gebhart/patrepeval huggingface dataset:
Multiplexed fibre Fizeau interferometer and fibre Bragg grating sensor system for simultaneous measurement of quasi-static strain and temperature using discrete wavelet transform (2006)

We present a multiplexed fibre Fizeau interferometer (FFI) and fibre Bragg grating (FBG) sensor system for simultaneous measurement of quasi-static strain and temperature. A combined spatial-frequency and wavelength-division multiplexing scheme is employed to multiplex the FFI and FBG sensors.
Radiotherapy-induced emesis. An overview. (1998)

Studies with total body irradiation, fractionated treatment and high-dose single exposures have clearly demonstrated the value of 5-HT3-receptor antagonist antiemetics. There is a response between 60 and 97%. There is no difference in the efficacy of the different 5-HT3-antagonists. High-risk patients should be prophylactic treated with 5-HT3-antagonists. The additional administration of glucocorticoids and benzodiazepins can optimize the response.
Sex differences in light sensitivity impact on brightness perception, vigilant attention and sleep in humans (2017)

Artificial light endows a "round-the-clock", 24-h/7-d society. Chronic exposure to light at night contributes to health hazards for humans, including disorders of sleep. Yet the influence of inter-individual traits, such as sex-differences, on light sensitivity remains to be established. Here we investigated potential sex-differences to evening light exposure of 40 lx at 6500 K (blue-enriched) or at 2500 K (non-blue-enriched), and their impact on brightness perception, vigilant attention and sleep physiology. In contrast to women, men had higher brightness perception and faster reaction times in a sustained attention task during blue-enriched light than non-blue-enriched. After blue-enriched light exposure, men had significantly higher all-night frontal NREM sleep slow-wave activity (SWA: 2-4 Hz), than women, particularly during the beginning of the sleep episode. Furthermore, brightness perception during blue-enriched light significantly predicted men's improved sustained attention performance and increased frontal NREM SWA. Our data indicate that, in contrast to women, men show a stronger response to blue-enriched light in the late evening even at very low light levels (40lux), as indexed by increased vigilant attention and sleep EEG hallmarks. Collectively, the data indicate that sex differences in light sensitivity might play a key role for ensuring the success of individually-targeted light interventions.
DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data (2019)

Methods for single-cell RNA sequencing (scRNA-seq) have greatly advanced in recent years. While droplet- and well-based methods have increased the capture frequency of cells for scRNA-seq, these technologies readily produce technical artifacts, such as doublet cell captures. Doublets occurring between distinct cell types can appear as hybrid scRNA-seq profiles, but do not have distinct transcriptomes from individual cell states. We introduce DoubletDecon, an approach that detects doublets with a combination of deconvolution analyses and the identification of unique cell-state gene expression. We demonstrate the ability of DoubletDecon to identify synthetic, mixed-species, genetic, and cell-hashing cell doublets from scRNA-seq datasets of varying cellular complexity with a high sensitivity relative to alternative approaches. Importantly, this algorithm prevents the prediction of valid mixed-lineage and transitional cell states as doublets by considering their unique gene expression. DoubletDecon has an easy-to-use graphical user interface and is compatible with diverse species and unsupervised population detection algorithms.
Conductivity tensor mapping of the human brain using diffusion tensor MRI (2001)

Knowledge of the electrical conductivity properties of excitable tissues is essential for relating the electromagnetic fields generated by the tissue to the underlying electrophysiological currents. Efforts to characterize these endogenous currents from measurements of the associated electromagnetic fields would significantly benefit from the ability to measure the electrical conductivity properties of the tissue noninvasively. Here, using an effective medium approach, we show how the electrical conductivity tensor of tissue can be quantitatively inferred from the water self-diffusion tensor as measured by diffusion tensor magnetic resonance imaging. The effective medium model indicates a strong linear relationship between the conductivity and diffusion tensor eigenvalues (respectively, final sigma and d) in agreement with theoretical bounds and experimental measurements presented here (final sigma/d approximately 0.844 +/- 0.0545 S small middle dots/mm(3), r(2) = 0.945). The extension to other biological transport phenomena is also discussed.
Biomarkers for neurodegenerative diseases (2005)

