gebhart/patrepeval huggingface dataset:
High-resolution genomic profiling of Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL) patients identified novel recurrent copy number variations involved in both pathogenesis and resistance to tyrosine kinase inhibitors (2014)

Background: The Ph chromosome is the most frequent karyotypic aberration in adults with ALL and it represents the single most significant adverse prognostic marker. Despite the encouraging results achieved with imatinib, resistance develops rapidly and is quickly followed by disease progression. Recently, the introduction of array-based analysis of single nucleotide polymorphism (SNP) has allowed the rapid determination of genome-wide allelic information at high density for a DNA sample.&#13;\nPatients and Methods: In order to identify, at submicroscopic level, genetic lesions which can escape standard cytogenetic observations and may contribute to leukemogenesis and resistance, we profiled, until now, the genomes of 18 patients out of 55 Ph+ ALL patients treated in our institute with imatinib or dasatinib. 250 ng of genomic DNA were processed on 500K SNP array according to protocols provided by the manufacturer (Affymetrix Inc., Santa Clara, CA, USA). Copy number state was calculated with respect to a set of 48 Hapmap normal individuals and a diploid reference set of samples obtained from acute leukaemia cases in remission using Partek® Genomics Suite. Fluorescence in situ hybridization (FISH) and real-time quantitative PCR were performed to validate our results.&#13;\nResults: We identified multiple copy number alterations per case, with deletions outnumbering amplification almost 3:1. Lesions varied from loss or gain of complete chromosome arms (trisomy 4, monosomy 7, loss of 9p, 10q, 14q, 16q and gain of 1q and 17q) to microdeletions and microduplications targeting genomic intervals. The common microdeletions included 1p36.21 (PRAMEF), 3q29 (TFCR), 8p23 (DEFB105A), 14q11.2 (DAD1), 16p13.11 (PDXDC1, NTAN1, RRN3), 16p11.2 (SPN) and 19p13.2 (CARM1, SMARCA4). Some genomic alterations were identified in genes regulating B-lymphocyte differentiation, such as PAX5 (n=3), BLNK (n=1) and VPREB1 (n=6), IKZF1 (n=7) and in genes with an established role in leukemogenesis, such as MDS, BTG1, MLLT3, RUNX1. The most frequently affected genes were those controlling G1/S cell cycle transition (e.g. CDKN2A and CDKN2B). Furthermore, many of the deletions detected included genes encoded for phosphatase proteins (e.g. PTPRD, PPP1R9B, PTPN18) and for zinc-finger proteins. It is noteworthy that some lesions felt in regions lacking annotated genes.&#13;\nDiscussion: Using high-resolution genome wide approach we showed that multiple sub-microscopic genomic anomalies, which may be suspected to contribute to leukemogenesis and used as targets for existing or novel drugs, frequently occur in Ph+ ALL
Self-reconfigurable control for dual-quaternion/dual-vector systems (2013)

In this paper we suggest self-reconfigurable control for dual-quaternion systems with unknown control direction. The technique is based on the creation of multiple equilibrium surfaces for the system in the extended state space. We describe the mathematical tools of dual quaternions and technique required to design such system. Examples are presented to illustrate the proposed method.
An Application of Distributed Spatial Formation Control with Multiplex Information Networks over Directed Graphs (2022)

View Video Presentation: https://doi.org/10.2514/6.2022-1219.vid Increasing complexity of civilian, military, and scientific tasks requires the spatial properties of agent teams to change in real-time. However, the single layer networked structure of existing distributed control algorithms may not provide the necessary flexibility to address complicated tasks through local interactions. To provide a remedy for controlling the spatial properties of multiagent formations in real-time, multiplex information networks (that is, networks having multiple layers) have been recently introduced over undirected graphs. In this paper, our contribution is to provide an important system-theoretical generalization over directed graphs. Specifically, we present a distributed control architecture that has multiple directed graph layers. The key aspect of our architecture is that the size and the orientation of a given formation can be controlled in real-time through local interactions when each directed graph layer has a spanning tree property. In addition to providing a rigorous stability analysis of our architecture, an illustrative numerical example is also included to demonstrate its efficacy.
X-ray diffraction investigations of collagen fibril structure in dermatosparactic lamb tissues. (1980)

