gebhart/patrepeval huggingface dataset:
Reverse-Phase Microarray Analysis Reveals Novel Targets in Lymph Nodes of Bacillus anthracis Spore-Challenged Mice (2015)

Anthrax is a frequently fatal infection of many animal species and men. The causative agent Bacillus anthracis propagates through the lymphatic system of the infected host; however, the specific interactions of the host and microbe within the lymphatics are incompletely understood. We report the first description of the phosphoprotein signaling in the lymph nodes of DBA/2 mice using a novel technique combining the reverse-phase microarray with the laser capture microdissection. Mice were challenged into foot pads with spores of toxinogenic, unencapsulated Sterne strain. The spores quickly migrated to the regional popliteal lymph nodes and spread to the bloodstream as early as 3 h post challenge. All mice died before 72 h post challenge from the systemic disease accompanied by a widespread LN tissue damage by bacteria, including the hemorrhagic necrotizing lymphadenitis, infiltration of CD11b+ and CD3+ cells, and massive proliferation of bacteria in lymph nodes. A macrophage scavenger receptor CD68/macrosialin was upregulated and found in association with vegetative bacteria likely as a marker of their prior interaction with macrophages. The major signaling findings among the 65 tested proteins included the reduced MAPK signaling, upregulation of STAT transcriptional factors, and altered abundance of a number of pro- and anti-apoptotic proteins with signaling properties opposing each other. Downregulation of ERK1/2 was associated with the response of CD11b+ macrophages/dendritic cells, while upregulation of the pro-apoptotic Puma indicated a targeting of CD3+ T-cells. A robust upregulation of the anti-apoptotic survivin was unexpected because generally it is not observed in adult tissues. Taken together with the activation of STATs it may reflect a new pathogenic mechanism aimed to delay the onset of apoptosis. Our data emphasize a notion that the net biological outcome of disease is determined by a cumulative impact of factors representing the microbial insult and the protective capacity of the host.
The Chemistry Institute (2015)

Chemistry at the Collège de France has received particular attention over the last few years. After the departures of Profs Jean-Marie Lehn and Jacques Livage, new ambition for developing this discipline has led to the creation of several Chairs: Prof. Marc Fontecave’s Chair of Chemistry of Biological Processes in 2008, Prof. Clément Sanchez’ Chair of Chemistry of Hybrid Materials in 2011, and the Chair of Chemistry of Materials and Energy, which Prof. Jean-Marie Tarascon has held since 2014....
Charge-Induced Chromatic Transition of Amino Acid-Derivatized Polydiacetylene Liposomes (1998)

Polydiacetylene liposomes have useful potential in biosensor research. To investigate the role of the headgroup in the colorimetric transition, a series of amino acid-derivatized 10,12-pentacosadyanoic acid lipids have been synthesized. The UV-polymerized liposomes undergo an irreversible color change from blue to red in response to a change of specific solution pH. In this system, the color change appears to be due to charge-induced headgroup rearrangement which perturbs the conjugated backbone assembly. Considering the reduced degree of freedom for lipid molecules in polymeric liposomes, a rigid, staggered conformational change in polydiacetylene conjugation is suggested as a likely mechanism for the colorimetric transition.
Transport properties and vortex-glass melting inTlnBa2Ca2Cu3Ox(n=1,2) films: Correlation of scaling exponents with crystal anisotropy (1995)

We present transport measurements for ${\mathrm{Tl}}_{\mathit{n}}$${\mathrm{Ba}}_{2}$${\mathrm{Ca}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{\mathit{x}}$ (n=1,2) films. The current-voltage characteristics clearly show a curvature change in the ln(E)-ln(J) plot, presence (T\ensuremath{\gtrsim}${\mathit{T}}_{\mathit{g}}$) and absence (T${\mathit{T}}_{\mathit{g}}$) of linear resistivity, and scaling behavior with measured critical exponents z=7--8 and \ensuremath{\nu}=1--1.3, suggesting a vortex-glass--liquid phase transition. The critical exponents reported so far are lacking in universality, but dependent upon both systems (${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7}$, ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{Ca}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{10}$, etc.) and samples (crystal, film, etc.). We discuss the possibility of an anisotropic correlation length of a vortex glass for an anisotropic superconductor, a finite correlation length due to inhomogeneous pinning for defective samples, and technical problems in the scaling procedure.
Foreword to the Applied Data Science (2017)

