gebhart/patrepeval huggingface dataset:
Supplementary Materials and Methods, Figures S1-5 and Tables S1-8 from Redesigning a Monospecific Anti-FGFR3 Antibody to Add Selectivity for FGFR2 and Expand Antitumor Activity (2023)

&lt;p&gt;Supplementary Materials and Methods, Figures S1-5 and Tables S1-8. Supplementary Materials and Methods: More detailed description of Materials and Methods for experiments. Figure S1: Structural analysis of the FGFR3-IIIb and R3Mab complex. Figure S2: Sequence analysis of the CDR H2 of selected FGFR2-positive clones. Figure S3: Superimposition of crystal structures of FGFR2-D2:2B.1.3 and FGFR3-D2D3:R3Mab. Figure S4: in vitro and in vivo studies of the 2B.1 antibody variants using the breast cancer cell line MFM-223x2.2. Figure S5: FGFR2 and FGFR3 expressions in gastric cancer cell line SNU-16. Table S1: Library design for recruiting FGFR2 binding specificity for R3Mab. Table S2: Library design for removing FGFR4 binding specificity from 2B.1.3. Table S3: Sequence identities between human FGFR. Table S4: Bidning affinities of selected 2B.1 variants for FGFR2 and FGFR3. Table S5: X-ray crystallography data collection and refinement statistics. Table S6: Binding affinities of R3Mab and 2B.1.3 for the D2 alone and D2D3 constructs of FGFR2 and FGFR3. Table S7: Residue differences between FGFR2 and FGFR4 at the positions making potential contacts with 2B.1.3. Table S8: 2B.1.3 variants that retain FGFR2 binding and show diminished binding to FGFR4.&lt;/p&gt;
Molecular bridging of aging and cancer (2010)

Collaborator of ARF (CARF) was first cloned as an ARF partner in yeast two-hybrid screens. It enhances ARF-dependent and -independent p53 functions, which are central to the control of cell growth and tumor suppression in human cells. CARF interacts with ARF, p53, and MDM2 proteins, and in turn gets regulated by MDM2-mediated degradation, suggesting a self-regulatory loop. CARF is upregulated during replicative, oncogenic, and stress-induced senescence. Overexpression of CARF induced premature senescence in normal human fibroblasts that was mediated by upregulation of p53-p21(CIP1/WAF1) and p16(INK4a)- pRB pathways. Knockdown of CARF resulted in mitotic arrest leading to excessive chromosomal condensation, aneuploidy, and apoptosis, suggesting that CARF is essential for cell survival. Most recently, we have found that CARF causes bidirectional regulation of p53 and pRB pathways, either arresting or promoting growth, and thus, it could be a potential threshold link between aging and cancer.
Wide-Range Many-Core SoC Design in Scaled CMOS: Challenges and Opportunities (2021)

The system-on-chip (SoC) designs for future Internet of Things (IoT) systems, spanning client platforms to cloud datacenters, need to deliver uncompromising and scalable performance with extreme energy efficiency for diverse workloads and applications, while satisfying a wide range of energy budgets, as well as platform cooling and power delivery constraints. Low-latency, burst-mode responsiveness, and scalable high-throughput performance must be delivered on demand for a range of thread-parallel, task-parallel, and data-parallel workloads covering traditional and emerging applications. This article discusses the challenges and opportunities for many-core SoC design in scaled CMOS process operating over a wide voltage-frequency range including near-threshold-voltage (NTV) that can meet the compute demands of the future at scale, flexibly, and efficiently. This article covers: 1) circuit design techniques for NTV cores; 2) mitigation techniques for within-die parameter variations via multivoltage frequency schemes; 3) digital integrated voltage regulators (VRs) for fine-grain and wide-range voltage modulation; and 4) radiation-induced soft error rate (SER) characterization and mitigation techniques to enable reliable operation at NTV. Silicon prototype examples will be used to illustrate the different techniques and highlight future research directions.
The Port Delivery System with Ranibizumab for Neovascular Age-Related Macular Degeneration (2019)

In the phase 2 Ladder trial, the PDS was generally well tolerated and demonstrated a dose response across multiple end points in patients with nAMD. The PDS 100-mg/ml arm showed visual and anatomic outcomes comparable with monthly intravitreal ranibizumab 0.5-mg injections but with a reduced total number of ranibizumab treatments. The PDS has the potential to reduce treatment burden in nAMD while maintaining vision.
Learning Actionable Representations from Visual Observations (2018)

