups to high-throughput sequencing: human induced pluripotent stem cells (hiPSCs) prior to differentiation, mature hiPSC-derived sensory neurons, mature co-cultures containing hiPSC-derived astrocytes and sensory neurons, mouse dorsal root ganglion (DRG) tissues, and mouse DRG cultures. Co-culture of nociceptors and astrocytes promotes expression of transcripts enriched in DRG tissues. Comparisons of the hiPSC models to tissue samples reveal that many key transcripts linked to pain are present. Markers indicative of a range of neuronal subtypes present in the DRG were detected in mature hiPSCs. Intriguingly, translation factors were maintained at consistently high expression levels across species and culture systems. As a proof of concept for the utility of this resource, we validated expression of eukaryotic initiation factor 5A (eIF5A) in DRG tissues and hiPSC samples. eIF5A is subject to a unique posttranslational hypusine modification required for its activity. Inhibition of hypusine biosynthesis prevented hyperalgesic priming by inflammatory mediators in vivo and diminished hiPSC activity in vitro. Collectively, our results illuminate the transcriptomes of hiPSC sensory neuron models. We provide a demonstration for this resource through our investigation of eIF5A. Our findings reveal hypusine as a potential target for inflammation associated pain in males.
A wideband bulk acoustic wave filter with modified lattice configuration (2015)

This paper proposes a modified lattice configuration of aluminum nitride (AlN) based bulk acoustic wave bandpass filter, which effectively broadens the pass band width without sacrificing the insertion loss and out-of-band rejection. The novel topology comprises two auxiliary inductors paralleled in the balanced input and output of the conventional lattice topology. The performance of the filter is evaluated theoretically as well as experimentally. It is found that, in multistage configuration, the number of auxiliary inductors decreases exponentially, enabling the compact integration of filter chips. This topology is further validated from the experiment, with the filter bandwidth measured to be 400 MHz at central frequency of 3.25 GHz (12.3 % relative bandwidth), which is in excellent agreement with the simulation.
Engineered biosynthesis of an ansamycin polyketide precursor in Escherichia coli (2003)

Ansamycins such as rifamycin, ansamitocin, and geldanamycin are an important class of polyketide natural products. Their biosynthetic pathways are especially complex because they involve the formation of 3-amino-5-hydroxybenzoic acid (AHBA) followed by backbone assembly by a hybrid nonribosomal peptide synthetase/polyketide synthase. We have reconstituted the ability to synthesize 2,6-dimethyl-3,5,7-trihydroxy-7-(3'-amino-5'-hydroxyphenyl)-2,4-heptadienoic acid (P8/1-OG), an intermediate in rifamycin biosynthesis, in an extensively manipulated strain of Escherichia coli. The parent strain, BAP1, contains the sfp phosphopantetheinyl transferase gene from Bacillus subtilis, which posttranslationally modifies polyketide synthase and nonribosomal peptide synthetase modules. AHBA biosynthesis in this host required introduction of seven genes from Amycolatopsis mediterranei, which produces rifamycin, and Actinosynnema pretiosum, which produces ansamitocin. Because the four-module RifA protein (530 kDa) from the rifamycin synthetase could not be efficiently produced in an intact form in E. coli, it was genetically split into two bimodular proteins separated by matched linker pairs to facilitate efficient inter-polypeptide transfer of a biosynthetic intermediate. A derivative of BAP1 was engineered that harbors the AHBA biosynthetic operon, the bicistronic RifA construct and the pccB and accA1 genes from Streptomyces coelicolor, which enable methylmalonyl-CoA biosynthesis. Fermentation of this strain of E. coli yielded P8/1-OG, an N-acetyl P8/1-OG analog, and AHBA. In addition to providing a fundamentally new route to shikimate and ansamycin-type compounds, this result enables further genetic manipulation of AHBA-derived polyketide natural products with unprecedented power.
Fabrication and characterization of Mg 2 Si pn-junction photodiode with circular electrode (2014)

