gebhart/patrepeval huggingface dataset:
Abstract 1033: Patient-derived xenografts for prognostication and personalized treatment for head and neck squamous cell carcinoma (2018)

Abstract Overall outcomes for HPV-negative head and neck squamous cell carcinoma (HNSCC) remain poor with 5-year overall survival rates of 50-60%. Oral squamous cell carcinoma (OSCC), the most common subtype of HPV-negative HNSCC, is typically treated with surgery, and clinico-pathologic features are used to identify patients in need of adjuvant therapies such as radiation therapy (RT), or radiation plus concurrent chemotherapy (CRT). It is clear from the rate of loco-regional or distant failures that more accurate methods of risk stratification would greatly improve outcomes for OSCC patients. This requires biomarkers to identify patients that will benefit from adjuvant RT or CRT but currently there are no validated molecular biomarkers that have been clinically implemented for the personalized treatment of OSCC. In addition to biomarkers for better risk stratification, there is also a need for novel therapeutic strategies leading to improved outcomes. Recently patient-derived xenografts (PDXs) have been shown to faithfully recapitulate human tumor biology and predict drug responses, supporting their relevance as preclinical models for new drug development. Upon subcutaneous implantation of HNSCC specimens into NOD/SCID/IL2Rγ-/- mice, 161 of 243 samples (66%) successfully formed patient-derived xenografts (PDX). Using univariable and multivariable analyses, the ability to form a PDX correlated significantly with adverse clinical outcomes, and specifically, patients with palpable PDX-formation within 8 weeks experienced particularly poor outcomes (hazard ratio for overall survival = 3.0). A cohort of engrafting and non-engrafting samples were sequenced using a targeted sequencing panel designed for both mutational and copy number alteration detection. The overall frequency of somatic genomic alterations detected was similar to The Cancer Genome Atlas cohort and interestingly, successful engraftment correlated to amplification of the CCND1 gene. Twelve PDX models were treated with the CDK4/6 inhibitor, abemaciclib; 5 of 6 models with CCND1 amplifications and/or CDKN2A mutations responded to abemaciclib treatment, whereas only 1 of 6 models lacking these alterations responded. These results demonstrate the potential of using PDX models to identify novel targeted therapies for HNSCC patients who have the poorest outcomes. In the future, PDX avatars could also be exploited to individualize treatment for patients at high risk of relapse following definitive treatment. Citation Format: Christina Karamboulas, Jeffrey P. Bruce, Andrew J. Hope, Jalna Meens, Shao Hui Huang, Jie Su, Fei-Fei Liu, Trevor J. Pugh, Scott V. Bratman, Wei Xu, Laurie E. Ailles. Patient-derived xenografts for prognostication and personalized treatment for head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1033.
Hydrogels oscillants en interaction fluide/structure : vers le design de plis vocaux biomimétiques (2021)

International audience
EUROPEAN BREWERY CONVENTION THE E.B.C. SCALE OF BITTERNESS (1967)

A fuller acceptance of the Committee's views on the characteristics of the bittering compounds of hopped beers has led to a revision of the units of calculation, which are now called “E.B.C. Bitterness Units.” For the Klopper or the Brenner, Vigilante & Owades methods the calculation recommended is:— E.B.C. Bitterness Units = Extinction at 275 mμ multiplied by 50 The change from the results given previously by the different methods of calculation will only be small, since the new method gives results which lie between those given by the different previous methods. Nevertheless, for uniformity it is recommended that the change to E.B.C. Bitterness Units should be made on 1st January, 1968.
Spontaneous vs. gaze shift-induced blinks for assessing driver drowsiness/inattention by electrooculography (2013)

Driver monitoring systems with focus on drowsiness and inattention aim to reduce car-crashes. To achieve this goal, previous research has shown that driver eye blink features (blink frequency, duration etc.) are correlated to some extent with drowsiness. Hence, within a level of uncertainty they can contribute to driver drowsiness warning systems. In order to improve such systems, we investigated blink characteristics with respect to their different origins. We observed that in a real road experiment using electrooculography, blinks occur both spontaneously or due to gaze shift. Gaze shifts between fixed positions, which occurred due to secondary visuomotor task, induced and modulated the occurrence of blinks. Moreover, the direction of the gaze shift affected the occurrence of such blinks. Based on the eye movements during another experiment in a driving simulator without a secondary task, we found that the amount of gaze shift (between various positions) is positively correlated with the probability of the blink occurrence. Therefore, the paper recommends handling gaze shift-induced blinks (e.g. during visual distraction) differently from those occurring spontaneously in drowsiness warning systems. (Paper No. 20-P).
High resolution CINE imaging of guided knee motion using golden-angle radial MRI and a novel knee loading device (2023)