In this work we explore a new approach for robots to teach themselves about the world simply by observing it. In particular we investigate the effectiveness of learning task-agnostic representations for continuous control tasks. We extend Time-Contrastive Networks (TCN) that learn from visual observations by embedding multiple frames jointly in the embedding space as opposed to a single frame. We show that by doing so, we are now able to encode both position and velocity attributes significantly more accurately. We test the usefulness of this self-supervised approach in a reinforcement learning setting. We show that the representations learned by agents observing themselves take random actions, or other agents perform tasks successfully, can enable the learning of continuous control policies using algorithms like Proximal Policy Optimization (PPO) using only the learned embeddings as input. We also demonstrate significant improvements on the real-world Pouring dataset with a relative error reduction of 39.4% for motion attributes and 11.1% for static attributes compared to the single-frame baseline. Video results are available at https://sites.google.com/view/actionablerepresentations.
Regulation of expression of the erythropoietin gene (1998)

Erythropoietin, a hormone produced in the adult kidney, controls erythrocyte production. In response to ischemic or hypoxic hypoxia, the level of expression of the gene increases markedly. We have a limited understanding of the factors governing the tissue specificity of erythropoietin gene expression but considerable progress has been made toward understanding the mechanisms that increase erythropoietin gene expression in response to hypoxia. An increase in transcription occurs, mediated (at least in part) by formation of a heterodimeric DNA binding complex termed hypoxia inducible factor 1. Transcriptional regulation mediated by this complex has now been shown to modulate the expression of a number of other genes in a wide range of cell types.
SAVVY: A Semantic Associative Browsing System for Heterogeneous Knowledge Resources (2009)

This paper presents a semantic associative browsing system called Semantic Association Various Viewpoint sYstem (SAVVY). Recently, the number of users who employ search engines for not only retrieving Web pages but also understanding or learning an arbitrary concept has been increasing. It is difficult to understand and learn an arbitrary concept by using most of the current search engines, because they provide a list of results according to the input keywords. The proposed approach represents the various relationships between arbitrary concepts as an outline. For example, it is assumed that a user wants information related to an input keyword. Current search engines represent a list of contents that match the keyword. The proposed approach dynamically represents various related concepts and contents on heterogeneous fields by using multiple views that are mutually synchronized. It helps to obtain various contents related to heterogeneous resources while understanding or learning an arbitrary concept.
Versatile Applications of microRNA in Anti-Cancer Drug Discovery: From Therapeutics to Biomarkers (2010)

Over the past several years, microRNAs (miRNAs) have been identified as a fine-tuner in a wide array of biological processes, including development, cell growth and metabolism. Recent studies have shown that many kinds of miRNAs act as oncomirs or tumor suppressors in tumors where the miRNA genes are up- or down- regulated, respectively. These dysregulations occur through a variety of mechanisms, such as genetic alterations, epigenetic repression or altered expression of transcription factors which target miRNAs. The aberrant expressions of miRNAs are observed not only in tumor lesions but also in plasma and serum of cancer patients. These characteristics of miRNAs have created extensive interest in tapping into them for diagnosis and prognosis as well as drug discovery in cancer therapy. In this literature, the significance of miRNAs in tumor initiation and development is first reviewed. Second topic is extracellular miRNAs as biomarkers for cancer classification and prediction. Further, we focus on secretory machinery of miRNAs and share new evidence suggesting that extracellular miRNAs can play biological roles beyond mere biomarkers. Extending this concept, our hypothetical model that extracellular miRNAs may function as a signaling molecule in a crosstalk between cancer cells and their surrounding cells is presented. Finally, we discuss the potential of miRNAs for therapeutic applications in clinical oncology.
Dedicated dental volumetric and total body multislice computed tomography: a comparison of image quality and radiation dose (2007)