The Applied Data Science (ADS) Invited Talks Track at KDD-2017 is a continuation of what has now become a "7-year tradition" at KDD conferences. This is the second year the track operates under the ADS name, an evolution from its origins at KDD-2011 as the "Industry Practice Expo". The KDD Conference on Knowledge Discovery and Data Mining (KDD) is the world's first, largest and best conference on Data Science, Data Mining, and Knowledge Discovery. It brings together a healthy mix of academic researchers, industry and government researchers, and practitioners from a wide range of institutions and fields. The primary focus on KDD is on peer-reviewed research contributions and the academic advancement of the field. This is an important goal and in fact the KDD conference is now recognized as the most competitive and prestigious forum for presenting high quality research results. KDD, being fundamentally an applied field, needs the strong representation of applied work of big impact. Over the years of running the conference we observed that our initial speaker-selection approach needed to be re-thought because of the important contributions made to the field outside traditional academic, industrial and government research laboratories. The result of this re-thinking was to create a forum that exposes important contributions to Data Science through Big Data Applications that address strategic problems. We wanted to effectively capture the rising importance of Data Science and Machine Learning especially in the Big Data environment where structured and unstructured data create special challenges, and of course present new opportunities. The goal of the Invited Talks Track is to curate contributions from leaders in our field who have made important contributions through the development of a system, the creation of a new and important business, or the development and market introduction of a product,. Some of these important contributions may never see an academic paper or detailed peer-reviewed paper written about them, yet they are of critical importance to our very applied field. To give you an idea of how rapidly growing this area is, and how this sector of our industry and promises to be highly disruptive across many industries, we cite a couple of articles out of a plethora of such coverage: According to IDC, the global revenues from Big Data and business will grow from $130.1 billion in 2016 to more than $203 billion in 2020, at a compound annual growth rate (CAGR) of 11.7% [1]. Furthermore, to quote from a Forbes article: "Data monetization" will become a major source of revenues, as the world will create 180 zettabytes of data (or 180 trillion gigabytes) in 2025, up from less than 10 zettabytes in 2015.? [2]
Performance estimation of the state-of-the-art convolution neural networks for thermal images-based gender classification system (2020)

Gender classification has found many useful applications in the broader domain of computer vision systems including in-cabin driver monitoring systems, human–computer interaction, video surveillance systems, crowd monitoring, data collection systems for the retail sector, and psychological analysis. In previous studies, researchers have established a gender classification system using visible spectrum images of the human face. However, there are many factors affecting the performance of these systems including illumination conditions, shadow, occlusions, and time of day. Our study is focused on evaluating the use of thermal imaging to overcome these challenges by providing a reliable means of gender classification. As thermal images lack some of the facial definition of other imaging modalities, a range of state-of-the-art deep neural networks are trained to perform the classification task. For our study, the Tufts University thermal facial image dataset was used for training. This features thermal facial images from more than 100 subjects gathered in multiple poses and multiple modalities and provided a good gender balance to support the classification task. These facial samples of both male and female subjects are used to fine-tune a number of selected state-of-the-art convolution neural networks (CNN) using transfer learning. The robustness of these networks is evaluated through cross validation on the Carl thermal dataset along with an additional set of test samples acquired in a controlled lab environment using prototype uncooled thermal cameras. Finally, a new CNN architecture, optimized for the gender classification task, GENNet, is designed and evaluated with the pretrained networks.
Path-dependent human identification using a pyroelectric infrared sensor and fresnel lens arrays (2006)

This paper presents a design and development of a low power consumption, and low cost, human identification system using a pyroelectric infrared (PIR) sensor whose visibility is modulated by a Fresnel lens array. The optimal element number of the lens array for the identification system was investigated and the experimental results suggest that the lens array with more elements can yield a better performance in terms of identification and false alarm rates. The other parameters of the system configuration such as the height of sensor location and sensor-to-object distance were also studied to improve spectral distinctions among sensory data of human objects. The identification process consists of two parts: training and testing. For the data training, we employed a principal components regression (PCR) method to cluster data with respect to different registered objects at different speed levels. The feature data of different objects walking along the same path in training yet at random speeds are then tested against the pre-trained clusters to decide whether the target is registered, and which member of the registered group it is.
From surface coatings to polymer nanofilms: lifting off polymer brushes (2013)