An MRI-safe device guiding knee motion/loading with a rotary encoder was used during MRI measurements of multiple knee flexion-extension cycles using radial gradient echo imaging with the golden-angle as a radial increment. Reproducibility of knee motion was investigated and anatomical CINE images were reconstructed for different knee angles by synchronizing the encoder data with the MRI data and selective gating, enabling evaluation of musculoskeletal conditions.
Eukaryotic RNAse H shares a conserved domain with caulimovirus proteins that facilitate translation of polycistronic RNA (1994)

RNAse H (RNH1 protein) from the trypanosomatid Crithidia fasciculata has a functionally uncharacterized N-terminal domain dispensable for the RNAse H activity. Using computer methods for database search and multiple alignment, we show that the N-terminal domains of RNH1 and its homologue encoded by a cDNA from chicken lens are related to the conserved domain in caulimovirus ORF VI product that facilitates translation of polycistronic virus RNA in plant cells. We hypothesize that the N-terminal domain of eukaryotic RNAse H performs an as yet uncharacterized regulatory function, possibly in mRNA translation or turnover.
Guest Editors' Introduction: On-Chip Interconnects for Multicores (2007)

This special issue of IEEE Micro brings readers the latest advances in the field of on-chip interconnects for multicores. The guest editors specifically selected articles to focus on novel on-chip networks realized on actual silicon--partly to showcase a few silicon prototypes of on-chip networks being used in multicore processors and SoCs; partly to bring to attention the implementation issues facing architects and designers. Along with six articles that gather insights from the designers of actual on-chip interconnects for multicores, the special issue includes two articles that delve into the design infrastructure support for on-chip networks and an article that summarizes the grand research challenges for realizing next-generation on-chip networks and multicores.
Novel Single Photon Sensors for Highly Sensitive Fluorescence Detection Systems (2009)

Stony Brook University Libraries.\nSBU Graduate School in Electrical and Computer Engineering.\nLawrence Martin (Dean of Graduate School), Vera Gorfinkel – Dissertation Advisor\nAssociate Professor, Department of Electrical and Computer Engineering, Hang-Sheng Tuan – Chairperson of Defense\nProfessor, Department of Electrical and Computer Engineering, Dmitri Donetski\nAssistant Professor, Department of Electrical and Computer Engineering.
Correlation Between Neonatal Cranial Ultrasound, MRI in Infancy and Neurodevelopmental Outcome in Infants with a Large Intraventricular Haemorrhage with or without Unilateral Parenchymal Involvement (1998)

Combining neonatal US with MRI in infancy enhances our understanding of the long-term effects of severe haemorrhagic brain lesions, occurring in preterm infants.
LNEMLC: Label Network Embeddings for Multi-Label Classification (2018)

Multi-label classification aims to classify instances with discrete non-exclusive labels. Most approaches on multi-label classification focus on effective adaptation or transformation of existing binary and multi-class learning approaches but fail in modelling the joint probability of labels or do not preserve generalization abilities for unseen label combinations. To address these issues we propose a new multi-label classification scheme, LNEMLC - Label Network Embedding for Multi-Label Classification, that embeds the label network and uses it to extend input space in learning and inference of any base multi-label classifier. The approach allows capturing of labels' joint probability at low computational complexity providing results comparable to the best methods reported in the literature. We demonstrate how the method reveals statistically significant improvements over the simple kNN baseline classifier. We also provide hints for selecting the robust configuration that works satisfactorily across data domains.
Extensible and similarity-based grouping for data integration (2003)

