gebhart/patrepeval huggingface dataset:
Exonic Splicing Enhancer Motif Recognized by Human SC35 under Splicing Conditions (2000)

Exonic splicing enhancers (ESEs) are important cis elements required for exon inclusion. Using an in vitro functional selection and amplification procedure, we have identified a novel ESE motif recognized by the human SR protein SC35 under splicing conditions. The selected sequences are functional and specific: they promote splicing in nuclear extract or in S100 extract complemented by SC35 but not by SF2/ASF. They can also function in a different exonic context from the one used for the selection procedure. The selected sequences share one or two close matches to a short and highly degenerate octamer consensus, GRYYcSYR. A score matrix was generated from the selected sequences according to the nucleotide frequency at each position of their best match to the consensus motif. The SC35 score matrix, along with our previously reported SF2/ASF score matrix, was used to search the sequences of two well-characterized splicing substrates derived from the mouse immunoglobulin M (IgM) and human immunodeficiency virus tat genes. Multiple SC35 high-score motifs, but only two widely separated SF2/ASF motifs, were found in the IgM C4 exon, which can be spliced in S100 extract complemented by SC35. In contrast, multiple high-score motifs for both SF2/ASF and SC35 were found in a variant of the Tat T3 exon (lacking an SC35-specific silencer) whose splicing can be complemented by either SF2/ASF or SC35. The motif score matrix can help locate SC35-specific enhancers in natural exon sequences.
Data from Biomarkers for EGFR-Antagonist Response: In the Genes and on the Genes! (2023)

&lt;div&gt;Abstract&lt;p&gt;Patients with non–small cell lung carcinoma containing epidermal growth factor receptor (EGFR)–activating mutations benefit from EGFR-antagonist therapy. EGFR-antagonist sensitivity is also correlated with epithelial–mesenchymal transition, which Walter and colleagues show to be marked by DNA-methylation changes. If validated, these markers could help identify patients with wild-type EGFR who will benefit from EGFR therapy. &lt;i&gt;Clin Cancer Res; 18(8); 2121–3. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Correlation of free radical copolymerization behavior and copolymer properties with the strength of π‐π stacking interactions between aromatic fluorocarbons and aromatic hydrocarbons: Comparison of the copolymerization behavior of 2,3,4,5,6‐pentafluorostyrene with styrene, 1‐vinylnaphthalene and 2‐vinylnaphthalene (2008)

Abstract 2,3,4,5,6‐Pentafluorostyrene (PFS) was copolymerized with 1‐vinylnaphathalene (1VN) in bulk by radical copolymerization at 25 °C (r 1VN r PFS = 0.070) using t ‐butylperoxy pivalate as the inititator, at 70 °C ( r 1VN r PFS = 0.11) using benzyol peroxide as the initiator, and at 120 °C ( r 1VN r PFS = 0.28) using t ‐butyl peroxide as the initiator; PFS was also copolymerized with 2‐vinylnaphathalene (2VN) in bulk by radical copolymerization at 70 °C ( r 2VN r PFS = 0.15) under similar conditions. Their reactivity ratios were determined at low monomer conversions using the nonlinear least‐squares method of analysis, which demonstrated that both comonomer pairs tend to alternate, and that their alternating tendency increases with decreasing temperature, similar to the radical copolymerizations of PFS with styrene (St) in bulk. The glass transition temperatures determined by differential scanning calorimetry are elevated relative to their mole‐average values, with the extent of elevation being greater for the 1VN‐PFS copolymers than for the 2VN‐PFS copolymers, which is greater than that for St‐PFS copolymers. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 331–345, 2009
Evaluation of fermi level pinning in low, midgap and high workfunction metal cate electrodes on ALD and MOCVD HfO/sub 2/ under high temperature exposure (2005)

The workfunction behavior and stability of several candidate metal gate electrodes on HfO/sub 2/ was carefully examined and correlated with processing parameters such as anneal temperatures and oxygen exposures. Transition metals and their nitrides, binary metal alloys and refractory metals were studied on MOCVD HfO/sub 2/ dielectrics of varying thicknesses. Binary low work function Mo-Ta alloys were also investigated on HfO/sub 2/.
Novel Strategy for Sulfapyridine Detection Using a Fully Integrated Bio-MEMS: Application to Honey Analysis (2017)