In this contribution we introduce a technique for the fabrication of a new kind of organic nanofilm from polymer brushes. For this, we grew poly(styrene) brushes on a thin film of poly(vinyl alcohol) (PVA). The resulting graft polymer film was patterned into square-shaped sections using photolithographic techniques. Afterwards the PVA layer was dissolved in water, thus lifting off the extremely thin layer of brush material. We obtained dimensionally stable, square shaped objects with a thickness in the nanometer size region, dispersed in water. When dried on a substrate, these nanofilms showed a unique folding behavior.
QoE evaluation for video streaming over eMBMS (2013)

As the multicast standard for Long Term Evolution (LTE), Enhanced Multimedia Broadcast Multicast Service (eMBMS) was introduced by Third Generation Partnership Project (3GPP) to facilitate delivery of popular content to multiple users over a cellular network. If a large number of users is interested in the same content, for e.g., live sports, news clips, etc., multicast transmission can significantly lower the cost and make better use of the spectrum as compared to unicast transmission. In this paper, we study and analyze the quality of experience (QoE) at the end user during live video streaming over eMBMS. We consider a comprehensive end-to-end MBMS streaming frame-work based on H.264/AVC encoded video content delivered in a chunked format over multiple segments using the File Delivery over Unidirectional Transport (FLUTE) protocol, combined with application layer (AL) forward error correction (FEC) based on Raptor and RaptorQ codes. Specifically, our study involves QoE evaluation in terms of startup delay, rebuffering percentage and Peak Signal-to-Noise Ratio (PSNR) metrics and provides performance evaluations to characterize the impact of various MBMS streaming, transport and AL-FEC configurations on the end user QoE. We also propose a decoding strategy that takes into consideration the systematic structure of AL-FEC codes to enhance performance when a source block decoding fails.
Integrated determination of sensitivity derivatives for an aeroelastic transonic wing (1996)

The incremental iterative technique is used to effectively couple for three-dimensional transonic flow about a twisted unswept rectangular wing, an aerodynamic solution for the pressure distribution with a structural solution for the corresponding deflections and, using the quasianalytical approach, simultaneously obtain the aerodynamic, structural, and coupling sensitivity derivatives for the fully coupled system. The solution includes aerodynamic sensitivities for nine design variables at all flowfield points, structural sensitivities for four design variables at 490 points on the wing, and 450 coupling sensitivities. Subsequently, fully coupled system sensitivity derivatives are obtained. The results often show significant differences between the discipline and system sensitivity derivatives and that the system derivatives are sensitive to the location and number of coupling derivatives.
Tuning a Protein‐Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation (2018)

Abstract Activated esters are widely used to label proteins at lysine side chains and N termini. These reagents are useful for labeling virtually any protein, but robust reactivity toward primary amines generally precludes site‐selective modification. In a unique case, fluorophenyl esters are shown to preferentially label human kappa antibodies at a single lysine (Lys188) within the light‐chain constant domain. Neighboring residues His189 and Asp151 contribute to the accelerated rate of labeling at Lys188 relative to the ≈40 other lysine sites. Enriched Lys188 labeling can be enhanced from 50–70 % to &gt;95 % by any of these approaches: lowering reaction temperature, applying flow chemistry, or mutagenesis of specific residues in the surrounding protein environment. Our results demonstrated that activated esters with fluoro‐substituted aromatic leaving groups, including a fluoronaphthyl ester, can be generally useful reagents for site‐selective lysine labeling of antibodies and other immunoglobulin‐type proteins.
347 Histopathology of Necrotic Spinal Cord Tissue Exudate Collected During Surgical Implantation of a Biodegradable Scaffold Following Acute Spinal Cord Injury (2017)

Lee, K Stuart MD, FACS; Boyer, Philip J MD, PhD; Hsieh, Patrick C MD, MSc; Hurth, Kyle M MD, PhD; Guest, James D MD, PhD; Aimetti, Alex PhD; Layer, Richard T PhD; Moore, Simon W PhD; Ulich, Thomas
Synthesis of Group 4 Complexes That Contain the Tridentate Diamido/Donor Ligands [(ArylNCH2CH2)2O]2- and Zirconium Complexes That Contain [(ArylNCH2CH2)2S]2- and an Evaluation of Their Activity for the Polymerization of 1-Hexene (1998)

