gebhart/patrepeval huggingface dataset:
Metastatic potential prediction by a visual grading system of cell motility: prospective validation in the Dunning R-3327 prostatic adenocarcinoma model. (1988)

A method for accurate prediction of prognosis in individual patients with prostatic carcinoma does not exist. The limitations of pathological grading systems may result from the failure of standard pathological examination of fixed dead tissue to accurately assess the biological and metastatic behavior of live tumor cells. Many of the sublines of the Dunning R-3327 rat prostatic adenocarcinoma are histologically similar yet differ in metastatic potential. Cells from the Dunning model were grown in culture and filmed by time-lapse videomicroscopy. These cells exhibited characteristic membrane ruffling, pseudopodal extension, and cellular translation that could be graded with 80% reproducibility. Individual cells from sublines with high metastatic potential were separated from cells from sublines of low metastatic potential in 96% of cases. We have applied our cell motility grading system to prospectively classify the metastatic potential of neoplastic cells. The mean motility grades of sublines of high and low metastatic potential differed significantly (Mann-Whitney-Wilcoxon, P less than 0.0005). Among seven sublines in which the grading system was developed, individual cells were correctly classified as high or low metastatic in 71% of cases by ruffling or pseudopodal extension, 73% of cases by translation, and 75% of cases by motility index, an average of the three parameters of motility. Among four newly tested sublines, cells from a low metastatic and high metastatic sublines were perfectly classified. Cells from two other low metastatic sublines were misclassified. When all 88 cells from the 11 sublines were classified, high metastatic cells were detected with 94% sensitivity and 50% specificity. The predictive value of a determination of low metastatic was 93%, whereas the predictive value of an assignment of high metastatic was 52%. The ability to detect and accurately classify most highly metastatic cells while rarely erring in a classification of low metastatic potential suggests that a grading system of cancer cell motility should be evaluated in human prostatic carcinoma. The motility of live prostatic carcinoma cells may predict patient prognosis better than standard pathological grading systems.
Validation of a Simple Risk Stratification Tool for Patients Implanted with Cardiac Resynchronization Therapy: The VALID-CRT Risk Score (2015)

The VALID-CRT risk score, which is based on routine, readily available clinical variables, reliably predicted the long-term total and cardiovascular mortality in patients undergoing CRT. While this score cannot be used to predict the benefit of CRT, it may be useful for predicting survival after CRT. This may have useful implications for follow-up.
Interleukin-15 superagonist (N-803) treatment of PML and JCV in a post–allogeneic hematopoietic stem cell transplant patient (2020)

Key Points Therapy with an IL-15 superagonist resulted in immune and clinical responses in a transplant recipient with PML.
Mini-review Applied aspects of neonicotinoid uses in crop protection † (2008)

Neonicotinoid insecticides comprise seven commercially marketed active ingredients: imidacloprid, acetamiprid, nitenpyram, thiamethoxam, thiacloprid, clothianidin and dinotefuran. The technical profiles and main differences between neonicotinoid insecticides, including their spectrum of efficacy, are described: use for vector control, systemic properties and versatile application forms, especially seed treatment. New formulations have been developed to optimize the bioavailability of neonicotinoids through improved rain fastness, better retention and spreading of the spray deposit on the leaf surface, combined with higher leaf penetration. Combined formulations with pyrethroids and other insecticides are also being developed with the aim of broadening the insecticidal spectrum of neonicotinoids and to replace WHO Class I products from older chemical classes. These innovative developments for life-cycle management, jointly with the introduction of generic products, will, within the next few years, turn neonicotinoids into the most important chemical class in crop protection.  2008 Society of Chemical Industry
Supplementary Data from <i>FGFR2</i> Extracellular Domain In-Frame Deletions Are Therapeutically Targetable Genomic Alterations That Function as Oncogenic Drivers in Cholangiocarcinoma (2023)

&lt;p&gt;Supplemental Tables and Figures&lt;/p&gt;
ChemInform Abstract: A Novel Synthetic Route to Fused Propenochlorin (I) and Benzochlorin (II) Photodynamic Therapy Probes. (2002)

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.
Removal behavior of Sn and Pb contaminants on EUV mask after EUV exposure (2022)