Sulfapyridine (SPy) as a category of sulfonamides, have been widely used as veterinary drugs for prophylactic and therapeutic purposes. However, several classes of bacteria have become resistant to this drugs due to their abusive uses. This practice can also signify a potential risk to human health since many diseases may emerge, such as thyroid cancer and anaphylactic reactions. We report in the present work the development of a highly sensitive Biomicro-electro-mechanical systems (BioMEMS) gold transducers as working micro electrodes (WEs) for the detection of SPy residues in honey at the low ppb concentration. The detection of SPy by this method is highly promising to give a stable measurement and a rapid response, with a detection limit of 0.28 ng kg-1 in honey.
Clinical Scenarios in Acute Kidney Injury-Parenchymal Acute Kidney Injury - Vascular Diseases (2016)

Acute cortical necrosis and hemolytic uremic syndrome (HUS) are 2 clinical scenarios of parenchymal acute kidney injury (AKI) related to renal microvascular injury. Acute cortical necrosis is a rare condition related to an ischemic necrosis of renal cortex. Necrotic lesions can be due to several injuries and may be focal, multifocal or diffuse. Renal necrotic lesions become visible with ultrasound only after renal recovery. HUS is a rare disease characterized by hemolytic anemia, thrombocytopenia and AKI. Color Doppler ultrasound is useful during diagnostic and follow-up phase. Renal artery thrombosis and renal vein thrombosis may also cause parenchymal AKI. Acute renal infarction is a rare pathological condition that occurs due to clots or cholesterol aggregates occluding renal artery or its branches. Several causes may lead to partial or massive kidney ischemic necrosis. Contrast-enhanced CT allows definitive diagnosis in 80% of cases and, at present, it is the first imaging technique used. Ultrasound (US) sensitivity and specificity significantly increases with color Doppler and contrast-enhanced US (CEUS). In AKI patients, in whom the use of iodinated contrast media is contraindicated, color Doppler and CEUS may be valid alternatives for the diagnosis of acute renal infarction. Renal vein thrombosis may be primary or secondary to retroperitoneal neoplasm or inflammatory diseases. It rarely causes an acute worsening of renal function because of the presence of several anastomosis that prevent parenchymal necrosis due to venous congestion. Color Doppler US could detect thrombus within the lumen and document the absence of venous flow.
An analytical mass spectrometry method of determining binding constants between chemokine, posttranslationally modified chemokine receptor N‐terminal peptides, and glycosaminoglycan (2010)

Chemokines play roles in inducing chemotaxis, extravasation, and activation of leukocytes. Tyrosine sulfation of the chemokine receptor is crucial for binding to its ligands and signaling. A robust analytical method for measuring the contribution of this posttranslational modification to the receptor to binding of its ligand is lacking. Using Nano‐electrospray time‐of‐flight mass spectrometry, we determined the association constant of chemokine, CCL7 to variably sulfated CCR2 peptides. Association constants between CCL7‐CCR2, CCL7‐monosulfated CCR2, and CCL7‐ disulfated CCR2 were determined to be 1.1 x 10 4 M −1 , 3.9 x 10 4 M −1 , and 4.0 x 10 5 M −1 , respectively. Chemokines also bind to glycosaminoglycans (GAGs). Mutation studies suggest a partial overlap between the GAG and receptor binding domains, but it has been debatable whether a ternary complex forms. Using mass spectrometry we did not observe significant ternary complex formation. Thus, competitive binding experiments between Arixtra and disulfated CCR2 were conducted. As the concentration of disulfated CCR2 is increased from 0μM to 10μM two observations are made suggesting that CCR2 competes with GAG for CCL7 binding: 1. more noncovalent complexes between CCL7 and CCR2; 2. Less noncovalent interactions between CCL7 and Arixtra.
Simple Quantitative Measurement of Glycogen in Shell Ligament Using Disposable Blood Glucose Sensor. (1997)

使い捨て型血糖値センサを利用して,真珠養殖用アコヤガイ貝柱内のグリコーゲン定量を検討した.貝柱-酸加熱-冷却-上澄み採取-pH調整-定溶-血糖値センサ測定からなる簡易法を従来法と比較した結果, このセンサ出力と従来法によるグリコーゲン含有率との間で相関係数0.99の直線関係が得られた.また,グリコーゲン含有率2.0%の貝柱を試料にした場合の変動係数は2.8%(n=10)であった.この結果,比較的簡単な設備だけで貝柱内のグリコーゲン量を迅速に測定できるようになった.
Diverse Applications of Nanomedicine (2017)