The general concept of grouping and aggregation appears to be a fitting paradigm for various issues in data integration, but in its common form of equality-based grouping, a number of problems remain unsolved. We propose a generic approach to user-defined grouping as part of a SQL extension, allowing for more complex functions, for instance integration of data mining algorithms. Furthermore, we discuss high-level language primitives for common applications.
Mood management and nicotine gum in smoking treatment: A therapeutic contact and placebo-controlled study. (1996)

Earlier research indicated that a 10-session mood management (MM) intervention was more effective than a 5-session standard intervention for smokers with a history of major depressive disorder (MDD). In a 2 x 2 factorial design, the present study compared MM intervention to a contact-equivalent health education intervention (HE) and 2 mg to 0 mg of nicotine gum for smokers with a history of MDD. Participants were 201 smokers, 22% with a history of MDD. Contrary to the earlier findings, the MM and HE interventions produced similar abstinence rates: 2 mg gum was no more effective than placebo. History-positive participants had a greater increase in mood disturbance after the quit attempt. Independent of depression diagnosis, increases in negative mood immediately after quitting predicted smoking. No treatment differences were found in trends over time for measures of mood, withdrawal symptoms, pleasant activities and events, self-efficacy, and optimism and pessimism. History-positive smokers may be best treated by interventions providing additional support and contact, independent of therapeutic content.
Robust Path Construction for Reliable Data Transmissions in Node Disjoint Multipath Routing (2015)

Wireless Sensor Networks (WSNs) are prone to node breakdowns due to energy constraints, which contribute to frequent topology changes. Moreover, since sensor nodes have restricted transmission range, multiple hops are needed by the node in order to forward the packets from one node to the other and this raises very challenging issues when designing routing protocols. Most of the proposed single path routing schemes use a periodic low-rate flooding of data in order to recover from path failures, which causes higher consumption in sensor node resources. So multipath routing is an optimal approach to enhance the network lifetime. In this paper, a robust path construction for a reliable data transmission in node-disjoint multipath routing (RNDMR) is proposed for WSNs. The proposed RNDMR has the ability to provide a low overhead path construction as well as provide data transmission reliability by using XOR-based coding algorithm, which entails low utilization of resources, such as low storage space and lesser computing power. In the proposed RNDMR, the procedure involves the splitting up of all transmitted messages into many different segments of equal size, before adding the XOR-based error correction codes and distributing it among multiple paths simultaneously in order to boost reliable data transmission and to be assured that the essential fragment of the packet arrives at the sink node without any additional consumption of energy and undue delay. By using simulations, the performance of RNDMR was assessed and compares it with ReInForm routing. The results illustrate that RNDMR attains low energy consumption, records low average delay and routing overhead, as well as increased packet delivery ratio when compared with ReInForm Routing.
Simulations of the pressure profiles of the PETRAIII frontends (2008)

PETRA III will be a high brilliance third generation synchrotron radiation source The undulators will provide photon beams with small beam size and therefore the components in the frontend are as compact as feasible. The resulting narrow cross sections of the vacuum system will yield a small conductance in the whole beamline. The design of the frontends has reached an advanced state so that the initial design of the vacuum system can be finalized now. The vacuum specification of the beamline components [2] demands for a hydrocarbon and dust free vacuum systems. To provide this, the beamline will be initially pumped down with dry pumping stations [9] to a pressure of at least 10 -6 mbar. At this pressure a set of ion pumps will be switched on to pump the beamline continuously. For lifetime reasons of the ion pumps it is necessary that during operation the pressure in the pumps is below 10 - 6 mbar. During the start up of the beamline system a high amount of gas will be photo desorbed especially at the high power slit systems. To cope with this, the pumping concept of the beamline has been revised. Monte Carlo simulations of the pressure profiles in the beamline show that additional pumping near the slit systems is mandatory for a long lifetime of the ionpumps. The paper reports the layout process of the pumping system.
Reversible tuning of luminescence and magnetism in a structurally flexible erbium–anilato MOF (2022)

