gebhart/patrepeval huggingface dataset:
A rapid single-cell RNA-seq approach to identify neoantigen-specific T-cell receptors targeting tumor-specific mutations for use in gene-engineered T-cell immunotherapy (2017)

Abstract Accumulated evidence suggested that effective cancer immunotherapies were associated with neoantigen-reactive T cells, and adoptive transfer of neoantigen-reactive tumor infiltrating lymphocytes (TILs) could result in tumor regressions. To improve the efficacy of adoptive T-cell therapy targeting tumor-specific mutations, we have proposed a new therapeutic approach, which involves the genetic modification of autologous T cells with neoantigen-specific TCRs and the transfer of these T cells back to cancer patients. However, the current techniques to isolate neoantigen-specific TCRs are labor-intensive, time-consuming and technically challenging, not suitable for clinical applications. To facilitate this process, a new approach was developed, which included the co-culture of TILs with tandem minigene (TMG)-pulsed antigen-presenting cells, single-cell RNA-seq analysis of T cells and the identification of paired TCR sequences associated with cells expressing high levels of IFN-γ and IL-2 mRNA. In this study, TIL fragment cultures were grown from tumors resected from three patients with metastatic gastrointestinal cancers, and then were screened against TMG libraries encoding tumor-specific mutations identified by whole-exome sequencing. Following this new approach, three TCRs were identified, synthesized and cloned into a retroviral vector. These TCRs were then transduced into donor T cells, and these transduced T cells were shown to specifically recognize the following neoantigens encoded by the TMGs: USP8 (R667H), KRAS (G12D) and NBAS (C144S). In conclusion, this approach provides a rapid procedure to isolate neoantigen-specific TCRs for basic and translational research, as well as clinical applications.
Unilateral inguinofemoral lymphadenectomy in patients with early-stage vulvar squamous cell carcinoma and a unilateral metastatic sentinel lymph node is safe (2022)

The risk of contralateral lymph node metastases in patients with early-stage VSCC and a unilateral metastatic SN is low. It appears safe to limit groin treatment to unilateral IFL or inguinofemoral radiotherapy in these cases.
Using the ICC V4 Reference Medium Gamut in a real-world color workflow (2008)

The ICC V4 Perceptual Reference Medium Gamut (PRMG) has been proposed as a &#x201C;fuzzy&#x201D; rendering target that vendors can use to achieve consistent color reproduction in multi-vendor workflows. By defining a device independent &#x201C;device referenced&#x201D; rendering target, vendors are able to improve the inter-operability of ICC profiles. This paper describes an implementation of the ICC V4 workflow in which the color preferencing can be applied on the host, and discusse how to work around some problems in using such a workflow.
Pseudomonas fragi biofilm on stainless steel (at low temperatures) affects the survival of Campylobacter jejuni and Listeria monocytogenes and their control by a polymer molybdenum oxide nanocomposite coating (2023)

Pseudomonas spp. are widely distributed bacteria on surfaces in the food production and processing environment, where they form extracellular polymeric substance rich biofilms that interact with other bacteria. In this study, the influence of biofilm of Pseudomonas fragi ATCC 4973 on Listeria monocytogenes ATCC 19115 and Campylobacter jejuni NCTC 11168 was investigated at 5 °C and 15 °C on stainless steel in broth and food homogenates (fish or chicken meat). Stainless steel was then coated with PVDF-HFP/PVP/MoO<sub>3</sub> nanocomposite and examined for surface changes (scanning electron microscope, static contact angle, Vickers hardness and elastic modulus). The effect of the prepared nanocomposite coating on P. fragi and on L. monocytogenes and C. jejuni was evaluated in mono- and co-culture. P. fragi produced more biofilm at 15 °C than at 5 °C, especially when food homogenates were used as growth media. Co-cultivation with pathogens did not affect biofilm production by P. fragi, but significant changes were observed in L. monocytogenes and C. jejuni, resulting in a decrease and increase, respectively, in the determined number of culturable biofilm cells. The first change was probably due to competition for the surface, and the second to the oxygen gradient. Stainless steel was then coated with a PVDF-HFP/PVP/MoO<sub>3</sub> nanocomposite, which was characterised by lower roughness and higher wettability, but lower hardness compared to uncoated stainless steel. The prepared nanocoating showed bactericidal activity when tested in phosphate buffered saline. When used in food homogenates, a reduction of over 95 % in bacterial counts was observed. An abundant biofilm of P. fragi proved protective to L. monocytogenes and C. jejuni against the functionalised nanocomposite surface when tested in food homogenates. The control of spoilage Pseudomonas spp., which are common in the food production and processing environment, is important for reducing the contamination of food with spoilage bacteria and with pathogens such as L. monocytogenes and C. jejuni, which may be present in the same environment. The PVDF-HFP/PVP/MoO<sub>3</sub> nanocomposite showed good potential for use as a coating for food contact surfaces, but possible migration of nanoparticles from the nanocomposite coating to food should be evaluated before its commercial use.
Coupling Apoptosis Resistance to the Cellular Sress Response: The IAP-Hsp90 Connection in Cancer (2004)