Aim of this work is to compare the performances of a Xoran Technologies i-CAT Cone Beam CT for dental applications with those of a standard total body multislice CT (Toshiba Aquilion 64 multislice) used for dental examinations. Image quality and doses to patients have been compared for the three main i-CAT protocols, the Toshiba standard protocol and a Toshiba modified protocol. Images of two phantoms have been acquired: a standard CT quality control phantom and an Alderson Rando<sup>®</sup> anthropomorphic phantom. Image noise, Signal to Noise Ratio (SNR), Contrast to Noise Ratio (CNR) and geometric accuracy have been considered. Clinical image quality was assessed. Effective dose and doses to main head and neck organs were evaluated by means of thermo-luminescent dosimeters (TLD-100) placed in the anthropomorphic phantom. A Quality Index (QI), defined as the ratio of squared CNR to effective dose, has been evaluated. The evaluated effective doses range from 0.06 mSv (i-CAT 10 s protocol) to 2.37 mSv (Toshiba standard protocol). The Toshiba modified protocol (halved tube current, higher pitch value) imparts lower effective dose (0.99 mSv). The conventional CT device provides lower image noise and better SNR, but clinical effectiveness similar to that of dedicated dental CT (comparable CNR and clinical judgment). Consequently, QI values are much higher for this second CT scanner. No geometric distortion has been observed with both devices. As a conclusion, dental volumetric CT supplies adequate image quality to clinical purposes, at doses that are really lower than those imparted by a conventional CT device.
Adaptive Transmission Bandwidth Based Packet Scheduling for LTE Uplink (2008)

UTRAN long term evolution is currently under standardization within 3GPP with the aim of providing a spectral efficiency 2 to 4 times higher than its predecessor HSUPA/HSDPA release 6. Single carrier FDMA has been selected as multiple access for the uplink. This technology requires the subcarriers allocated to a single user to be adjacent. The consequence is a reduced allocation flexibility which makes it challenging to design effective packet scheduling algorithms. This paper proposes a channel aware packet scheduling algorithm which exploits the bandwidth flexibility offered by the system to perform an allocation which closely resembles the frequency domain envelope of the metric to be optimized. Compared to a fixed bandwidth approach, the proposed algorithm provides a greater flexibility given the inbuilt adaptation to different scenarios and loads, as well as an improvement in term of performance for the Macro 3 case. In this case the uplink capacity is increased by approximately 20% in average cell throughput and 10% in UE outage compared to a fixed bandwidth channel aware approach.
Thermal Conductivities，Rheological Behaviors and Photo-thermal Properties of Ethylene Glycol -based Nanofluids Containing Carbon Black Nanoparticles (2012)

Nanofluid is a new class of heat transfer fluids containing nano-sized particles, fibers, or tubes that are stably suspended in a carrier liquid. In this article, carbon black nanofluids were prepared by dispersing the pre-treated carbon black powder into ethylene glycol. The thermal conductivities, rheological behaviors and photo-thermal properties of the nanofluids were investigated. The results showed that the thermal conductivities of carbon black nanofluids increased with particle loading and temperature. The nanofluids performed a shear thinning behavior. The shear viscosity increased with particle loading while decreased with temperature at the same shear rate. Carbon black nanofluids had good absorption ability of solar energy and could effectively enhance the solar absorption efficiency.
Transcriptional Regulation (2000)

The eukaryotic cell is remarkably versatile. Whether it is destined to spend its existence producing antibodies for immune response or moving mucus over the epithelial sheets of the colon is determined by the myriad of proteins that it manufactures. Some processes are shared by all cells. Therefore, most cells contain a subset of common proteins, including proteins involved in forming the cytoskeleton, proteins intrinsic to the membranes of the golgi and endoplasmic reticulum, ribosomal proteins, and other “housekeeping proteins.” In contrast, subsets of proteins are expressed only in specialized cells, where they serve specific and often unique functions. Cellular specialization is controlled by gene expression, in which groups of genes are activated or repressed in response to internal and external stimuli. Moreover, the integrity with which gene expression is controlled can determine whether a cell performs its function in harmony and collaboration with its surroundings or defies the controls of growth and proliferation and invades territories normally reserved for other cells, resulting in malignancy.
ChemInform Abstract: Isolable Gold(I) Complexes Having One Low‐Coordinating Ligand as Catalysts for the Selective Hydration of Substituted Alkynes at Room Temperature Without Acidic Promoters. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
VISUAL FIELD AND RETINAL NERVE FIBRE LAYER IN EARLY GLAUCOMA AFTER OPTIC DISC HAEMORRHAGE (1983)