By combining 3,6-<i>N</i>-ditriazolyl-2,5-dihydroxy-1,4-benzoquinone (H<sub>2</sub>trz<sub>2</sub>An) with NIR-emitting Er<sup>III</sup> ions, two different 3D neutral polymorphic frameworks (1a and 1b), differing in the number of uncoordinated water molecules, formulated as [Er<sub>2</sub>(trz<sub>2</sub>An)<sub>3</sub>(H<sub>2</sub>O)<sub>4</sub>] <sub><i>n</i></sub> ·<i>x</i>H<sub>2</sub>O (<i>x</i> = 10, a; <i>x</i> = 7, b), have been obtained. The structure of 1a shows layers with (6,3) topology forming six-membered rings with distorted hexagonal cavities along the <i>bc</i> plane. These 2D layers are interconnected through the N4 atoms of the two pendant arms of the trz<sub>2</sub>An linkers, leading to a 3D framework, where neighboring layers are eclipsed along the <i>a</i> axis, with hexagonal channels filled with water molecules. In 1b, layers with (6,3) topology in the [101] plane are present, each Er<sup>III</sup> ion being connected to three other Er<sup>III</sup> ions through bis-bidentate trz<sub>2</sub>An linkers, forming rectangular six-membered cavities. 1a and 1b are multifunctional materials showing coexistence of NIR emission and field-induced slow relaxation of the magnetization. Remarkably, 1a is a flexible MOF, showing a reversible structural phase transition involving shrinkage/expansion from a distorted hexagonal 2D framework to a distorted 3,6-brickwall rectangular 3D structure in [Er<sub>2</sub>(trz<sub>2</sub>An)<sub>3</sub>(H<sub>2</sub>O)<sub>2</sub>] <sub><i>n</i></sub> ·2H<sub>2</sub>O (1a_des). This transition is triggered by a dehydration/hydration process under mild conditions (vacuum/heating to 360 K). The partially dehydrated compound shows a sizeable change in the emission properties and an improvement of the magnetic blocking temperature with respect to the hydrated compound, mainly related to the loss of one water coordination molecule. Theoretical calculations support the experimental findings, indicating that the slight improvement observed in the magnetic properties has its origin in the change of the ligand field around the Er<sup>III</sup> ion due to the loss of a water molecule.
Lipid Membrane; A Novel Target for Viral and Bacterial Pathogens (2006)

Lipid rafts are defined as specialized, dynamic microdomains that can be found in plasma membrane, and they are enriched with cholesterol and sphingolipids. Since lipid rafts' first debut in the mid 1990's, their existence, function and biological relevance have been a subject of intense scrutiny within the scientific community. Throughout this debate, we have learned a great deal regarding how cargos (both pathogens and cellular factors) are transported into and out of the cell through raft-dependent or raft-independent pathways. It is now apparent that a number of toxins, bacterial-, and viral-pathogens are able to exploit cholesterol and/or lipid rafts to gain a foot hold in their target hosts. The objective of this review is to describe our current appreciation on how selected pathogens utilise cholesterol and/or lipid rafts to support their propagation and to speculate on how some of these observations can be explored for the development of novel strategies that target plasma membrane lipids to control the spread of these viral- and bacterial-pathogens.
Characteristics of Bismuth Layered SrBi2Ta2O9 Thin-Film Capacitors and Comparison with Pb(Zr, Ti)O3 (1995)

We have developed the series of thin-film bismuth layer structured ferroelectric (BLSF) materials such as SrBi 2 Ta 2 O 9 , SrBi 2 Nb 2 O 9 , SrBi 4 Ti 4 O 15 and their solid solutions using metallo-organic-decomposition (MOD) spin-on coating techniques. We found that SrBi 2 Ta 2 O 9 is one of the best potential candidate materials for ferroelectric nonvolatile memories. The SrBi 2 Ta 2 O 9 thin-film capacitor had the remanent polarization ( P r+ - P r- ) of 20 µ C/cm 2 , coercive field of 35 kV/cm and dielectric constant of 250. SrBi 2 Ta 2 O 9 thin film on platinum electrode has fatigue-free characteristics for up to 2×10 11 cycles without requiring any complicated electrode system such as conductive oxide. Moreover, SrBi 2 Ta 2 O 9 thin film has many advantages, e.g. , high signal/noise ratio of 8 at 1.2 V, low-voltage operation at as low as 1 V, long data-retention, little surface effect, superior imprint properties and low leakage current. We considered that these advantages are due to (1) less space charge and (2) the inherent domain motion.
Silicon 2&#x00D7;2 optical switch based on optimized multimode interference coupler to minimize power consumption (2015)