Understanding how tumor cells manage to survive and proliferate in ever-changing and often harmful microenvironments is a daunting challenge in tumor biology, and a major cause of treatment failure in the oncology clinic. Recent data have now demonstrated a direct link between the molecular chaperone Hsp90 and survivin, a dual regulator of cell proliferation and cell death over-expressed in virtually every human tumor. While the survivin-Hsp90 association may help tumor cells elevate their anti-apoptotic threshold and promote their proliferation, it may also provide new opportunities for rational cancer therapy.
Towards oscillation control in a vibrating cantilever nonlinear NEMS (2007)

This paper presents a control method for initiating and maintaining oscillations of a given amplitude in some nanoelectromechanical device. The control law is based on some nonlinear feedback design and state reconstruction. The achieved performances are illustrated via simulations.
Photochemical keratodesmos as an adjunct to sutures for bonding penetrating keratoplasty corneal incisions (2004)

Photochemical keratodesmos may be a useful adjunct to sutures for approximating PKP corneal incisions in the immediate postoperative period. This process does not induce high temperature, and thus denaturation can be avoided and structural integrity restored.
Survival With Cemiplimab in Recurrent Cervical Cancer (2022)

(Abstracted from N Engl J Med 2022;386(6):544–555) Despite widespread implementation of cervical cancer screening and prevention programs including cytologic assessment and high-risk human papillomavirus DNA detection as well as effective vaccines, the incidence of cervical cancer remains high. Treatment varies based on stage and grade and involves a combination of surgery, platinum-based chemotherapy, bevacizumab, chemoradiation, and intracavitary brachytherapy.
Alternative, Nonapoptotic Programmed Cell Death (2004)

Programmed cell death (pcd) may take the form of apoptosis or of nonapoptotic pcd. Whereas cysteine aspartyl-specific proteases (caspases) mediate apoptosis, the mediators of nonapoptotic cell death programs are much less well characterized. Here we report that alternative, nonapoptotic pcd induced by the neurokinin-1 receptor (NK(1)R) activated by its ligand Substance P, is mediated by a MAPK phosphorylation cascade recruited by the scaffold protein arrestin 2. The activation of the protein kinases Raf-1, MEK2, and ERK2 is essential for this form of nonapoptotic pcd, leading to the phosphorylation of the orphan nuclear receptor Nur77. NK(1)R-mediated cell death was inhibited by a dominant negative form of arrestin 2, Raf-1, or Nur77, by MEK1/2-specific inhibitors, and by RNA interference directed against ERK2 or MEK2 but not ERK1 or MEK1 and against Nur77. The MAPK pathway is also activated in neurons in primary culture undergoing NK(1)R-mediated death, since the MEK inhibitor PD98059 inhibited Substance P-induced death in primary striatal neurons. These results suggest that Nur77, which is regulated by a MAPK pathway activated via arrestin 2, modulates NK(1)R-mediated nonapoptotic pcd.
Water State Measurements on Turbid Thick Tissue Phantoms and in vivo Breast Tissues using Broadband Diffuse Optical Spectroscopy (2008)

Molecular disposition of water has been measured non-invasively in the NIR using Diffuse Optical Spectroscopy in thick tissues. The water binding state has provided significant pathological information of breast tissues.
Modeling of dilute two-phase multispecies solid/gas flows (1986)

The report gives a detailed description of the analytical modeling that underlies the numerical code for predicting the flow of dilute solid/gas flows in pipes. The model is two-phase multispecies. Particles of one size are treated as one species and the equations of particle dynamics include terms to account for momentum transfer between species and the wall friction on each species of particles. New expressions for particle/particle interaction and wall friction for multispecies flow are derived. Results of parametric studies based on the new expressions are described. The predictions of this model for gas/powder flow through a venturi are compared with experimental measurements. The model's capability for predicting the flow in Argonne's Solid/Gas Flow Test Facility will be the subject of a companion report. 26 refs., 16 figs.
Area-optimized FPGA implementation of a digital FM modulator (2003)