pyrolytic graphite (PG) crucibles (Ibiden Co.). Mg2Si substrates of 3 x 3 mm 2 , 1-mm-thick were polished on both sides by fumed silica (AKASEL, water-free, 0.2 μm). The pn-junction photodiodes with the Au-ring electrode were fabricated by the conventional photolithography process. The p-type region with the diameter (D) of 150 μm, 200 μm, and 300 μm was made by the rapid thermal diffusion of Ag metal layer at 550 °C for 10 min [11, 10]. The diffusion source of Ag metal with the appropriate diameter was formed on the Mg2Si substrate with the Au capping metal by the lift-off process using a conventional heat-resistive evaporator. After the diffusion of the Ag metal source, the surface of the substrate was polished to flat, and then 100 nm-thick SiO2 passivation layer was deposited on the top surface by chemical vapor deposition method. After that, the Au-ring electrodes with the inner diameter (ID) of 50 μm, 100 μm and 200 μm were formed on top of the p-type region with the D of 150 μm, 200 μm, and 300 μm, respectively. Fig.1(a) and (b) show the top view of the fabricated pn-junction photodiode with the ID = 100 μm and the cross sectional device structure of the photodiode, respectively. Photoresponse properties of the photodiode were measured under a zero bias condition at room temperature using a halogen lamp chopped and passed through an IR filter (cut-off = 1.2 m) and a single monochromator (JASCO CT-50) with a focal length of 500 mm [10]. We also evaluated the ideality factor n and surface leakage current density Jsurf from the current-voltage (I-V) characteristics of the photodiode by the following equations [12];
Burkholderia thailandensis E125 Harbors a Temperate Bacteriophage Specific for Burkholderia mallei (2002)

Burkholderia thailandensis is a nonpathogenic gram-negative bacillus that is closely related to Burkholderia mallei and Burkholderia pseudomallei. We found that B. thailandensis E125 spontaneously produced a bacteriophage, termed phiE125, which formed turbid plaques in top agar containing B. mallei ATCC 23344. We examined the host range of phiE125 and found that it formed plaques on B. mallei but not on any other bacterial species tested, including B. thailandensis and B. pseudomallei. Examination of the bacteriophage by transmission electron microscopy revealed an isometric head and a long noncontractile tail. B. mallei NCTC 120 and B. mallei DB110795 were resistant to infection with phiE125 and did not produce lipopolysaccharide (LPS) O antigen due to IS407A insertions in wbiE and wbiG, respectively. wbiE was provided in trans on a broad-host-range plasmid to B. mallei NCTC 120, and it restored LPS O-antigen production and susceptibility to phiE125. The 53,373-bp phiE125 genome contained 70 genes, an IS3 family insertion sequence (ISBt3), and an attachment site (attP) encompassing the 3' end of a proline tRNA (UGG) gene. While the overall genetic organization of the phiE125 genome was similar to lambda-like bacteriophages and prophages, it also possessed a novel cluster of putative replication and lysogeny genes. The phiE125 genome encoded an adenine and a cytosine methyltransferase, and purified bacteriophage DNA contained both N6-methyladenine and N4-methylcytosine. The results presented here demonstrate that phiE125 is a new member of the lambda supergroup of Siphoviridae that may be useful as a diagnostic tool for B. mallei.
De novo pathogenic variants in CHAMP1 are associated with global developmental delay, intellectual disability, and dysmorphic facial features (2015)

We identified five unrelated individuals with significant global developmental delay and intellectual disability (ID), dysmorphic facial features and frequent microcephaly, and de novo predicted loss-of-function variants in chromosome alignment maintaining phosphoprotein 1 (CHAMP1). Our findings are consistent with recently reported de novo mutations in CHAMP1 in five other individuals with similar features. CHAMP1 is a zinc finger protein involved in kinetochore-microtubule attachment and is required for regulating the proper alignment of chromosomes during metaphase in mitosis. Mutations in CHAMP1 may affect cell division and hence brain development and function, resulting in developmental delay and ID.
Subnanotesla quantum-interference magnetometry with a single spin in diamond (2015)