The x-ray diffraction of dermatosparactic lamb skin and tendon was compared with that from normal lamb tissues in order to investigate alterations in collagen fibril structure in the diseased tissues. Dermatosparactic tendon, which contains about 13 per cent pN-collagen, gave a normal x-ray pattern, whereas dermatosparactic skin, with 70 per cent pN-collagen, gave extremely weak meridional diffraction. The loss of meridional diffraction indicates a loss of long range axial alignment of the collagen molecules in the affected skin fibrils. Drying or reduction of dermatosparactic skin increased the meridional diffraction, indicating some restoration of the axial order.
Refroidissement de plaques bipolaires – Résultats et analyse des essais de plaques à géométries complexes, Rapport technique DTS DR 2006 34. (2006)

Refroidissement de plaques bipolaires – Résultats et analyse des essais de plaques à géométries complexes, Rapport technique DTS DR 2006 34.
Proteins: Materials Fabrication from Native and Recombinant Thermoplastic Squid Proteins (Adv. Funct. Mater. 47/2014) (2014)

Squid ring teeth complex extracted from Loligo vulgaris shows reversible solid to melt phase transition on page 7401. M. C. Demirel and team show how the direct extraction or recombinant expression of protein based thermoplastics opens up new avenues for materials fabrication and synthesis, which will eventually be competitive with the high-end synthetic oil based plastics.
Supplementary Materials and Methods from Targeted Metabolomics Identifies the Cytochrome P450 Monooxygenase Eicosanoid Pathway as a Novel Therapeutic Target of Colon Tumorigenesis (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
Feedlot efficiency implications on greenhouse gas emissions and sustainability1 (2011)

The term sustainable has many meanings, but in agriculture it generally refers to some balance between environmental, social, and economic goals. The objective of this project was to quantify inputs and outputs to assess the sustainability implications of 2 feedlot cattle management systems: Never Ever 3 (NE3) and a conventional (CON) system using metabolic modifiers. Angus-cross steers (n=104) were stratified by BW (337 kg ± 17) and randomly assigned to 4 pens per treatment group. The NE3 cattle received no feed additives or implants, whereas CON were implanted with 100 mg of trenbolone acetate and 14 mg of estradiol benzoate on d 1 and 70, and were additionally fed monensin [330 mg/(animal·d)] and tylosin phosphate [90 mg/(animal·d)] in their ration throughout the course of the study, and ractopamine hydrochloride at 254 mg/(animal·d) for the last 29 d on feed. Cattle were shipped on a constant average pen weight basis (596 kg ± 32 BW). The CON cattle had greater ADG (1.81 vs. 1.35 kg, P < 0.01) and were on feed fewer days (146 vs. 188 d, P < 0.01) than the NE3 cattle. No significant differences were observed in HCW (P = 0.072) or dressing percentage (P=0.62) between treatments (P > 0.05); however, CON carcasses averaged larger ribeye area (87 vs. 80 cm(2), P < 0.01), greater Warner-Bratzler shear force measurement (WBSF; 3.46 vs. 3.19 kg, P < 0.01), and smaller USDA marbling score (5.4 vs. 6.2, P < 0.01), and less backfat thickness (1.64 vs. 1.84 cm, P < 0.05) and yield grade (3.38 vs. 3.95, P < 0.01) than NE3 carcasses. Overall, CON cattle consumed 393 kg less DM in the feedlot (1,250 vs. 1,643 kg; P < 0.05). No treatment effects were observed for daily methane (CH(4); P=0.62) or nitrous oxide (N(2)O; P=0.7) emissions per steer. Assuming a constant emission rate on a DMI basis throughout the course of the feedlot trial, CON feedlot management resulted in a 31% decrease in emissions per finished steer compared with NE3 management. Expressing CH(4) emissions on a carbon dioxide equivalent (CO(2)-eq) basis revealed a 1.10-kg CO(2)-eq difference per kilogram BW gain (5.02 kg of NE3 vs. 3.92 kg of CON) between the 2 feedlot management systems. Although the metabolic modifiers resulted in additional costs for the CON treatment group, the cost per kilogram of feedlot BW gain was significantly less ($1.12/kg vs. $1.35/kg; P < 0.05) than NE3. Both production systems satisfied some sustainability criteria, although neither concurrently fulfilled all of the environmental, social, and economic goals of agricultural sustainability.
Data from Differential Toxicity in Patients with and without DNA Repair Mutations: Phase I Study of Carboplatin and Talazoparib in Advanced Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The PARP inhibitor (PARPi) talazoparib may potentiate activity of chemotherapy and toxicity in cells vulnerable to DNA damage.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; This phase I study evaluated the safety, tolerability, pharmacokinetics, and efficacy of talazoparib and carboplatin. Pharmacokinetic modeling explored associations between DNA vulnerability and hematologic toxicity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Twenty-four patients (eight males; 16 females) with solid tumors were enrolled in four cohorts at 0.75 and 1 mg daily talazoparib and weekly carboplatin (AUC 1 and 1.5, every 2 weeks or every 3 weeks), including 14 patients (58%) with prior platinum treatment. Dose-limiting toxicities included grade 3 fatigue and grade 4 thrombocytopenia; the MTD was not reached. Grade 3/4 toxicities included fatigue (13%), neutropenia (63%), thrombocytopenia (29%), and anemia (38%). After cycle 2's dose, delays/reductions were required in all patients. One complete and two partial responses occurred in germline BRCA1/2 (gBRCA1/2) patients. Four patients showed stable disease beyond 4 months, three of which had known mutations in DNA repair pathways. Pharmacokinetic toxicity modeling suggests that after three cycles of carboplatin AUC 1.5 every 3 weeks and talazoparib 1 mg daily, neutrophil counts decreased 78% [confidence interval (CI), 87–68] from baseline in gBRCA carriers and 63% (CI, 72–55) in noncarriers (&lt;i&gt;P&lt;/i&gt; &lt; 0.001). Pharmacokinetic toxicity modeling suggests an intermittent, pulse dosing schedule of PARP inhibition, differentiated by gBRCA mutation status, may improve the benefit/risk ratio of combination therapy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Carboplatin and talazoparib showed efficacy in DNA damage mutation carriers, but hematologic toxicity was more pronounced in gBRCA carriers. Carboplatin is best combined with intermittent talazoparib dosing differentiated by germline and somatic DNA damage mutation carriers. &lt;i&gt;Clin Cancer Res; 23(21); 6400–10. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Brain Source Localization using Constrained Low Rank Canonical Polyadic Decomposition (2018)