An architecture and a prototype implementation of a digital frequency modulator are presented. The system features a direct digital synthesizer with a highly compressed ROM and a low-area Interpolator for the audio input signal. The frequency synthesizer has a spurious free dynamic range of more than 75 dB. The implementation occupies less than 200 configurable logic blocks on a Xilinx XC4000E-series field programmable gate array.
Novel mutant KRAS addiction signature predicts response to the combination of ERBB and MEK inhibitors in lung and pancreatic cancers (2023)

KRAS mutations are prevalent in pancreatic and lung cancers, but not all mutant (mt) KRAS tumors are addicted to mt KRAS. Here, we discovered a 30-gene transcriptome signature "KDS30" that encodes a novel EGFR/ERBB2-driven signaling network and predicts mt KRAS, but not NRAS or HRAS, oncogene addiction. High KDS30 tumors from mt KRAS lung and pancreatic cancer patients are enriched in genes upregulated by EGFR, ERBB2, mt KRAS or MEK. EGFR/ERBB2 (neratinib) and MEK (cobimetinib) inhibitor combination inhibits tumor growth and prolongs mouse survival in high, but not low, KDS30 mt KRAS lung and pancreatic xenografts, and is synergistic only in high KDS30 mt KRAS patient-derived organoids. Furthermore, mt KRAS high KDS30 lung and pancreatic cancer patients live significantly shorter lives than those with low KDS30. Thus, KDS30 can identify lung and pancreatic cancer patients whose tumors are addicted to mt KRAS, and predicts EGFR/ERBB2 and MEK inhibitor combination response.
X-Band Low Noise Figure T/R Switch-Module Using a Superconducting T/ R Switch (2018)

We have developed an X-band low noise figure (NF) T/R switch-module using a superconducting T/R switch. The superconducting T/R switch was realized by combining a six-port network, two impedance transformers and two varactor diodes. The six-port network consists of one λ/4 transmission line, two λ/2 transmission lines and one 3λ/4 transmission line. For each λ/2 transmission line, a single varactor diode was connected to the center of a given λ/2 transmission line by using one of the aforementioned impedance transformers. The superconducting T/R switch was fabricated using a high- Tc superconducting material called YBCO. An insertion loss of 0.3 dB was measured in Rx mode. By combining the superconducting T/R switch with a limiter and a low noise amplifier (LNA), a low NF T/R switch-module was designed. Measurements performed at X-band show an NF of 0.7 dB, which confirms the design procedure of a low NF T/R switch- module.
Measuring bending rigidity and spatial renormalization in bicontinuous microemulsions (2001)

We demonstrate a new approach to determine the bending rigidity of the amphiphile film in microemulsions and sponge phases from neutron scattering data. This method is precise enough to measure the logarithmic scale dependence of the bending rigidity and its universal prefactor for the first time. Furthermore, we show that in the mushroom regime the bending rigidity of a membrane decorated by amphiphilic block copolymers increases linearly with the polymer concentration on the membrane; the amplitude is found to be about a factor 1.5 larger than theoretical results for ideal chains.
Ornithine Transcarbamylase Deficiency with Persistent Abnormality in Cerebral Glutamate Metabolism in Adults (2009)

Treatments that improve cerebral glucose metabolism and glutamate neurotransmission may improve neurologic outcome in patients with OTCD, in whom prevention and treatment of hyperammonemic episodes appear to be insufficient.
Genome-wide scan in a nationwide study sample of schizophrenia families in Finland reveals susceptibility loci on chromosomes 2q and 5q (2001)

We have previously carried out two genome-wide scans in samples of Finns ascertained for schizophrenia from national epidemiological registers. Here, we report data from a third genome scan in a nationwide Finnish schizophrenia study sample of 238 pedigrees with 591 affected individuals. Of the 238 pedigrees, 53 originated from a small internal isolate (IS) on the eastern border of Finland with a well established genealogical history and a small number of founders, who settled in the community 300 years ago. The total study sample of over 1200 individuals were genotyped, using 315 markers. In addition to the previously identified chromosome 1 locus, two new loci were identified on chromosomes 2q and 5q. The highest LOD scores were found in the IS families with marker D2S427 (Z(max) = 4.43) and in the families originating from the late settlement region with marker D5S414 (Z(max) = 3.56). In addition to 1q, 2q and 5q, some evidence for linkage emerged at 4q, 9q and Xp, the regions also suggested by our previous genome scans, whereas, in the nationwide study sample, the region at 7q failed to show further evidence of linkage. The chromosome 5q finding is of particular interest, since several other studies have also shown evidence for linkage in the vicinity of this locus.
The Casimir effect for silicon and gold slabs (2007)