The design and use of materials in the nanoscale size range for addressing medical and health-related issues continues to receive increasing interest. Research in nanomedicine spans a multitude of areas, including drug delivery, vaccine development, antibacterial, diagnosis and imaging tools, wearable devices, implants, high-throughput screening platforms, etc. using biological, nonbiological, biomimetic, or hybrid materials. Many of these developments are starting to be translated into viable clinical products. Here, we provide an overview of recent developments in nanomedicine and highlight the current challenges and upcoming opportunities for the field and translation to the clinic.
Microfracture network evolution leading to catastrophic failure: hearing and seeing. (2020)

The process of strain localisation is critical in the evolution of deformation leading to catastrophic failure. However, the precise mechanisms of how cracks, pores and grain boundaries interact locally under an applied stress field have yet to be determined. To understand the microscopic processes and their control of system-sized failure, a novel x-ray transparent cell was used for deformation experiments of rock samples, which permits integration of acoustic monitoring with fast synchrotron x-ray imaging. To increase temporal characterization of damage beyond the temporal resolution of the fast 3D synchrotron system, acoustic emission (AE) feedback control was used to regulate the applied stress and slow down the deformation processes. As a result, the increment deformation between x-ray scanned states was relatively homogeneous, simplifying comparison between AE events and x-ray scans. In this paper, we present the acoustic data acquisition, conditioning and processing used to characterize the velocity evolution of the rock samples, and the location and characteristics of individual AE events during deformation. Time-lapse velocity measurements are linked to internal stress changes and structural damage corresponding to seismic and aseismic deformation processes, while acoustic emissions are a direct indication of local cracking. We show that we can successfully locate AE events in 3D, using only two sensors on either end of the sample, based on ellipsoid mapping. We further test AE location using Coda Wave Interferometry (CWI), which has only been analysed so far synthetically, with CWI earthquake location techniques previously applied exclusively to field scale. By exploring the kinematic and dynamic signatures of AE events, we characterise and locate seismic deformation processes and examine how those are linked to the strain field in the samples measured with incremental Digital Volume Correlation between pairs of recorded x-ray tomograms.
Supplementary Figure Legends 1-4, Table Legend from DCAMKL-1 Regulates Epithelial–Mesenchymal Transition in Human Pancreatic Cells through a <i>miR-200a</i>–Dependent Mechanism (2023)

Supplementary Figure Legends 1-4, Table Legend from DCAMKL-1 Regulates Epithelial–Mesenchymal Transition in Human Pancreatic Cells through a &lt;i&gt;miR-200a&lt;/i&gt;–Dependent Mechanism
Data from Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Although local tissue-based immune responses are critical for elucidating direct tumor–immune cell interactions, peripheral immune responses are increasingly recognized as occupying an important role in anticancer immunity. We evaluated serial blood samples from patients with advanced epithelial ovarian cancer (EOC) undergoing standard-of-care neoadjuvant carboplatin and paclitaxel chemotherapy (including dexamethasone for prophylaxis of paclitaxel-associated hypersensitivity reactions) to characterize the evolution of the peripheral immune cell function and composition across the course of therapy.&lt;/p&gt;Experimental Design:&lt;p&gt;Serial blood samples from 10 patients with advanced high-grade serous ovarian cancer treated with neoadjuvant chemotherapy (NACT) were collected before the initiation of chemotherapy, after the third and sixth cycles, and approximately 2 months after completion of chemotherapy. T-cell function was evaluated using &lt;i&gt;ex vivo&lt;/i&gt; IFNγ ELISpot assays, and the dynamics of T-cell repertoire and immune cell composition were assessed using bulk and single-cell RNA sequencing (RNAseq).&lt;/p&gt;Results:&lt;p&gt;T cells exhibited an improved response to viral antigens after NACT, which paralleled the decrease in CA125 levels. Single-cell analysis revealed increased numbers of memory T-cell receptor (TCR) clonotypes and increased central memory CD8&lt;sup&gt;+&lt;/sup&gt; and regulatory T cells throughout chemotherapy. Finally, administration of NACT was associated with increased monocyte frequency and expression of HLA class II and antigen presentation genes; single-cell RNAseq analyses showed that although driven largely by classical monocytes, increased class II gene expression was a feature observed across monocyte subpopulations after chemotherapy.&lt;/p&gt;Conclusions:&lt;p&gt;NACT may alleviate tumor-associated immunosuppression by reducing tumor burden and may enhance antigen processing and presentation. These findings have implications for the successful combinatorial applications of immune checkpoint blockade and therapeutic vaccine approaches in EOC.&lt;/p&gt;&lt;/div&gt;
Crystal Structure Analysis of Multiwalled Carbon Nanotube Forests by Newly Developed Cross-Sectional X-ray Diffraction Measurement (2010)