The ideal biomarker needs to be easy to quantify and measure, reproducible, not subject to wide variation in the general population and unaffected by co-morbid factors. For evaluation of therapies the biomarker needs to change linearly with disease progression and closely correlate with established clinico-pathological parameters of the disease. It is unlikely that any one biomarker will fulfil all these characteristics, and it is likely that more than one biomarker will be needed for early diagnosis and similarly for evaluation of disease progression for therapeutic trials. For example, the combination of more detailed clinical assessments encompassing specific cognitive and neurophysiological testing, in addition to imaging, biochemical and genomic profiling, is likely to be needed.
Diversity of human endogenous retrovirus class II-like sequences. (1999)

Class II human endogenous retroviruses (HERVs), often referred to as mouse mammary tumour virus (MMTV)-like or HERV-K elements, have similarities to several animal infectious retroviruses. Single clones from each of nine class II HERV groups (NMWV 1 to NMWV 9), isolated from a human breast cancer cell genomic library, were sequenced over a 244 bp stretch of the conserved reverse transcriptase region. These sequences were aligned to related exogenous and endogenous retroviruses and a phylogenetic tree was constructed. Sequences with more than 80% identity were considered as members of one group and we report here that the class II HERV family consists of at least ten groups. Three of the sequenced clones, from groups NMWV 3, 7 and 9, could not be related to any other previously identified elements and constituted their own groups. NMWV 8 had no similarity to any retroviral sequences in the sequenced region and is so far considered to be non-retroviral.
Towards a Formal Distributional Semantics: Simulating Logical Calculi with Tensors (2013)

The development of compositional distributional models of semantics reconciling the empirical aspects of distributional semantics with the compositional aspects of formal semantics is a popular topic in the contemporary literature. This paper seeks to bring this reconciliation one step further by showing how the mathematical constructs commonly used in compositional distributional models, such as tensors and matrices, can be used to simulate different aspects of predicate logic. This paper discusses how the canonical isomorphism between tensors and multilinear maps can be exploited to simulate a full-blown quantifier-free predicate calculus using tensors. It provides tensor interpretations of the set of logical connectives required to model propositional calculi. It suggests a variant of these tensor calculi capable of modelling quantifiers, using few non-linear operations. It finally discusses the relation between these variants, and how this relation should constitute the subject of future work.
Ultra-stable organic fluorophores for single-molecule research (2013)

Fluorescence provides a mechanism for achieving contrast in biological imaging that enables investigations of molecular structure, dynamics, and function at high spatial and temporal resolution. Small-molecule organic fluorophores have proven essential for such efforts and are widely used in advanced applications such as single-molecule and super-resolution microscopy. Yet, organic fluorophores, like all fluorescent species, exhibit instabilities in their emission characteristics, including blinking and photobleaching that limit their utility and performance. Here, we review the photophysics and photochemistry of organic fluorophores as they pertain to mitigating such instabilities, with a specific focus on the development of stabilized fluorophores through derivatization. Self-healing organic fluorophores, wherein the triplet state is intramolecularly quenched by a covalently attached protective agent, exhibit markedly improved photostabilities. We discuss the potential for further enhancements towards the goal of developing "ultra-stable" fluorophores spanning the visible spectrum and how such fluorophores are likely to impact the future of single-molecule research.
Itch: Mechanisms and Management of Pruritus (1994)

Itching (pruritis) is the classic symptom in skin disease, yet the identification of its cause remains a common and frustrating problem for the dermatologist and non-dermatologist alike. This book is a practical guide to the variety of underlying causes and a comprehensive review of relevant treatments. The approach throughout is clinical with systematic coverage of virtually all conditions, common and rare, which can evoke itching.
Preformulation Studies on Solid Dispersions Containing Triamterene or Temazepam in Polyethylene Glycols or Gelucire 44/14 for Liquid Filling of Hard Gelatin Capsules (1991)

