gebhart/patrepeval huggingface dataset:
Longitudinal evaluation and decline of antibody responses in SARS-CoV-2 infection (2020)

Abstract Antibody (Ab) responses to SARS-CoV-2 can be detected in most infected individuals 10-15 days following the onset of COVID-19 symptoms. However, due to the recent emergence of this virus in the human population it is not yet known how long these Ab responses will be maintained or whether they will provide protection from re-infection. Using sequential serum samples collected up to 94 days post onset of symptoms (POS) from 65 RT-qPCR confirmed SARS-CoV-2-infected individuals, we show seroconversion in &gt;95% of cases and neutralizing antibody (nAb) responses when sampled beyond 8 days POS. We demonstrate that the magnitude of the nAb response is dependent upon the disease severity, but this does not affect the kinetics of the nAb response. Declining nAb titres were observed during the follow up period. Whilst some individuals with high peak ID 50 (&gt;10,000) maintained titres &gt;1,000 at &gt;60 days POS, some with lower peak ID 50 had titres approaching baseline within the follow up period. A similar decline in nAb titres was also observed in a cohort of seropositive healthcare workers from Guy’s and St Thomas’ Hospitals. We suggest that this transient nAb response is a feature shared by both a SARS-CoV-2 infection that causes low disease severity and the circulating seasonal coronaviruses that are associated with common colds. This study has important implications when considering widespread serological testing, Ab protection against re-infection with SARS-CoV-2 and the durability of vaccine protection.
The sequence of the nucleoprotein gene of human influenza A virus, strain A/NT/60/68 (1982)

The nucleotide sequence of the nucleoprotein gene of influenza A/NT/60/68 was established after using improved cloning methods to obtain full length cDNA clones in pBr322. The gene is 1565 residues long and codes for a basic protein of 498 amino acids. There are only 30 amino acid differences between it and the homologous sequence in A/PR/8/35, all occurring as point mutations. Assuming a common lineage, the evolutionary rate of divergence of the two strains is 0.18% amino acid per year. This confirms there is a slow but significant rate of evolution.
STRAP Is a Strong Predictive Marker of Adjuvant Chemotherapy Benefit in Colorectal Cancer (2004)

If confirmed, the STRAP gene copy status might provide a parameter to decide about the use of 5-FU-based adjuvant chemotherapy.
An essential role for RasGRP1 in mast cell function and IgE-mediated allergic response (2006)

Cross-linking of the FcepsilonRI activates the phosphatidyl inositol 3 kinase (PI3K) and mitogen-activated protein kinase pathways. Previous studies demonstrate that Ras guanyl nucleotide-releasing protein (RasGRP)1 is essential in T cell receptor-mediated Ras-Erk activation. Here, we report that RasGRP1 plays an important role in FcepsilonRI-mediated PI3K activation and mast cell function. RasGRP1-deficient mice failed to mount anaphylactic allergic reactions. RasGRP1-/- mast cells had markedly reduced degranulation and cytokine production. Although FcepsilonRI-mediated Erk activation was normal, PI3K activation was diminished. Consequently, activation of Akt, PIP3-dependent kinase, and protein kinase C delta was defective. Expression of a constitutively active form of N-Ras could rescue the degranulation defect and Akt activation. We further demonstrated that RasGRP1-/- mast cells were defective in granule translocation, microtubule formation, and RhoA activation. Our results identified RasGRP1 as an essential regulator of mast cell function.
Visible and near-infrared responsivity of femtosecond-laser microstructured silicon photodiodes (2005)

We investigated the current-voltage characteristics and responsivity of photodiodes fabricated with silicon that was microstructured by use of femtosecond-laser pulses in a sulfur-containing atmosphere. The photodiodes that we fabricated have a broad spectral response ranging from the visible to the near infrared (400-1600 nm). The responsivity depends on substrate doping, microstructuring fluence, and annealing temperature. We obtained room-temperature responsivities as high as 100 A/W at 1064 nm, 2 orders of magnitude higher than for standard silicon photodiodes. For wavelengths below the bandgap we obtained responsivities as high as 50 mA/W at 1330 nm and 35 mA/W at 1550 nm.
Characterization of electronic transitions in complex molecules (1950)