A new tensor-based source localization algorithm is presented in this paper. It is a single-step algorithm in which tensor decomposition with an efficient rank estimation and source localization are performed in only one single step. Contrary to the previous single-step tensor-based STS-SISSY (Space-Time-Spike Source Imaging based on Structured Sparsity) method recently proposed by our group, the proposed method is robust to tensor over-factoring and gives more accurate results. In addition to the structural constraints on the sources required for their localization, group sparsity constraints on the loading over-estimated matrices of the constructed STS tensor is used to estimate its rank. The numerical results show the efficiency of the proposed method over the STS-SISSY one.
Structural Optimization of Quinolon-4(1<i>H</i>)-imines as Dual-Stage Antimalarials: Toward Increased Potency and Metabolic Stability (2013)

Discovery of novel effective and safe antimalarials has been traditionally focused on targeting erythrocytic parasite stages that cause clinical symptoms. However, elimination of malaria parasites from the human population will be facilitated by intervention at different life-cycle stages of the parasite, including the obligatory developmental phase in the liver, which precedes the erythrocytic stage. We have previously reported that N-Mannich-based quinolon-4(1H)-imines are potent antiplasmodial agents but present several stability liabilities. We now report our efforts to optimize quinolon-4(1H)-imines as dual-stage antiplasmodial agents endowed with chemical and metabolic stability. We report compounds active against both the erythrocytic and exoerythrocytic forms of malaria parasites, such as the quinolon-4(1H)-imine 5p (IC50 values of 54 and 710 nM against the erythrocytic and exoerythrocytic forms), which constitute excellent starting points for further lead optimization as dual-stage antimalarials.
PCF Hi-Bi 2-section fibre Lyot depolarisers (2006)

A 2-section photonic crystal fibre (PCF) highly birefringent (Hi-Bi) Lyot depolariser is demonstrated. Because of the high birefringence of the PCF Hi-Bi, the fibre length required to make such a device was an order of magnitude lower than if conventional Hi-Bi is employed. The residual degree of polarisation was found to be as low as 0.25%.
Breaking Down the Supramolecular Ensemble: Single-Molecule Studies of the Concentration Dependence of Main-Chain Supramolecular Polymer Molecular Weight Distributions on Surfaces (2010)