Solid dispersions of triamterene or temazepam in polyethylene glycols or gelucire 44/14 have been investigated. The phase equilibria of the drugs and carriers were determined by Differential Thermal Analysis and Hot Stage Microscopy. Particle Size Analysis was carried out using double image microscopy, whilst phase solubility techniques and dissolution methods were used to study solubility, dissolution and ageing.It has been shown that triamterene forms monotectics with polyethylene glycols and gelucire 44/14 and temzepam shows partial solubility. The effect of the carriers on particle size depends on the solubility of the drug in the carrier and size reduction is observed where the drug is soluble in the carrier.
Synthesis and isolation of iodocarbazoles. Direct iodination of carbazoles by N‐iodosuccinimide and N‐iodosuccinimide‐silica gel system (2001)

Abstract Carbazole ( 1 ) undergoes electrophilic aromatic substitution with various iodinating reagents. Although, 3‐iodocarbazole ( 1b ) and 3,6‐diiodocarbazole ( 1d ) obtained by iodination of carbazole were isolated and characterized sometime ago, 1‐iodocarbazole ( 1a ), 1,6‐diiodocarbazole ( 1c ) and 1,3,6‐triiodocarbazole ( 1e ) had never been isolated from the reaction mixture. The preparation and subsequent isolation and characterization of 1a, 1b, 1c, 1d and 1e are reported (mp, t r , R f , 1 H‐nmr, 13 C‐nmr and ms). As iodinating reagents, NaIO 4 /I 2 and NaIO 4 /KI mixtures in (i) ethanol doped with catalytical amount of sulfuric acid and in (ii) acetic acid, and N ‐odosuccinimide and N ‐iodosuccinimide‐silica gel in dichloromethane and in chloroform have been used and their uses have been compared. The iodination reaction of different carbazole derivatives such as 2‐acetoxycarbazole ( 2 ), 3‐bromocarbazole (3) and 3‐nitrocarbazole ( 4 ) was also studied and the corresponding iododerivatives, 2a, 2b, 2c, 3a, 3b, 4a and 4b , are described for the first time. Semiempirical PM3 calculations have been performed in order to predict reactivity of carbazole ( 1 ), substituted carbazoles (2‐4) and iodocarbazoles ( 1a‐1e, 2a‐2c, 3a‐3b, 4a and 4b ) (Scheme 1). Theoretical and experimental results are discussed briefly.
Codon insertion mutants of the adenovirus terminal protein. (1986)

A series of codon insertion mutants was isolated following restriction site-directed linker insertion mutagenesis of the open reading frame for the type 5 adenovirus terminal protein precursor. The conditionally lethal mutant H5sub100 bears an insertion mutation upstream of the first AUG in the reading frame, fails to replicate its DNA under nonpermissive conditions, and was assigned to the terminal protein complementation group. These data establish that terminal protein is an essential polypeptide required for DNA replication in vivo and indicate that the NH2-terminal region of the precursor is encoded in an upstream mRNA leader. The extended eclipse period of the viral replication cycle in H5in179-infected cells is probably a consequence of delayed onset of DNA replication. Analysis of DNA replication in coinfections with wild-type virus shows that the in179 mutation has cis and trans effects. The trans-dominant, negative-complementing in179 terminal protein precursor inhibits wild-type DNA replication in a dose-dependent manner. Replication of parental in179 templates is not stimulated by an excess of coinfecting wild-type virus, indicating that the mutant terminal protein covalently bound to the in179 template in some way interferes with the replication of that template. The implications of these results for the structure and function of the terminal protein are discussed.
In Vitro Bone Production Using Stem Cells Derived From Human Dental Pulp (2006)

To harvest bone for autologous grafting is a daily problem encountered by craniofacial and oral surgeons. Stem cells derived from human dental pulp are able to differentiate in osteoblasts and are a potential source of autologous bone produced in vitro. The authors describe their preliminary results in this new field with its potential application in craniomaxillofacial surgery. Dental pulp was gently extracted from 34 human permanent teeth (all third molars) of patients 19 to 37 years of age. After they were digested, the cells were selected using a cytometer for c-kit, STRO-1, CD34, CD45, and then for CD44 and RUNX-2. This study, made on a considerable number of cases, provided evidence that dental pulp is extremely rich in stem cells, which were c-kit+/CD34+/STRO-1+/CD45-, capable of differentiation toward several stromal-derived differentiated cells and mainly osteoblasts. These findings, supported by the large number of cases, are of great interest for tissue regeneration, tissue-based clinical therapies, and transplantation.
Enthesitis in spondyloarthropathy (1999)