Tin (Sn) and Lead (Pb) particles released from the EUV scanner can contaminate the EUV mask causing serious yield and throughput problems. These contaminants can worsen during EUV exposure and become difficult to remove, leading to damaging the EUV mask in the process. To effectively remove contaminants without substrate damage, it is necessary to understand the removal behavior of the contaminants. In this study, the removal behavior of Sn and Pb particles was studied by simulating the EUV exposure heated by rapid thermal annealing. The removal forces between the thermally aged Sn and Pb particles and EUV substrate surfaces were quantitatively measured using atomic force microscopy (AFM). With the thermal aging time, the contact area of the deformed particle increases which requires a high removal force. After particle removal, the footprint of the contaminants was investigated to understand the surface quality of where the particles sat under the various exposure conditions. This study helps to better understand the adhesion mechanism and removal behavior of thermally deformed Sn and Pb particles on different EUV substrates.
Ionic Liquids as Additives to Polystyrene-Block-Poly(Methyl Methacrylate) Enabling Directed Self-Assembly of Patterns with Sub-10 nm Features (2018)

Polystyrene- block-poly(methyl methacrylate) (PS- b-PMMA) is one of the prototypical block copolymers in directed self-assembly (DSA) research and development, with standardized protocols in place for processing on industrially relevant 300 mm wafers. Scaling of DSA patterns to pitches below 20 nm using PS- b-PMMA, however, is hindered by the relatively low Flory-Huggins interaction parameter, χ. Here, we investigate the approach of adding small amounts of ionic liquids (ILs) into PS- b-PMMA, which selectively segregates into the PMMA domain and effectively increases the χ parameter and thus the pattern resolution. The amount of IL additive is small enough to result in limited changes in PS- b-PMMA's surface and interfacial properties, thus maintaining industry-friendly processing by thermal annealing with a free surface. Three different ILs are studied comparatively regarding their compositional process window, capability of increasing χ, and thermal stability. By adding ∼3.1 vol % of the champion IL into a low-molecular-weight PS- b-PMMA ( M<sub>n</sub> = 10.3k- b-9.5k), we demonstrated DSA on chemically patterned substrates of lamellar structures with feature sizes <8.5 nm. Compatibility of the PS- b-PMMMA/IL blends with the standardized processes that have been previously developed suggests that such blend materials could provide a drop-in solution for sub-10 nm lithography with the processing advantages of PS- b-PMMA.
Modeling an evanescent field absorption optical fiber sensor (1995)

Using the weakly guiding and exact field solutions of an optical fiber, we wrote a FORTRAN program to determine the fractional power that reaches the end of an optical fiber with an absorptive cladding. We have assumed that each mode of the fiber is equally excited. This corresponds to incoherent source excitation. The results were compared to a previous approximation published by Payne and Hale in 1993. We have found that, at low <i>V</i>-numbers, <i>V</i><20, Payne and Hale's approximation deviate by more than 20% from the weakly guiding solution. At high <i>V</i>-numbers, the approximation deviates by less than 10%. When compared to Payne and Hale's approximation, both the weakly guiding and exact solutions are closer to the data points obtained experimentally by Degrandpre and Burgess in 1988. Although closer than Payne and Hale's approximation, our solution still deviates from the Degrandpre and Burgess results. The difference may result from the assumption that all modes were excited equally. Another possibility was the fact that we have neglected leaky modes in our treatment.
HLA-DP Variation as Additional Risk Factor in IDDM (1990)

A significant increase in the frequency of DPw3/6 alleles defined by restriction-fragment-length polymorphism is observed in insulin-dependent diabetes mellitus (IDDM) patients relative to healthy control subjects (34.6 vs. 10.5%, P less than 0.009). Log-linear modeling demonstrates that this association is independent of HLA-DR3 and -DR4 and IDDM association and cannot be attributed to linkage disequilibrium between HLA-DP and -DR. The analysis also demonstrates an absence of interactive effects among the antigens in conferring IDDM susceptibility. The strength of the DPw3/6 association is not significantly less than that of either DR3 or DR4.
Monocyte subsets associated with the efficacy of anti‑PD‑1 antibody monotherapy (2023)