The authors have noticed an error in the numerical results plotted in fig. 3 of their paper. The correct values are given.
ChemInform Abstract: TRANSITION METAL INITIATED CATIONIC PHOTOPOLYMERIZATION (1978)

Abstract In Lösungen von Ag‐Salzen (AgBF 4 , AgPF 6 , AgSbF 6 und AgOSO 2 CF 3 ) in THF, die bei Dunkelheit völlig stabil sind, erfolgt bei UV‐Bestrahlung (254 nm) THF‐Polymerisation unter gleichzeitiger Abscheidung von metallischem Ag.
Digitally linearized wide-band photonic link (2001)

A photonic analog-to-digital (A/D) link with third-order distortion suppression is proposed and demonstrated. Experimental results with single-and two-tone analog input signals and a one giga-sample per second (GSPS) photonic A/D system with 500-MHz instantaneous bandwidth are presented. The application of a simple time-domain linearization scheme results in distortion suppression approaching 30 dB and allows optical modulation depths over 80%.
Current status and prospects for pancreatic cancer diagnosis by exosome-based liquid biopsy (2023)

自覚症状の乏しい膵臓癌においては早期発見を行うためのバイオマーカーが必須であり，膵臓癌の発見が遅れることは，ただでさえ，予後が不良な膵臓癌の死亡率の増加に繋がっている．現在，リキッドバイオプシーによる検査法の開発が世界中で進められており，本邦でも保険適用に至った検査方法もある．リキッドバイオプシーの解析対象となるマテリアルはいくつかあるが，細胞が分泌するエクソソームが新たなリキッドバイオプシーのマテリアルとして注目を浴びている．本稿では，血液などの体液からエクソソームが含む分子を解析・検出し，診断するエクソソーム・リキッドバイオプシーについて，早期診断という観点を中心にいくつかの実例を紹介し，エクソソームが秘める膵臓癌診断へのポテンシャルを概説する．
The Role of Connective Tissue Growth Factor (CTGF/CCN2) in Skeletogenesis (2011)

Connective tissue growth factor (CTGF) is a 38 kDa, cysteine rich, extracellular matrix protein composed of 4 domains or modules. CTGF has been shown to regulate a diverse array of cellular functions and has been implicated in more complex biological processes such as angiogenesis, chondrogenesis, and osteogenesis. A role for CTGF in the development and maintenance of skeletal tissues first came to light in studies demonstrating its expression in cartilage and bone cells, which was dramatically increased during skeletal repair or regeneration. The physiological significance of CTGF in skeletogenesis was confirmed in CTGF-null mice, which exhibited multiple skeletal dysmorphisms as a result of impaired growth plate chondrogenesis, angiogenesis, and bone formation/mineralization. Given the emerging importance of CTGF in osteogenesis and chondrogenesis, this review will focus on its expression in skeletal tissues, its effects on osteoblast and chondrocyte differentiation and function, and the skeletal implications of ablation or over-expression of CTGF in knockout or transgenic mouse models, respectively. In addition, this review will examine the role of integrin-mediated signaling and the regulation of CTGF expression as it relates to skeletogenesis. We will emphasize CTGF studies in bone or bone cells, and will identify opportunities for future investigations concerning CTGF and chondrogenesis/osteogenesis.
Vaccines, emerging viruses, and how to avoid disaster (2014)