Optical switches based on multimode interference (MMI) couplers can reduce footprint and increase tolerance against fabrication deviations. Furthermore, a 50% power consumption reduction has been demonstrated by designing a trenched MMI for thermal isolation without penalizing insertion losses and crosstalk.
Relation of “agammaglobulinemia” sera to rheumatoid agglutination reactions (1958)

Abstract In an effort to elucidate the nature of the polyarthritis and other systemic Lesions occurring during the course of hypogammaglobulinemia, sera from patients with hypogammaglobulinemia were tested by serveral procedures for demonstration of the rheumatoid factor or its inhibitor. Neither agglutinator of inhibitor was present in the twelve patients studied, six of whom had arthritis. A possible relationship between the arthritis of agammaglobulinemia and rheumatoid arthritis culd not be confirmed. However, for reasons described, such a relationship could not be excluded. Con le objectivo de elucidar le natura del polyarthritis e del altere lesiones systemic que occurre in le curso de hypogammaglobulinemia, seros ab patientes con hypogammaglobulinemia esseva testate per varie technicas pro le presentia del factor rheumatoide o de su inhibitor. In le dece‐duo patientes studiate, incluse sex con arthritis, ni agglutinator ni inhibitor esseva presente. Le existentia possibile de un relation inter le arthritis de agammaglobulinemia e arthritis rheumatoide non poteva esser confirmate. Tamen, pro rationes describite, excluder le existentia de ille relation esseva etiam impossibile.
Crystal Structures of Stapled and Hydrogen Bond Surrogate Peptides Targeting a Fully Buried Protein–Helix Interaction (2014)

Constrained α-helical peptides are an exciting class of molecule designed to disrupt protein-protein interactions (PPIs) at a surface-exposed helix binding site. Complexes that engage more than one helical face account for over a third of structurally characterized helix PPIs, including several examples where the helix is fully buried. However, no constrained peptides have been reported that have targeted this class of interaction. We report the design of stapled and hydrogen bond surrogate (HBS) peptides mimicking the helical tail of the malaria parasite invasion motor myosin (myoA), which presents polar and hydrophobic functionality on all three faces in binding its partner, myoA tail interacting protein (MTIP), with high affinity. The first structures of these different constrained peptides bound to the same target are reported, enabling a direct comparison between these constraints and between staples based on monosubstituted pentenyl glycine (pGly) and disubstituted pentenyl alanine (pAla). Importantly, installation of these constraints does not disrupt native interactions in the buried site, so the affinity of the wild-type peptide is maintained.
Expression of Hepatocyte Growth Factor and Its Receptor c-metin the Ovine Uterus1 (2000)

Epithelial-mesenchymal interactions (EMI) are necessary for epithelial cell proliferation, differentiation, and function in the uterus and are mediated, in part, by paracrine growth factors of stromal origin. The objective of this study was to determine if hepatocyte growth factor (HGF, scatter factor) and its receptor c-met were present in the ovine uterus and to characterize their temporal and spatial expression during the estrous cycle and pregnancy. Reverse transcription-polymerase chain reaction was used to clone partial cDNAs for ovine HGF and c-met from endometrial total RNA. Northern blot analysis of endometrial RNA revealed expression of a 6-kb mRNA for HGF and an 8-kb mRNA for c-met in ovine endometrium. In situ hybridization demonstrated that HGF mRNA was expressed by stromal cells of the endometrium, whereas c-met mRNA was localized exclusively to luminal and glandular epithelial cells. In the early conceptus, HGF mRNA was expressed by chorioallantoic mesenchyme, and c-met was expressed by trophectoderm. Steady-state levels of endometrial c-met mRNA increased after Day 9 in both cyclic and pregnant ewes. The HGF mRNA was expressed during both the estrous cycle and early pregnancy. Results indicate that HGF is a stromal-derived paracrine growth factor in the ovine uterus and placenta that is potentially involved in endometrial epithelial-stromal interactions and chorioallantoic stromal-trophectodermal interactions. In the ovine uterus, HGF may stimulate epithelial morphogenesis and differentiated function required for establishment and maintenance of pregnancy, conceptus implantation, and placentation.