A novel cross-sectional X-ray diffraction method was developed to evaluate crystal structures of multiwalled carbon nanotube (CNT) forests. Aligned degree of the graphene volume in the CNT forest could be quantified by this analysis. The domain sizes of the CNTs in the forests were estimated using a modified Scherrer's equation for bending multilayered graphene sheets. The statistical information of the crystal structure of the CNT forests including the degree of alignment, domain size, layer numbers, and interlayer spacing d002 will contribute to developing applications of CNT forests for devices and functional materials.
Iridium(I)-Catalyzed α-C(sp3)–H Alkylation of Saturated Azacycles (2020)

Saturated azacycles are commonly encountered in bioactive compounds and approved therapeutic agents. The development of methods for functionalization of the α-methylene C-H bonds of these highly privileged building blocks is of great importance, especially in drug discovery. While much effort has been dedicated toward this goal by using a directed C-H activation approach, the development of directing groups that are both <i>general</i> as well as <i>practical</i> remains a significant challenge. Herein, the design and development of novel amidoxime directing groups is described for Ir(I)-catalyzed α-C(sp<sup>3</sup>)-H alkylation of saturated azacycles using readily available olefins as coupling partners. This protocol extends the scope of saturated azacycles to piperidines, azepane, and tetrahydroisoquinoline that are incompatible with our previously reported directing group. A variety of olefin coupling partners, including previously unreactive disubstituted terminal olefins and internal olefins, are compatible with this transformation. The selectivity for a branched α-C(sp<sup>3</sup>)-alkylation product is also observed for the first time when acrylate is used as the reaction partner. The development of practical, one-step installation and removal protocols further adds to the utility of amidoxime directing groups.
Simultaneous bidirectional propagation of cold atoms in a “stadium” shaped magnetic waveguide ring (2004)

we report the bidirectional propagation of atom sample around a “stadium” shaped magnetice waveguide. The atoms are cooled and trapped at one side of the magnetic “stadium”. Optical standingwave can evenly divide the atoms to propagate in opposite directions around the ring, which recombine at starting position after traversing the same closed path. The ring encloses an area of 8.0 cm2. The flux density of the guided atoms reaches 1011 sec−1 cm−2.
Infrastructure Mobility (2014)

Mobile computing has traditionally implied mobile clients connected to a static infrastructure. This paper breaks away from this point of view and envisions the possibility of injecting mobility into infrastructure. We envision a WiFi access point on wheels, that moves to optimize desired performance metrics. Movements need not necessarily be all around the floor of a home or office, neither do they have to operate on batteries, or connect wirelessly to the Internet. At homes, they could remain tethered to power and Ethernet outlets while moving in small areas (perhaps under the study table). In offices of the future, perhaps APs could move on tracks installed on top of false ceilings.
Supplemental Figure 5 from Mast Cell–Derived Prostaglandin D<sub>2</sub> Inhibits Colitis and Colitis-Associated Colon Cancer in Mice (2023)

&lt;p&gt;Supplemental Figure&lt;/p&gt;
Power-performance management on an IBM POWER7 server (2010)

The processor and cooling subsystems of high-performance servers consume a significant portion of total system power. In this paper, we use the server energy-efficiency benchmark SPECpower_ssj2008 to assess dynamic power management strategies for these sub-systems on an IBM POWER 750 platform.
Increase in Expression of IL-4 and IL-5 Mrna in the Nasal Mucosa of Patients with Perennial Allergic Rhinitis during Natural Allergen Exposure (1997)