Immune checkpoint inhibitors (ICIs) are among the most notable advances in cancer immunotherapy; however, reliable biomarkers for the efficacy of ICIs are yet to be reported. Programmed death (PD)-ligand 1 (L1)-expressing CD14<sup>+</sup> monocytes are associated with shorter overall survival (OS) time in patients with cancer treated with anti-PD-1 antibodies. The present study focused on the classification of monocytes into three subsets: Classical, intermediate and non-classical. A total of 44 patients with different types of cancer treated with anti-PD-1 monotherapy (pembrolizumab or nivolumab) were enrolled in the present study. The percentage of each monocyte subset was investigated, and the percentage of cells expressing PD-L1 or PD-1 within each of the three subsets was further analyzed. Higher pretreatment classical monocyte percentages were correlated with shorter OS (r=-0.32; P=0.032), whereas higher non-classical monocyte percentages were correlated with a favorable OS (r=0.39; P=0.0083). PD-L1-expressing classical monocytes accounted for a higher percentage of the total monocytes than non-classical monocytes with PD-L1 expression. In patients with non-small cell lung cancer (NSCLC), a higher percentage of PD-L1-expressing classical monocytes was correlated with shorter OS (r=-0.60; P=0.012), which is similar to the observation for the whole patient cohort. Comparatively, higher percentages of non-classical monocytes expressing PD-L1 were significantly associated with better OS, especially in patients with NSCLC (r=0.60; P=0.010). Moreover, a higher percentage of non-classical monocytes contributed to prolonged progression-free survival in patients with NSCLC (r=0.50; P=0.042), with similar results for PD-L1-expressing non-classical monocytes. The results suggested that the percentage of monocyte subsets in patients with cancer before anti-PD-1 monotherapy may predict the treatment efficacy and prognosis. Furthermore, more classical monocytes and fewer non-classical monocytes, especially those expressing PD-L1, are involved in shortening OS time, which may indicate the poor efficiency of anti-PD-1 treatment approaches.
Tunable Bifunctional Silyl Ether Cross-Linkers for the Design of Acid-Sensitive Biomaterials (2010)

Responsive polymeric biomaterials can be triggered to degrade using localized environments found in vivo. A limited number of biomaterials provide precise control over the rate of degradation and the release rate of entrapped cargo and yield a material that is intrinsically nontoxic. In this work, we designed nontoxic acid-sensitive biomaterials based on silyl ether chemistry. A host of silyl ether cross-linkers were synthesized and molded into relevant medical devices, including Trojan horse particles, sutures, and stents. The resulting devices were engineered to degrade under acidic conditions known to exist in tumor tissue, inflammatory tissue, and diseased cells. The implementation of silyl ether chemistry gave precise control over the rate of degradation and afforded devices that could degrade over the course of hours, days, weeks, or months, depending upon the steric bulk around the silicon atom. These novel materials could be useful for numerous biomedical applications, including drug delivery, tissue repair, and general surgery.
Carbohydrate steroid hybrid architectures: the viewpoint of amphiphilicity and self-organisation (2016)

International audience
Microenvironmental sensing by fibroblasts controls macrophage population size (2022)

Animal tissues comprise diverse cell types. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we report that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and TGF-β target genes are both regulated by cell density. We found YAP1, the transcriptional coactivator of the Hippo signaling pathway, directly regulates expression of <i>Csf1</i>, the lineage-specific growth factor for macrophages, through an enhancer of <i>Csf1</i> that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates <i>Csf1</i> expression and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical force through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition.
The CD226/CD155 Interaction Regulates the Proinflammatory (Th1/Th17)/Anti-Inflammatory (Th2) Balance in Humans (2013)

CD226 costimulatory signals strongly promote Th1 differentiation, enhancing IFN-γ production by naive T cells. We recently reported that knockdown of CD226 on human T cells resulted in a decrease in T-bet and IFN-γ expression. However, the role of CD226 on Th2 and Th17 cells remains unknown. In this study, we found that CD226 and its ligand CD155 were decreased on Th2-polarized naive T cells, whereas both were highly expressed under Th17 conditions. Most IFN-γ- and IL-17-producing cells expressed high levels of CD226, but production of IL-13 did not correlate with CD226 expression. CD226 knockdown by lentiviral transduction resulted in increased STAT-6 phosphorylation, enhanced GATA3 expression, and consequently higher production of IL-4 and IL-13. Under Th17 conditions, CD226-depleted cells showed slightly impaired IL-17 secretion, suggesting that CD226 contributes, in part, to IL-17 production but is dispensable for Th17 cell generation. In line with these results, CD226 blockade with neutralizing Abs efficiently inhibited T cell activation and proliferation and production of IFN-γ and IL-17, whereas IL-13 secretion remained functional. Taken together, our results establish an important role for CD226 in differentially regulating the proinflammatory (Th1/Th17)/anti-inflammatory (Th2) balance, suggesting that the CD226/CD155 interaction could potentially be targeted in therapeutic approaches to human autoimmune diseases.
Le concept de défense immunitaire (2001)

Le systeme immunitaire est un ensemble de cellules qui communiquent par interaction directe mais aussi indirecte par des mediateurs solubles, les cytokines. Il assure l'integrite de l'organisme dans un environnement dont la diversite est la marque et dont il partage la selection par la survie comme mode de selection, mais aussi de fonctionnement assurant une memoire immunitaire. La connaissance actuelle des mecanismes generant la diversite de reconnaissance des antigenes et leur presentation fondent l'immunologie. Le developpement du systeme immunitaire, qui en assure la plasticite en l'adaptant a l'organisme dans lequel il evolue, conduit, en assurant un compromis permettant sa coexistence avec celui -ci, a la tolerance immunitaire.
Inertial Confinement Fusion Propulsion for Deep Space Missions Revisited (2010)