Computerized visual field testing with the Competer automatic perimeter including automatic profile perimetry revealed early glaucomatous field loss in 9 of 10 eyes with photographically demonstrable retinal nerve fibre layer (RNFL) defects after optic disc haemorrhages despite the fact than conventional routine perimetry had failed to do so. In 7 of these cases the Competer central pattern test was abnormal; in 2 cases field defects could be shown only when automatic high-resolution static profile perimetry was performed and directed according to the information present in wide-angle RNFL photographs. A field defect was also found in one of five eyes with no photographic RNFL changes. Visual field defects seem to occur in a higher proportion of cases with RNFL defects than was previously thought, but they can be very subtle and hard to find. There are, however, cases where in spite of the presence of an indisputable RNFL defect no visual field defects can be shown even with painstaking technique and conversely field defects may be present without RNFL defects. Automatic perimetry and RNFL photography complement each other in early detection and quantitation of glaucomatous damage.
Re: Overexpression of Androgen Receptor Enhances the Binding of the Receptor to the Chromatin in Prostate Cancer (2012)

No AccessJournal of UrologyInvestigative Urology1 Feb 2013Re: Overexpression of Androgen Receptor Enhances the Binding of the Receptor to the Chromatin in Prostate Cancer Anthony AtalaM.D. Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2012.10.106AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Overexpression of Androgen Receptor Enhances the Binding of the Receptor to the Chromatin in Prostate Cancer." The Journal of Urology, 189(2), pp. 769–770 © 2013 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 189Issue 2February 2013Page: 769-770 Advertisement Copyright & Permissions© 2013 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...
STRUCTURE AND VIBRATIONAL PREDISSOCIATION OF THE $HcI_{2}$ VAN DER WALLS' COMPLEX. (1976)

The $HeI_{2}$ van der Waals’ complex was prepared from a dilute mixture of iodine in helium at a pressure of 100 atm by supersonic expansion through a nozzle into a vacuum. Laser-induced fluorescence excitation spectra were recorded for the $\\tilde{B} \\leftarrow \\tilde{X}$ transition of $HeI_{2}$ as well as corresponding spectra for the $He_{2}I_{2}$ and $I_{2}$ species also found in the expanded gas. These species are observed to have extremely low internal temperatures as a result of the supersonic expansion: $T_{rot} \\approx 0.4K, T_{vib} \\approx 50K$. Evidence was found for vibrational predissociation of the $HeI_{2}$ complex in both the $\\tilde{X}$ and $\\tilde{B}$ electronic states. The vibrational predissociation rate was found to depend weakly upon the degree of excitation of the I-I stretching mode, $\\nu_{1}.$ For $\\nu_{1} = 1$ in the $\\tilde{X}$ state the predissociation rate was found to be greater then $5 \\times 10^{6} sec^{-1}$ in the B state vibrational predissociation rate is $\\sim 5 \\times 10^{10} sec^{-1}$ for $v_{1}=27,$ decreasing to $&lt; 5\\times 10^{9} sec^{-1}$ for $\\nu_{1} \\leq 7$. A study of the dispersed fluorescence from the $I_{2}$ fragment produced in the predissociation indicated that the $\\Delta\\nu = -1$ channel accounts for over 98% of all predissociation. Our progress in the interpretation of the detailed rotational structure of these transitions and in the measurement of the relative importance of the possible values for $\\Delta J$ in the vibrational predissociation will be discussed.
Screening for Angiotensin 1-Converting Enzyme Inhibitory Activity of Ecklonia cava (2005)

Seven brown algal species (Ecklonia cava, Ishige okamurae, Sargassum fulvellum, Sargassum horneri, Sargassum coreanum, Sargassum thunbergii and Scytosiphon lomentaria) were hydrolyzed using five proteases (Protamex, Kojizyme, Neutrase, Flavourzyme and Alcalase) and screened for angiotensin 1-converting enzyme (ACE) inhibitory activities. Most algal species examined showed good ACE inhibitory activities after the enzymatic hydrolysis. However, E. cava was the most potent ACE inhibitor of the seven species. Flavourzyme digest of E. cava exhibited an IC_(50) of around 0.3 ㎍/mL for ACE; captopril has an IC_(50) of ~0.05 ㎍/mL. The Flavourzyme digest was separated to three fractions by an ultrafiltration membrane (5, 10, 30 kDa MWCO) system according to the molecular weights. The active components were mainly concentrated in ＞30 kD fraction which are composed of the highest protein content (27%) and phenolic content (261 mg/100 mL) compared to the other two smaller molecular weight fractions. Therefore, the active compounds appear to be relatively high molecular weight complex molecules associated with protein (glycoprotein) and polyphenols. Therefore, E. cave is a potential source of antihypertensive compound.
Immunogenicity of an Ad26-based SARS-CoV-2 Omicron Vaccine in Naïve Mice and SARS-CoV-2 Spike Pre-immune Hamsters (2022)