Rino Rappuoli is a graduate of Siena University, where he also earned his PhD before moving to the Sclavo Research Center, the Italian vaccine institute, also in Siena. He then spent two years in the USA, mostly at Harvard with John Murphy and Alwin Pappenheimer working on a new diphtheria vaccine based on a non-toxic mutant of diphtheria toxin which has since become the basis for conjugate vaccines against haemophilus, meningococcus, and pneumococcal infections, before returning to the Sclavo Research Center where he developed an acellular vaccine based on a mutant pertussis toxin. With many achievements in vaccine development to his credit, he is now Global Head of Vaccines Research and Development for Novartis Vaccines in Siena, and has most recently pioneered reverse vaccinology, in which the genome of the pathogen is screened for candidate antigenic and immunogenic vaccine components. We spoke to him about the potential for outbreaks of the kind we are now seeing with Ebolavirus in West Africa, and what can be done to prevent them.
Three-Axis MEMS Threshold Accelerometer Switch for Enhanced Power Conservation of MEMS Sensors (2008)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
ChemInform Abstract: Enhanced Stereoselectivity in the Catalytic Dihydroxylation of Acyclic Allylic Alcohols. (2000)

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 DNA-Launched Nanoparticle Vaccine Elicits CD8+ T-cell Immunity to Promote In Vivo Tumor Control (2020)

Cytolytic T cells (CTL) play a pivotal role in surveillance against tumors. Induction of CTL responses by vaccination may be challenging, as it requires direct transduction of target cells or special adjuvants to promote cross-presentation. Here, we observed induction of robust CTL responses through electroporation-facilitated, DNA-launched nanoparticle vaccination (DLnano-vaccines). Electroporation was observed to mediate transient tissue apoptosis and macrophage infiltration, which were deemed essential to the induction of CTLs by DLnano-vaccines through a systemic macrophage depletion study. Bolus delivery of protein nano-vaccines followed by electroporation, however, failed to induce CTLs, suggesting direct <i>in vivo</i> production of nano-vaccines may be required. Following these observations, new DLnano-vaccines scaffolding immunodominant melanoma Gp100 and Trp2 epitopes were designed and shown to induce more potent and consistent epitope-specific CTL responses than the corresponding DNA monomeric vaccines or CpG-adjuvanted peptide vaccines. DNA, but not recombinant protein, nano-vaccinations induced CTL responses to these epitopes and suppressed melanoma tumor growth in mouse models in a CD8<sup>+</sup> T-cell-dependent fashion. Further studies to explore the use of DLnano-vaccines against other cancer targets and the biology with which they induce CTLs are important.
A New Synthesis of Functional Dyes from 2-Acenaphtho[1,2-c]pyrrole (2003)

Incorporation of acenaphtho[1,2-c]pyrrole units into the π-conjugated systems is very effective to get the narrow HOMO-LUMO gap materials, and the absorption spectra of π-conjugated polymers, porphyrins, and boron dipyrromethene dyes fused with acenaphthene rings are extensively red-shifted.The reaction of nitroalkenes with ethyl isocyanoacetate in the presence of a base gives ethyl 3, 4substituted pyrroles (Barton-Zard reaction), 1 which provide useful precursors for synthesis of porphyrins or biologically active pyrroles. 2This reaction has been extended to aromatic nitro compounds, and pyrroles fused with various aromatic rings such as benzene, naphthalene, phenanthrene, phenanththroline, quinoline, isoquinoline, fluoranthene, and acenaphthene have been prepared. 3,4Smith has found that nitro-porphyrins also undergo the Barton-Zard reaction to give pyrrolo-fused porphyrins. 5Such pyrroles are readily converted into the corresponding porphyrins.In 1996, we reported that the UV-VIS absorption spectra of tetraacenaphthoporphyrins were extremely red-shifted (Soret band: 525 nm).3b Lash reported that the introduction of phenyl ring at the meso position of tetraacenaphthoporphyrins induced the further red-shift of absorption (Soret band: 560 nm).4a Typical porphyrins such as octaethylporphyrin or meso-tetraphenylporphyrin absorb at about 400 nm (Soret band), and λ max is not much affected by the change of substituents on these porphyrins.Lash has claimed that fused acenaphthene rings induce large bathochromic shifts in the UV-VIS spectra of porphyrins, contrasting with the minimal influence of fused benzenoid aromatic systems. 6It is important to confirm whether the effect of acenaphthene is limited to porphyrins or not.In order to answer this question, π-conjugated oligomers, polymers, and cyclic HETEROCYCLES, Vol.61, 2003
Different Profiles of Wheat Antigens Are Recognised by Patients Suffering from Coeliac Disease and IgE-Mediated Food Allergy (2005)

This study thus demonstrates that wheat contains antigens/epitopes which are preferentially recognised by CD patients, whereas others elicit IgE-mediated food allergy. This finding suggests that the nature of a food antigen may influence the quality of the pathological immune response in the gut and has implications for the diagnosis and therapy of hypersensitivity to wheat.