We demonstrate a magnetometry technique using nitrogen-vacancy centres in diamond which makes use of coherent two-photon transitions. We find that the sensitivity to magnetic fields can be significantly improved in isotopically purified diamond. Furthermore, the long-term stability of magnetic field measurements is significantly enhanced, thereby reducing the minimum detectable long-term field variations for both quasi-static and periodic fields. The method is useful both for sensing applications and as a spin qubit manipulation technique.
The intestinal microbiota associated with cardiac valve calcification differs from that of coronary artery disease (2018)

Patients with VC and CAD suffer from different gut microbial dysbiosis. The gut microbiomes are associated with the clinical characteristics in these diseases and might be potential therapeutic targets.
Stimulant Drug Treatment in Childhood-Onset Schizophrenia with Comorbid ADHD: An Open-Label Case Series (2004)

The administration of psychostimulants to children with psychotic symptoms is controversial. This study reports the stimulant drug response of 5 children, aged 8-15 years, with childhood-onset schizophrenia (COS) and comorbid attention deficit hyperactivity disorder (ADHD). Four COS inpatients were given stimulants for comorbid ADHD after stabilization of psychosis on antipsychotic medication. A fifth COS inpatient received stimulants while still actively psychotic, despite concurrent neuroleptic treatment. Data from the 10-item Brief Conners Teachers Ratings Scale (BCTRS) were examined the week before, and the week after, stimulant addition. A paired t test, conducted using Conners Teachers data from these 4 subjects, indicated significant improvement in ADHD symptoms (p = 0.02). Data obtained from a retrospective chart review indicated no significant worsening of psychosis. The 2 subjects treated with mixed salts of dextroamphetamine sulfate and amphetamine sulfate remained on that medication at 6 months and at the 2-year follow-up. Our results suggest that ADHD comorbid with COS may be safely treated with a stimulant, once the psychosis is stabilized. A systematic investigation of this question may be warranted.
Energy-efficient wi-fi gateways for federated residential networks (2013)

Cooperation among federated APs in dense urban areas can yield energy saving by allowing under-used devices to hand over their wireless stations (WS) to nearby APs and temporarily switch off while meeting user expectations in terms of throughput. We demonstrate the effectiveness and the benefits of our energy-efficient cooperative protocol through a real deployment emulating a residential scenario. The demo we propose is highly interactive, as users can generate traffic within a BSS through a wireless station, like a smartphone or a notebook, and observe, through a web interface, the protocol behavior and the network topology changes caused by the new traffic scenario.
Solid-phase purification of gene synthesis products using magnetic beads (2008)

Herein we report three novel methods which utilize chemical conjugated magnetic beads to purify synthetic gene from its synthesis solution and prepare the synthesized gene in suitable buffer for downstream applications. Silica-coated magnetic beads are applied for non-specific DNA purification to remove short oligonucleotides and monomers. Streptavidin conjugated magnetic beads and (dT)<sub>25</sub> Oligo immobilized magnetic beads are introduced for specific DNA extraction. The performances of these methods are investigated and compared using gel electrophoresis. The optimal conditions for enhancing the extraction efficiency are discussed. In addition, the approach to integrate these solid-phase purification methods into microfluidic devices is presented.
Somatosensory‐evoked cortical potential during attacks of paroxysmal dysesthesia in multiple sclerosis (2005)

Paroxysmal dysesthesia is considered to be one of the characteristic symptoms of multiple sclerosis (MS), but the lesion responsible and the pathophysiology of this dysesthesia are not known. We report the interesting finding of somatosensory-evoked potentials (SEPs) in a patient with MS during a paroxysmal dysesthesia attack.
Fludarabine, cytarabine, and idarubicin with or without venetoclax in patients with relapsed/refractory acute myeloid leukemia (2023)