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant sparked concern due to its fast spread and the unprecedented number of mutations in the spike protein that enables it to partially evade spike-based COVID-19 vaccine-induced humoral immunity. In anticipation of a potential need for an Omicron spike-based vaccine, we generated an Ad26 vector encoding an Omicron (BA.1) spike protein (Ad26.COV2.S.529). Ad26.COV2.S.529 encodes for a prefusion stabilized spike protein, similar to the current COVID-19 vaccine Ad26.COV2.S encoding the Wuhan-Hu-1 spike protein. We verified that spike expression by Ad26.COV2.S.529 was comparable to Ad26.COV2.S. Immunogenicity of Ad26.COV2.S.529 was then evaluated in naïve mice and SARS-CoV-2 Wuhan-Hu-1 spike pre-immunized hamsters. In naïve mice, Ad26.COV2.S.529 elicited robust neutralizing antibodies against SARS-CoV-2 Omicron (BA.1) but not to SARS-CoV-2 Delta (B.1.617.2), while the opposite was observed for Ad26.COV2.S. In pre-immune hamsters, Ad26.COV2.S.529 vaccination resulted in robust increases in neutralizing antibody titers against both SARS-CoV-2 Omicron (BA.1) and Delta (B.1.617.2), while Ad26.COV2.S vaccination only increased neutralizing antibody titers against the Delta variant. Our data imply that Ad26.COV2.S.529 can both expand and boost a Wuhan-Hu-1 spike-primed humoral immune response to protect against distant SARS-CoV-2 variants.
Studies of Pseudomonas Aeruginosa Mucosus Strains Persistently Isolated from a Patient of Chronic Bronchitis and a Trial of Autogenous Vaccines as a Treatment (1970)

Pseudomonas aeruginosa mucosus (Ps-M) type strains were persistently cultured from sputa of a patient, 65 years old house wife, sufferring from chronic bronchitis since her middle age. Since her first admission to Toranomon Hospital in 1954, at her 59 years age, she has been intermittently hospitalized to that hospital because of the exacerbation of the disease. Every time, the same type of Ps-M was isolated and this fact led to the authors' judgement that Ps-M infection was the cause of her large amount of pyog enic sputa and the fever.In view of the recent concern about Ps-M and cystic fibrosis disease, the patient was observed for related signs to the latter such as pancreatic deficiency and sweat electrolytes abnormality. Isolated Ps-M strains were investigated for some biological properties, and finally, formaldehyde-treated autogenous vaccines made from isolated Ps-M strains were administrated to the patient as an immune therapy and its effects were evaluated.The results were as follows:1) No evidence of cystic fibrosis disease was detected on the patient.2) The following findings were revealed as biological properties of the Ps-M strains:a) The colony's strong mucoid productivity was observed on agar plates and the viscosity was further increased when horse serum was added to the plates. Though the mucoid productivity was lowered through 5-6 times repeated subcultures, it recovered by passing through peritoneal space of mice.b) Sero-type of all the strains of Ps-M isolated at different hospitalized periods was all identical (T3 type). It can prove that the patient has continuously infected for a long time with the same strain.c) The strain was less pathogenic against mice than P1-111 type strain which produces no mucus.d) Behaviors to phagocytosis of the lcucocytes were not much different between the Ps-M strain and the control P1-111.e) Immunized mice with the formaldehyde-treated vaccines of the Ps-M strains, sustained the challenge of the homologous live ones. The effects were almost equal to that of antibiotics (colistin and polymyxin B3) Above autogenous vaccines were administrated to the patient for 19 months, the total dose being 52mg (wet weight of the organism). The agglutination titer of the patient serum was not elevated and the pseudomonas was kept being isolated from the sputa, but, clinical signs such as expectorating large amount of pyogenic sputa or fever rise are thought to have been ameliorated by the vaccinations.