Inflammation at the insertions of ligaments, tendons, or joint capsules to bone, which is termed enthesitis, is a characteristic feature of spondyloarthropathy. Because of the relative inaccessibility of the enthesis, the inflammatory, microbiologic, and immunologic events at that site have been poorly defined. Recent magnetic resonance imaging studies have drawn attention to the ubiquitous nature of enthesitis in spondyloarthropathies, especially adjacent to synovial joints. This may have implications for the mechanisms of synovitis in spondyloarthropathies. Magnetic resonance imaging studies also suggest that enthesitis lesions may be extensive, which could explain the diffuse nature of bone changes seen in some patients with spondyloarthropathies. The importance of enthesitis as a skeletal phenomenon in spondyloarthropathies has gained further support from transgenic models in which either tumor necrosis factor-alpha or bone morphogenetic protein-6 overexpression result in entheseal-associated polyarthropathy.
Increased Virulence of Modified-Live Infectious Laryngotracheitis Vaccine Virus Following Bird-to-Bird Passage (1991)

Modified-live (ML) infectious laryngotracheitis (ILT) vaccine viruses, both tissue-culture-origin (TCO) and chicken-embryo-origin (CEO), were passaged 20 times in specific-pathogen-free chickens. After serial bird-to-bird passage, increased virulence was observed for CEO virus but not TCO virus. Increased mortality and increased severity and duration of respiratory disease were observed in chickens inoculated with chicken-passaged CEO viruses; only mild respiratory disease (no mortality) occurred in chickens inoculated with chicken-passaged TCO viruses. These findings suggest that ML ILT vaccine viruses may increase in virulence after bird-to-bird passage.
Human Parainfluenza Virus Type 1 Matrix and Nucleoprotein Genes Transiently Expressed in Mammalian Cells Induce the Release of Virus-Like Particles Containing Nucleocapsid-Like Structures (1999)

The matrix (M) protein plays an essential role in the assembly and budding of some enveloped RNA viruses. We expressed the human parainfluenza virus type 1 (hPIV-1) M and/or NP genes into 293T cells using the mammalian expression vector pCAGGS. Biochemical and electron microscopic analyses of transfected cells showed that the M protein alone can induce the budding of virus-like particles (vesicles) from the plasma membrane and that the NP protein can assemble into intracellular nucleocapsid-like (NC-like) structures. Furthermore, the coexpression of both the M and NP genes resulted in the production of vesicles enclosing NC-like structures, suggesting that the hPIV-1 M protein has the intrinsic ability to induce membrane vesiculation and to incorporate NC-like structures into these budding vesicles.
Coordinated management of multiple interacting resources in chip multiprocessors: A machine learning approach (2008)

Efficient sharing of system resources is critical to obtaining high utilization and enforcing system-level performance objectives on chip multiprocessors (CMPs). Although several proposals that address the management of a single microarchitectural resource have been published in the literature, coordinated management of multiple interacting resources on CMPs remains an open problem.
Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2011–2014 (2016)

OBJECTIVE To describe antimicrobial resistance patterns for healthcare-associated infections (HAIs) that occurred in 2011–2014 and were reported to the Centers for Disease Control and Prevention’s National Healthcare Safety Network. METHODS Data from central line–associated bloodstream infections, catheter-associated urinary tract infections, ventilator-associated pneumonias, and surgical site infections were analyzed. These HAIs were reported from acute care hospitals, long-term acute care hospitals, and inpatient rehabilitation facilities. Pooled mean proportions of pathogens that tested resistant (or nonsusceptible) to selected antimicrobials were calculated by year and HAI type. RESULTS Overall, 4,515 hospitals reported that at least 1 HAI occurred in 2011–2014. There were 408,151 pathogens from 365,490 HAIs reported to the National Healthcare Safety Network, most of which were reported from acute care hospitals with greater than 200 beds. Fifteen pathogen groups accounted for 87% of reported pathogens; the most common included Escherichia coli (15%), Staphylococcus aureus (12%), Klebsiella species (8%), and coagulase-negative staphylococci (8%). In general, the proportion of isolates with common resistance phenotypes was higher among device-associated HAIs compared with surgical site infections. Although the percent resistance for most phenotypes was similar to earlier reports, an increase in the magnitude of the resistance percentages among E. coli pathogens was noted, especially related to fluoroquinolone resistance. CONCLUSION This report represents a national summary of antimicrobial resistance among select HAIs and phenotypes. The distribution of frequent pathogens and some resistance patterns appear to have changed from 2009–2010, highlighting the need for continual, careful monitoring of these data across the spectrum of HAI types. Infect Control Hosp Epidemiol 2016;1–14
Cutting Edge: Stromal Cell-Derived Factor-1 Is a Costimulator for CD4+ T Cell Activation (2000)