Single molecule atomic force microscopy (AFM) studies of oligonucleotide-based supramolecular polymers on surfaces are used to examine the molecular weight distribution of the polymers formed between a functionalized surface and an AFM tip as a function of monomer concentration. For the concentrations examined here, excellent agreement with a multi-stage open association model of polymerization is obtained, without the need to invoke additional contributions from secondary steric interactions at the surface.
Tribological and Nanomechanical Properties of Unmodified and Crosslinked Ultra-High Molecular Weight Polyethylene for Total Joint Replacements (2004)

Wear of ultra-high molecular weight polyethylene (UHMWPE) continues to be a major obstacle limiting the longevity of total joint replacements. Efforts to solve the wear problem in UHMWPE have resulted in numerous studies dealing with the microstructure, morphology, and mechanical properties of this polymer. However, the fundamental wear mechanisms at different material length scales in total joint replacements remain elusive. Consequently, a systematic investigation of the initial stage of the wear process was performed in this study in order to obtain insight into the origins of wear in UHMWPE at submicrometer scales. Sliding experiments were performed with both unmodified and crosslinked (by gamma radiation treatment) UHMWPE subjected to reciprocating sliding against Co-Cr alloy in a bath of bovine serum under ranges of mean contact pressure and sliding speed typical of knee joints. Nanoindentation and optical, scanning electron, and transmission electron microscopy were used to examine the effect of crosslinking on the nanomechanical properties, dominant wear mechanisms, and microstructure of UHMWPE. The fundamental wear micromechanisms of unmodified and crosslinked UHMWPE are interpreted in the context of coefficient of friction, wear factor, creep, adhesion force, and microstructure results.
Thermal Lasers in Urologic Oncology (1998)

Urology is a surgical specialty that relies heavily on the endoscopic approach for diagnosis and treatment of disease. Electrosurgical instruments have been the standard vehicle for endoscopic tumor ablation. Over the last 30 years a number of investigators have explored the use of the medical laser as either an alternative or an adjunct to standard electrosurgical techniques. The development of small caliber flexible and rigid endoscopic application. In addition, the potential for very limited and precise distribution of laser energy in targeted tissue is clinically appealing for endoscopic applications. In this article, we review the use of thermal laser in urologic oncology.
Codage de source distribuées : comparaison de 2 systèmes approchant la borne de Wyner-Ziv (2003)

National audience
Development of a Novel, Low-Resistance Pediatric Artificial Lung for Long-Term Support (2021)

Background: For children with severe lung disease that cannot wean from ECMO, an implantable artificial lung would permit extubation and support gradual lung recovery from acute disease or provide a bridge to transplantation. We evaluate the function of the novel Pediatric MLung—an efficient, implantable, pumpless artificial lung developed specifically for children—in healthy animal subjects. Methods: Adolescent “mini sheep” weighing 12-20 …
A pure silica ytterbium-doped sol–gel-based fiber laser (2013)

In this letter it is demonstrated that the sol–gel route combined with fiber fabrication by the stack and draw method can be used to realize efficient fiber lasers. More precisely, a pure silica ytterbium-doped photonic crystal fiber with a core obtained by the sol–gel polymeric technique is studied, and a laser efficiency of more than 73% is achieved for a laser emission around 1034 nm. The optical and spectroscopic properties of the monolith and fiber are investigated, together with the sensitivity of the fiber to photodarkening. The dimensions of the ytterbium-doped monolith combined with the uniform doping and refractive index that are reported make this technique particularly interesting for the realization of large-mode area fibers.
Client Considerations (2019)

Children and adolescents present to therapy with unique strengths and challenges. Many of their challenges, often defined as disabilities, carry with them common concerns, such as making friends, academic struggles, low self-esteem, isolation and loneliness, abuse, and family dysfunction. Solution-focused therapy offers clients diagnosed with a disability hope by shedding light on client strengths and resources rather than their deficits. Further, by using creative and expressive materials, clients more willingly participate in therapy since the therapist uses techniques and approaches that lend themselves to focusing on strengths. However, the therapist must be cognizant of certain limitations clients present and make adaptations to therapy and the therapy environment, so that those with a disability can participate fully in the therapeutic process. The author provides suggestions for the therapist and possible adaptations of the therapeutic environment.
Tuning the Functionality by Splicing: Factor H and Its Alternative Splice Variant FHL-1 Share a Gene but Not All Functions (2020)