Treatment options for relapsed and refractory acute myeloid leukemia patients (R/R AML) are limited. This retrospective cohort study compares safety and efficacy of fludarabine, cytarabine, and idarubicin (FLA-IDA) without or with venetoclax (FLAVIDA) in patients with R/R AML. Thirty-seven and 81 patients received one course FLA-IDA with or without a 7-day course of venetoclax, respectively. The overall response rate (ORR) was significantly higher in FLAVIDA compared to FLAIDA- treated patients (78% vs. 47%; P=0.001), while measurable residual disease was negative at a similar proportion in responding patients (50% vs. 57%), respectively. Eighty-one percent and 79% of patients proceeded to allogeneic hematopoietic cell transplantation or donor lymphocyte infusion after FLAVIDA and FLA-IDA, respectively. Event-free and overall survival were similar in FLAVIDA- and FLA-IDA-treated patients. Refractory patients could be salvaged more successfully after FLA-IDA compared to FLAVIDA pretreatment. Neutrophil and platelet recovery times were similar in the venetoclax and the control group. In conclusion, short-term venetoclax in combination with FLA-IDA represents an effective treatment regimen in R/R AML identifying chemosensitive patients rapidly and inducing measurable residual disease-negative remission in a high proportion of R/R AML patients.
Roles of BCL6 in normal and transformed germinal center B cells (2012)

BCL6 is a transcriptional repressor required in mature B cells during the germinal center (GC) reaction. Multiple mechanisms act coordinately to timely modulate BCL6 expression at transcriptional and post-transcriptional levels. BCL6 prevents premature activation and differentiation of GC B cells and provides an environment tolerant of the DNA breaks associated with immunoglobulin gene remodeling mechanisms involved in the production of high-affinity antibodies of different isotypes. The critical functions exerted by BCL6 during normal B-cell development can be hijacked by the malignant transformation process. Indeed, BCL6 is targeted by genetic aberrations and acts as an oncogene in GC-derived lymphomas. The aberrations affecting BCL6 interfere with the multiple levels of regulation that grant a fine tuning of BCL6 expression and activity in physiologic conditions. This review summarizes the current knowledge on BCL6 function and its role in lymphomagenesis.
Explainable prediction of survival using clinical, molecular, and radiomic profiles in recurrent high-grade glioma patients treated with CAR T-cell therapy. (2021)

104 Background: High-grade glioma (HGG) is an aggressive heterogeneous primary CNS neoplasm with high recurrence rate and poor survival. Multiple ongoing clinical trials are leveraging targeted molecular and immunologic therapeutics (e.g., pembrolizumab, Chimeric Antigen Receptor [CAR] T-cell therapy) in effort to improve survival. Explainable predictive models have shown value in identifying biomarkers predictive of treatment response as well as informing prognosis. In this study, we developed an explainable machine learning model leveraging clinical, molecular and radiomic (imaging) features to predict overall survival in patients suffering from HGG treated with CAR T-cell therapy. Methods: In this IRB-approved phase 1 clinical trial, 60 patients (39 males, median age = 49) suffering from HGG underwent surgical resection and CAR T-cell therapy 1 . All patients underwent baseline MRI scans prior to both surgical resection and CAR T-cell administration in the resection cavity. Using contrast-enhanced T1-weighted MRIs, we segmented the enhancing tumor (ET) and generated radiomic features. For predictive modeling, we incorporated the following features: Age, gender, race, ethnicity, histology, tumor grade (WHO), IL-13 receptor alpha 2 (IL-13Rα2) expression (H score), unifocal or multifocal lesions, tumor location (lobe), shape-based radiomics (tumor volume, surface area, and sphericity). We utilized gradient-boosted tree models to classify whether survival is above or below 180 days with two-loop nested cross-validation. For the inner validation loop, we optimized the model with hyper-parameter tuning. For the outer validation loop, we tested the optimal model on the hold-out data and the predictions were used as survival scores (0 – 1). Larger scores imply better predicted survival. For prediction explanations, we adopted the Shapley additive explanation (SHAP) framework. Results: The outer validation loop Area Under the Receiver Operating Characteristic Curve and Area under the Precision-Recall Curve were 0.76 and 0.81, respectively. Among the top five most important features calculated from SHAP; patients with larger tumor surface area, tumor volume and age have reduced survival scores while patients with larger IL-13Rα2 and tumor sphericity have increased survival scores. We stratified the patients into two distinct prognostic sub-groups (30 patients each group) using the survival scores obtained from the outer loop, with a log-rank test p &lt; 0.01. Conclusions: In patients with HGG treated with CAR T-cell therapy, we found that tumor surface area/volume and age are inversely related to survival while increased IL-13Rα2 expression and tumor sphericity were positive predictor of survival. Our model can potentially be used to optimize clinical trial enrollment through more precise patient screening and treatment planning.
Fiber Bragg Grating Sensing-Based Online Torque Detection on Coupled Bending and Torsional Vibration of Rotating Shaft (2017)