To understand the role of cytokines in allergic nasal disease in humans, we designed this study to investigate the expression of cytokine mRNA in the nasal mucosa of 10 control subjects and 10 patients with perennial allergic rhinitis using a reverse transcription-polymerase chain reaction (RT-PCR) for IL-4, IL-5 (Th2 cytokines), and IFN-gamma (Th1 cytokine). Both IL-4 and IL-5 mRNAs were expressed in a significantly larger number of patients with allergic rhinitis than in control subjects. When the levels of expression of cytokines and beta-actin mRNA were quantitated, the mean density ratios (cytokine/beta-actin) for IL-4 and IL-5 were higher in patients with allergic rhinitis than in control subjects. In contrast, there were no differences in the number of subjects who showed expression of IFN-gamma mRNA, or in mean density ratios for IFN-gamma between the two groups. This study suggests that both IL-4 and IL-5 mRNAs are expressed almost universally in the nasal mucosa of patients with perennial allergic rhinitis during natural allergen exposure and also that Th2-type cytokines play a crucial role in the development of allergic nasal diseases in vivo.
Efficient methods for unsupervised learning of probabilistic models (2012)

High dimensional probabilistic models are used for many modern scientific and engineering data analysis tasks. Interpreting neural spike trains, compressing video, identifying features in DNA microarrays, and recognizing particles in high energy physics all rely upon the ability to find and model complex structure in a high dimensional space. Despite their great promise, high dimensional probabilistic models are frequently computationally intractable to work with in practice. In this thesis I develop solutions to overcome this intractability, primarily in the context of energy based models. 
A common cause of intractability is that model distributions cannot be analytically normalized. Probabilities can only be computed up to a constant, making training exceedingly difficult. To solve this problem I propose 'minimum probability flow learning', a variational technique for parameter estimation in such models. The utility of this training technique is demonstrated in the case of an Ising model, a Hopfield auto-associative memory, an independent component analysis model of natural images, and a deep belief network. 
A second common difficulty in training probabilistic models arises when the parameter space is ill-conditioned. This makes gradient descent optimization slow and impractical, but can be alleviated using the natural gradient. I show here that the natural gradient can be related to signal whitening, and provide specific prescriptions for applying it to learning problems. 
It is also difficult to evaluate the performance of models that cannot be analytically normalized, providing a particular challenge to hypothesis testing and model comparison. To overcome this, I introduce a method termed 'Hamiltonian annealed importance sampling,' which more efficiently estimates the normalization constant of non-analytically-normalizable models. This method is then used to calculate and compare the log likelihoods of several state of the art probabilistic models of natural image patches. 
Finally, many tasks performed with a trained probabilistic model (for instance, image denoising or inpainting and speech recognition) involve generating samples from the model distribution, which is typically a very computationally expensive process. I introduce a modification to Hamiltonian Monte Carlo sampling that reduces the tendency of sampling trajectories to double back on themselves, and enables statistically independent samples to be generated more rapidly. 
Taken together, it is my hope that these contributions will help scientists and engineers to build and manipulate probabilistic models.
Recommendations for conducting the rodent erythrocyte Pig‐a assay: A report from the HESI GTTCPig‐a Workgroup (2021)

The rodent Pig-a assay is a flow cytometric, phenotype-based method used to measure in vivo somatic cell mutation. An Organization for Economic Co-operation and Development (OECD) test guideline is currently being developed to support routine use of the assay for regulatory purposes (OECD project number 4.93). This article provides advice on best practices for designing and conducting rodent Pig-a studies in support of evaluating test substance safety, with a focus on the rat model. Various aspects of assay conduct, including laboratory proficiency, minimum number of animals per dose group, preferred treatment and blood sampling schedule, and statistical analysis are described.
Structure and Properties of Gallium-Rich Sodium Germano-Gallate Glasses (2018)

Glass compositions in the gallium-rich region of the ternary GaO3/2–GeO2–NaO1/2 vitreous system are studied as a function of the Na/Ga cationic ratio (ranging from 1.30 to 1.61) for a fixed GeO2 content. Glass structures are investigated by 71Ga magic angle spinning nuclear magnetic resonance, infrared, and Raman spectroscopies, and the thermal, optical, and physical properties are characterized. Vibrational spectra are interpreted with the help of density functional theory calculations. Gallium oxide generally enters the germania network in fourfold coordination, however, for a Na/Ga ratio below unity, gallium cations tend to charge balance with the formation of five- or six-fold coordination units. When the amount of sodium is greater than gallium, nonbridging oxygens are formed preferably on germanate tetrahedral units. These structural descriptions are used to understand the evolution of glass properties such as glass transition temperature, density, and refractive index.