The alternative pathway regulator Factor H-like protein 1 (FHL-1) is composed of the first 7 N-terminal complement control protein domains of Factor H (FH) and protects host surfaces from uncontrolled complement attack. Although FHL-1 shares the N-terminal regulatory domains with FH, it was thought to be a weaker regulator. Recently, the regulatory activity of FHL-1 was shown to be comparable to FH. Nonetheless, the question remained whether FHL-1 is an indispensable, unique regulator. The discovery that FHL-1 is the predominant regulator on Bruch's membrane, a critical site for the onset and progression of age-related-macular degeneration (AMD), showed that FHL-1 is essential for complement regulation. A common single nucleotide polymorphism in FH/FHL-1 that predisposes for AMD underlines the important role of FHL-1 in this context. Reports that some cancer tissues specifically upregulate FHL-1 expression, thereby evading immune surveillance, suggests a pronounced regulatory activity of the splice variant. Several microorganisms specifically recruit FHL-1 to evade complement attack. From a phylogenetic point of view, FHL-1 appears much later than other complement regulators, which could imply a specific role that is possibly not systemic but rather tissue specific. This review focuses on the current knowledge of FHL-1 and its physiological and pathophysiological roles.
Motion analysis for video coding and retrieval (1999)

We concentrate on showing how a robust, low-level motion estimator based on a Robust Hough Transform can be applied to a range of tasks, such as optical flow estimation, motion estimation for video coding and fundamental matrix estimation from video sequences. We show that by selecting a robust and reliable, low-level motion estimator, which derives not only pixels displacements but also provides direct motion segmentation and other motion-related clues, one can obtain good performance even within a very simple computational framework. We describe the low-level motion estimator based on the Robust Hough Transform. The application of the technique to optical-flow estimation is presented. Video coding and estimation of fundamental matrix is dealt with. (6 pages)
Data from Immunization against HIF-1α Inhibits the Growth of Basal Mammary Tumors and Targets Mammary Stem Cells &lt;i&gt;In Vivo&lt;/i&gt; (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Triple-negative breast cancer (TNBC) represents a cancer stem cell–enriched phenotype. Hypoxia-inducible factor-1α (HIF-1α) induces the expression of proteins associated with stemness and is highly upregulated in TNBC. We questioned whether HIF-1α was immunogenic and whether vaccination targeting HIF-1α would impact the growth of basal-like mammary tumors in transgenic mice.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We evaluated HIF-1α–specific IgG in sera from controls and patients with breast cancer. Class II epitopes derived from the HIF-1α protein sequence were validated by ELISPOT. To assess therapeutic efficacy, we immunized Tg-MMTVneu and C3(1)Tag mice with HIF-1α Th1-inducing peptides. Stem cells were isolated via magnetic bead separation. Levels of HIF-1α and stem cells in the tumor were quantitated by Western blotting and flow cytometry.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The magnitude (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) and incidence (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) of HIF-1α–specific IgG were elevated in TNBC patients compared with controls. Both breast cancer patients and donors showed evidence of HIF-1α–specific Th1 and Th2 immunity. Three HIF-1α–specific Th1 class II restricted epitopes that were highly homologous between species elicited type I immunity in mice. After HIF-1α vaccination, mammary tumor growth was significantly inhibited in only C3(1)Tag (basal-like/stem cell&lt;sup&gt;high&lt;/sup&gt;; &lt;i&gt;P&lt;/i&gt; &lt; 0.001) not TgMMTV-neu (luminal/neu/stem cell&lt;sup&gt;low&lt;/sup&gt;; &lt;i&gt;P&lt;/i&gt; = 0.859) murine models. Vaccination increased type I T cells in the tumor (&lt;i&gt;P&lt;/i&gt; = 0.001) and decreased cells expressing the stem cell marker, Sca-1, compared with controls (&lt;i&gt;P&lt;/i&gt; = 0.004).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; An HIF-1α vaccine may be uniquely effective in limiting tumor growth in TNBC. Inhibiting outgrowth of breast cancer stem cells via active immunization in the adjuvant setting may impact disease recurrence. &lt;i&gt;Clin Cancer Res; 23(13); 3396–404. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;