This paper has presented a novel approach based on fiber Bragg grating (FBG) sensing to analyze and decouple the coupled bending and torsional vibration of a rotating shaft. The theoretical FBG-based strain detection models under pure torsional vibration and coupled bending and torsional vibration have been derived. Two FBG sensors have been attached on the opposite sides of a rotating shaft with an angle of 45° with respect to the axial direction to support the use of the proposed decoupling method and determine the decoupled bending and torsion signals. A new supporting device has been designed to protect the fiber optical rotary joint from damage under large load impact, and ensure the stable signal transmit. The calibrated sensitivity of the pasted FBGs for measuring torque is 7.02 pm/N·m. Dynamic experiments on a rotor platform under different rotating speeds have been performed to effectively decouple the bending strain and torsional strain in real time. The decoupled torque measurements have shown a close agreement with the data detected from a commercial tacho-torquemeter, which demonstrated the effectiveness of the proposed decoupling method.
AI '92 : proceedings of the 5th Australian Joint Conference on Artificial Intelligence : Hobart, Tasmania, 16-18 November 1992 (1992)

Automated operation of complex machinery using plans extracted from numerical models - towards adaptive control of a stainless steel cold rolling mill, D. Stirling and S. Sevinc annealing networks and fractal landscapes - is the writing on the wall?, R. Lister a master/slave neural network architecture, P. Hingston classification with networks of fixed hidden units, A. Kowalczyk a comparison of image processing techniques and neural networks for an automated visual inspection problem, V. Ciesielski et al estimating sun direction from a single image, W. Chojnacki et al a framework for reasoning about modelling, N.Y. Foo a belief revision approach to nonmonotonic reasoning, W. Wobcke man-machine collaboration for knowledge acquisition, G.I. Webb learning with continuous classes, J.R. Quinlan induction of ripple-down rules, B.R. Gaines and P.J. Compton predicting situation outcomes on the basis of past cases, C. Bradburn and J. Zeleznikow. (Part contents)
ChemInform Abstract: An Expeditious I2‐Catalyzed Entry into 6H‐Indolo[2,3‐b]quinoline System of Cryptotackieine. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A computational protocol and software implementation (as a MATLAB application) for biomarker identification in infrared spectroscopy datasets (2010)

One attractive possibility of infrared (IR) spectroscopy is that it may be applied to investigate class (i.e., treatment, tissue type, etc)-specific alterations in the absorption signature. Such alterations can act as biomarkers of mechanism associated with pathways or effects. One may be interested in investigating such alterations from different standpoints including: (1) intensity; (2) statistical significance; and, (3) composite (multi-spectral-region) alterations. These three view-concepts were implemented computationally and named BM1, BM2 and BM3. They can be easily applied to datasets of classed IR spectra through a user-friendly MATLAB interface. BM1. Most intuitive of the methods. The mean spectrum from a given class is subtracted from the mean spectrum from a reference class (e.g., “vehicle control”) thus obtaining a “difference-between-means curve”. BM2. Each variable (wavenumber) is taken at a time as input to a univariate linear classifier thus obtaining a per-wavenumber “classification rate curve”1. Cross-validation is used to determine classification rates. This method is close to the t-test criterion2, but more precise. BM3. When multiple variables are assessed together, the joint-best variables for classification may differ substantially from the rank of the individual best variables. This method generates a histogram that represents how many times each wavenumber appeared within the TopVars (method parameter: number of “best variables”) “best variable set” achieved through feature selection, which is repeated many times according to NoBootstraps (method parameter: number of validation bootstraps). The aim of this protocol is identify and visualize class-related biomarkers in IR spectral datasets by means of a simple sequence of steps to be executed under a user-friendly interface (Figure 1). Two visual representations are provided where all BM results are presented concurrently allowing for comparison of results generated by each method.