Compounds of the type (ArylNHCH2CH2)2O (Aryl = 2,6-Me2C6H3 (H2[1a]), 2,6-Et2C6H3 (H2[1b]), 2,6-i-Pr2C6H3 (H2[1c])) can be prepared by treating (TsOCH2CH2)2O (TsO = tosylate) with the lithium anilides in THF. [1a,b]TiCl2, [1a,b]TiMe2, [1a]Ti(CH2Ph)2, [1a−c]M(NMe2)2 (M = Zr or Hf), [1a−c]MCl2, and [1a−c]MR2 (R = Me, Et, i-Bu) were prepared. An X-ray study of [1a]Ti(CH2Ph)2 revealed the structure to be a distorted trigonal bipyramid (type B) in which the two amido nitrogens and one benzyl ligand occupy equatorial positions. An X-ray study of [1a]ZrMe2 showed it to be a distorted trigonal bipyramid that contains “axial” amido groups (type A), while an X-ray study of [1c]HfEt2 revealed it to have a structure halfway between type A and type B, i.e., a distorted square pyramid with one alkyl in the apical position. Analogous compounds were also prepared that contain a sulfur donor instead of oxygen, i.e., [(2,6-Me2C6H3NHCH2CH2)2S] (H2[2a]), [(2,6-i-Pr2C6H3NHCH2CH2)2S] (H2[2c]), [2a,c]Zr(NMe2)2, [2a,c]ZrCl2, [2a,c]ZrMe2, and [2c]Zr(CH2CHMe2)2. An X-ray study of [2a]ZrMe2 revealed it to be closest to a type B structure. Addition of 1 equiv of [PhNMe2H][B(C6F5)4] in C6D5X (X = Br, Cl) to [1a,c]MMe2 (M = Zr, Hf) gave cationic complexes that contain coordinated dimethylaniline, with which free aniline does not exchange readily on the NMR time scale at 60 °C. Addition of excess ether to {[1a]MMe(NMe2Ph)}[B(C6F5)4] (M = Zr, Hf) led to {[1a]MMe(ether)}[B(C6F5)4] (M = Zr, Hf) complexes in high yield. Analogous cations can be prepared in the sulfur ligand system, but they do not appear to be as stable as in the oxygen ligand system. Zr and Hf dimethyl complexes that contain an oxygen donor or a sulfur donor ligand can be activated with [Ph3C][B(C6F5)4] to yield efficient catalysts for polymerization of 1-hexene, although the molecular weight of the poly(1-hexene) chains is limited to ∼20 000−∼25 000 under the conditions employed. Neither {[1c]ZrMe(ether)}[B(C6F5)4] nor {[1c]HfMe(ether)}[B(C6F5)4] will polymerize 1-hexene in C6D5Br at room temperature, and neither will polymerize ethylene readily at 1 atm and 25 °C. It is proposed that a solvated five-coordinate cation must lose the solvent in order to react with an olefin and that β-hydride elimination in the four-coordinate cation limits chain length.
18 kDa Translocator Protein in Mitochondria-Related Pathology: The Case of Traumatic Brain Injury (2018)

Translocator protein (TSPO) takes part in mitochondrial adenine triphosphate (ATP) production and transport. Mitochondrial TSPO is a part of the apoptotic and cell necrotic mechanism. Ligands to TSPO, endogenous and synthetic, have different effects on metabolism and protein expression in human well-differentiated metabolically active cells. In general, most of the TSPO ligands affect the cellular function or metabolism in the same general direction, but different specific TSPO ligands have their own unique effects in human cells. Regulation of gene expression via the actions of TSPO ligands on the mitochondrial TSPO may form an essential mechanism for the regulation of cellular functions, especially during acute organ injury, such as acute brain damage. The exact mode of action of the specific TSPO ligands is not clear enough and should be further investigated. TSPO is a potential target for therapeutic efforts to mitigate secondary tissue injury caused by programmed cell death.
Membrane-dependent oligomeric structure and pore formation of a β-hairpin antimicrobial peptide in lipid bilayers from solid-state NMR (2006)