Stromal cell-derived factor (SDF)-1 is a chemoattractant for T cells, precursor B cells, monocytes, and neutrophils. SDF-1alpha was also found to up-regulate expression of early activation markers (CD69, CD25, and CD154) by anti-CD3-activated CD4+ T cells. In addition, SDF-1alpha costimulated proliferation of CD4+ T cells and production of IL-2, IFN-gamma, IL-4, and IL-10. Stimulation with SDF-1alpha alone did not induce activation marker expression, proliferation, or cytokine production by the CD4+ T cells. SDF-1alpha-mediated costimulation was blocked by anti-CXC chemokine receptor-4 mAb. RANTES also increased activation marker expression by anti-CD3-stimulated peripheral CD4+ T cells, but less effectively than SDF-1alpha did, and did not up-regulate IL-2 production and proliferation. These results indicate that SDF-1 and CXC chemokine receptor-4 interactions not only play a role in T cell migration but also provide potent costimulatory signals to Ag-stimulated T cells.
Structural and biophysical determinants of αβ T‐cell antigen recognition (2011)

The molecular rules that govern MHC restriction, and allow T-cells to differentiate between peptides derived from healthy cells and those from diseased cells, remain poorly understood. Here we provide an overview of the structural constraints that enable the T-cell receptor (TCR) to discriminate between self and non-self peptides, and summarize studies that have attempted to correlate the biophysical parameters of TCR/peptide-major histocompatibility complex (pMHC) binding with T-cell activation. We further review how the antigenic origin of peptide epitopes affects TCR binding parameters and the 'quality' of a T-cell response. Understanding the principles that govern pMHC recognition by T-cells will unlock pathways to the rational development of immunotherapeutic approaches for the treatment of infectious disease, cancer and autoimmunity.
A Novel FRET-Based Biosensor for the Measurement of BCR-ABL Activity and Its Response to Drugs in Living Cells (2010)

In consideration of its quick and practical nature, this method is potentially a promising tool for the prediction of both current and future therapeutic responses in individual CML patients, which will be surely beneficial for both patients and clinicians.
Proposal of variable active-passive reactance (2003)

The concept of a variable active-passive reactance (VAPAR) which consists of an inverter and a passive element is proposed. The VAPAR behaves like a two-port reactive element and the produced active reactance works as a passive reactive component, including in the transient state. The authors present the principle of the VAPAR and two possible control schemes to realize the VAPAR. Through simulations and experiments, it is verified that the VAPAR shows two-port reactive characteristics not only in steady state but also in the transient state.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Role for the Protease Falcipain 1 in Host Cell Invasion by the Human Malaria Parasite (2002)

Cysteine proteases of Plasmodium falciparum are required for survival of the malaria parasite, yet their specific cellular functions remain unclear. We used a chemical proteomic screen with a small-molecule probe to characterize the predominant cysteine proteases throughout the parasite life cycle. Only one protease, falcipain 1, was active during the invasive merozoite stage. Falcipain 1-specific inhibitors, identified by screening of chemical libraries, blocked parasite invasion of host erythrocytes, yet had no effect on normal parasite processes such as hemoglobin degradation. These results demonstrate a specific role for falcipain 1 in host cell invasion and establish a potential new target for antimalarial therapeutics.