Laser-driven Inertial Confinement Fusion (ICF) is extremely attractive for deep space propulsion and has been the subject of several conceptual design studies. However, these studies were based on older ICF technology using either “direct “or “in-direct x-ray driven” type target irradiation. This leads to rather low energy gains. Plus, traditional DT fusion was selected, requiring tritium breeding and delivering 80% of the fusion energy in neutrons that cannot be directed thorough an exhaust nozzle. However, important new directions have developed for laser ICF in recent years following the development of “chirped” lasers capable of ultra-short pulses with powers of TW up to a few PW. This has led to the exciting concept of “fast ignition (FI)” where the peta-watt laser beam strikes a pre-compressed target, creating a hot spot in the interior of the target burn that propagates outward into the surrounding fuel. This then gives a much higher energy gain, since part of the input energy required is replaced by the propagating burn. In the present study, we employ a new type of FI, termed ignition. In this approach, a non-laser interaction causes a plasma block to be accelerated into the target to ignite the hot spot. This is very efficient in giving very high gains while maintaining a low electron temperature, allowing ignition of more demanding fusion fuels like p- 11 B. The p- 11 B reaction is employed here and releases energy by energetic alphas particles that can be very effectively guided through a magnetic nozzle to produce thrust while avoiding tritium involvement or neutron induced radioactivity. These advances are considered here and are shown to meet and exceed the requirements anticipated (but not then available) for optimum ICF fusion propulsion ship design.
CYCLOPE SYNDROME: A PROBLEM PRESENT BEFORE ARTHROSCOPIC RECONSTRUCTION OF THE ANTERIOR CRUCIATE LIGAMENT (2002)

Purpose: Cyclope syndrome is described in the literature as a postoperative complication of arthroscopic anterior cruciate ligament (ACL) grafts, leading to permanent flexion. The discovery of this syndrome in ten patients before reconstruction of the ACL led us to revisit the pathophysiology. Material and methods: Among 250 candidates for ACL grafts, ten presented a positive but dull Lachman-Trillat sign with permanent flexion greater than 10°. The rotation click was negative in two and dull in eight. KT 200 measured differential laxity greater than 4 mm in all. Nine patients were reviewed at consultation, one patient had recently undergone another operation. Clinical and radiographic findings recorded in the patient’s files and operation reports were reviewed by two observers different from the operator. Results: Arthroscopy revealed a partial tear of the ACL in three cases, a scarred ACL nourished by the PCL in five and a full thickness tear of the ACL in two. There was a fibrous barbell nodule inserted on the tibia in all cases, a characteristic feature of cyclope syndrome. The nodule was interposed between the femur and tibia at extension and was resected in all cases. Pathology reported a ligamentoid structure undergoing fibrous organisation. At last follow-up, greater than two years for nine patients, the IKDC rating was A for six patients and B for three patients. None of the patients had a defective extension differential. Discussion: Persistent flexion preoperatively in a patient with a torn anterior cruciate ligament suggests possible presence of a ligamento-fibrous nodule interposing between the femur and tibia at extension. This nodule can go unnoticed at arthroscopy but appears to be unmasked in the Cabott position after partial resection of the subpatellar fat. It is particularly important to look for this nodule when the stump of the torn ACL is not found and the patient has experienced a recent sprain. Since we started looking for this nodule in all cases with resection, we have no longer encountered postoperative cyclope syndrome. Conclusion: This group of arguments strongly suggests that the conditions necessary for the constitution of cyclope syndrome are probably present before reconstruction of the anterior cruciate ligament.
Table S1-S7 from Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies (2023)

&lt;p&gt;Table S1: Plasmids and primers used for protein expression.&lt;/p&gt;&lt;p&gt;Table S2: Characterization of MSLN expression constructs.&lt;/p&gt;&lt;p&gt;Table S3: Structural alignments of MSLN models.&lt;/p&gt;&lt;p&gt;Table S4: Lists of interactions.&lt;/p&gt;&lt;p&gt;Table S5: Buried surface area for three MSLN-Fab complexes.&lt;/p&gt;&lt;p&gt;Table S6: Observed saccharide attachments at predicted glycosylation sites.&lt;/p&gt;&lt;p&gt;Table S7: Dali search result.&lt;/p&gt;