We used solid-state NMR spectroscopy to investigate the oligomeric structure and insertion of protegrin-1 (PG-1), a beta-hairpin antimicrobial peptide, in lipid bilayers that mimic either the bacterial inner membrane [palmitoyloleoylphosphatidyl ethanolamine and palmitoyloleoylphosphatidylglycerol (POPE/POPG) bilayers] or the red blood cell membrane [neutral palmitoyloleoylphosphatidylcholine (POPC)/cholesterol bilayers]. (1)H spin diffusion from lipids to the peptide indicates that PG-1 contacts both the lipid acyl chains and the headgroups in the anionic membrane but resides far from the lipid chains in the POPC/cholesterol bilayer. (19)F spin diffusion data indicates that 75% of the beta-hairpins have homodimerized N strands and C strands in the anionic membrane. The resulting (NCCN)(n) multimer suggests a membrane-inserted beta-barrel enclosing a water pore. The lipids surrounding the beta-barrel have high orientational disorder and chain upturns, thus they may act as fillers for the pore. These results revise several features of the toroidal pore model, first proposed for magainin and subsequently applied to PG-1. In the POPC/cholesterol membrane, the N and C strands of PG-1 cluster into tetramers, suggesting the formation of beta-sheets on the membrane surface. Thus, the membrane composition plays a decisive role in defining the assembly and insertion of PG-1. The different oligomeric structures of PG-1 help to explain its greater toxicity for bacteria than for eukaryotic cells.
A color atlas for human assisted reproduction : laboratory and clinical insights (2003)

SECTION I: LABORATORY INSIGHTS The Biology of Fertilization in Humans 3 Laura Hewitson and Gerald P. Schatten The New Imaging Technique Applied to Human Reproduction 17 Cathy Boutin and Clifford Hoyt The Oocyte 25 Vanessa Guelman and Pasquale Patrizio Fertilization and Cleavage 49 Vanessa Guelman Classification of Pronuclei and Polarity of the Zygote: Correlations with Outcome 71 Lynette Scott Intracytoplasmic Sperm Injection 89 Vanessa Guelman and Michael J. Tucker Morphological Scoring of Human Embryos and Its Relevance to Blastocyst Transfer 99 Michael J. Tucker and Juergen Liebermann Assisted Hatching 109 Marc P. Portmann and Ronald F. Feinberg Oocyte and Embryo Cryopreservation 137 Michael J. Tucker and Juergen Liebermann Practical Aspects of Human Ovarian Tissue Storage 161 Debra A. Gook and David H. Edgar Polar Body Biopsy, Embryo Biopsy, and Fixation for Fluorescent In Situ Hybridization Analysis 179 Santiago Munne, Mireia Sandalinas, Esther Velilla, and Peter Nagy Nuclear and Cytoplasmic Transfer in Mouse and Human Oocytes 195 John Zhang, Hui Liu, Lewis Krey, and Jamie A. Grifo SECTION II: CLINICAL INSIGHTS The Clinical Component of Assisted Reproductive Technologies 209 Pasquale Patrizio The Technique of Ovarian Transplantation: Laboratory and Clinical Aspects 229 Kutluk Oktay and Erkan Buyuk SECTION III: ADDITIONAL TOPICS Media Used in the Assisted Reproductive Technologies Laboratories 241 Patrick Quinn Cryopreservation Protocols 257 Michael J. Tucker, Paula C. Morton, and Juergen Liebermann Quality Control and Accreditation 277 Brooks A. Keel and Tammie K. Schalue The Ethics of Stem Cell Therapy 297 Glenn McGee, Pasquale Patrizio, Vanessa Kuhn, and Claire Robertson-Kraft Subject Index 311
Vesicle-bound regulatory RNAs are associated with tissue aging (2021)

Previous work on murine models and human demonstrated global as well as tissue-specific molecular aging trajectories in solid tissues and body fluids 1–8 . Extracellular vesicles like exosomes play a crucial role in communication and information exchange in between such systemic factors and solid tissues 9,10 . We sequenced freely circulating and vesicle-bound small regulatory RNAs in mice at five time points across the average life span from 2 to 18 months. Intriguingly, each small RNA class exhibits unique aging patterns, which showed differential signatures between vesicle-bound and freely circulating molecules. In particular, tRNA fragments showed overall highest correlation with aging which also matched well between sample types, facilitating age prediction with non-negative matrix factorization (86% accuracy). Interestingly, rRNAs exhibited inverse correlation trajectories between vesicles and plasma while vesicle-bound microRNAs (miRNAs) were exceptionally strong associated with aging. Affected miRNAs regulate the inflammatory response and transcriptional processes, and adipose tissues show considerable effects in associated gene regulatory modules. Finally, nanoparticle tracking and electron microscopy suggest a shift from overall many small to fewer but larger vesicles in aged plasma, potentially contributing to systemic aging trajectories and affecting the molecular aging of organs.