M. Kasha, Discuss. Faraday Soc., 1950, 9, 14 DOI: 10.1039/DF9500900014
Generating strong primes (1986)

A new method of generating strong primes is presented. The method produces primes satisfying Gordon&apos;s strong prime requirements but which are not probabilistic. The expected time required to generate such a prime is comparable with previously proposed methods.
Frequently Asked Questions (FAQ) related to the EFSA assessment of Article 14 and 13.5 health claims applications (2009)

14 and 13.5 health claims applications 1 European Food Safety Authority (EFSA), Parma, Italy the applicant.In such cases applicants should ensure that all proprietary and non-proprietary data pertinent to the claimed effect are included in the application.The protection of proprietary data, as appropriate, falls within the responsibility of the European Commission. 11.How does EFSA treat confidential data?The applicant should keep the designation of confidential information to a minimum.
Exon Skipping as a Therapeutic Strategy Applied to an RYR1 Mutation with Pseudo-Exon Inclusion Causing a Severe Core Myopathy (2013)

Central core disease is a myopathy often arising from mutations in the type 1 ryanodine receptor (RYR1) gene, encoding the sarcoplasmic reticulum calcium release channel RyR1. No treatment is currently available for this disease. We studied the pathological situation of a severely affected child with two recessive mutations, which resulted in a massive reduction in the amount of RyR1. The paternal mutation induced the inclusion of a new in-frame pseudo-exon in RyR1 mRNA that resulted in the insertion of additional amino acids leading to the instability of the protein. We hypothesized that skipping this additional exon would be sufficient to restore RyR1 expression and to normalize calcium releases. We therefore developed U7-AON lentiviral vectors to force exon skipping on affected primary muscle cells. The efficiency of the exon skipping was evaluated at the mRNA level, at the protein level, and at the functional level using calcium imaging. In these affected cells, we observed a decreased inclusion of the pseudo-exon, an increased RyR1 protein expression, and a restoration of calcium releases of normal amplitude either upon direct RyR1 stimulation or in response to membrane depolarization. This study is the first demonstration of the potential of exon-skipping strategy for the therapy of central core disease, from the molecular to the functional level.
Urological Management in Patients With Spinal Cord Injuries (1996)

In the past, urologic complications contributed greatly to spinal cord injury mortality. With improved evaluation and treatment, this is no longer the case. Treatment should be guided by urodynamic data gathered after the resolution of spinal shock symptoms. Goals of treatment are to facilitate voiding, reduce incontinence, and prevent renal damage. Indwelling catheters are almost never indicated for long-term treatment of the neurogenic bladder. Commonly used treatments include intermittent catheterization, condom catheter drainage with sphincter ablation, and pharmaceutical manipulation. Electrical stimulation of sacral nerve roots shows promise for future therapy.
Dielectric‐EBG covered conical antenna for UWB applications (2010)

Purpose The purpose of this paper is to investigate of the ultra‐wide band (UWB) characteristics of a conical antenna covered by an electromagnetic band‐gap (EBG) structure composed of alternating high‐ and low‐permittivity dielectric spherical shells. Design/methodology/approach A finite difference time domain in spherical coordinates is implemented in order to characterize the antenna's performance and waveform fidelity in case an UWB pulse is used. The method of projected effective permittivity is used in order to treat accurately the dielectric interfaces between the dissimilar spherical shells. Findings The design achieves a very wide impedance bandwidth above 5.5 GHz and presents UWB radiation characteristics and high average gain over the whole bandwidth. The radiation patterns are monopole‐like and their frequency dependence is small in the whole UWB frequency band. A time domain study has shown that the antenna distorts the excitation pulse in a moderate way. Originality/value In this paper, a quasi‐planar wideband conical antenna coated on a dielectric EBG structure is proposed for what is believed to be the first time. It is mechanically stable and, relatively easy to build and integrate with the planar circuits.
Detecting alerts, notifying the physician, and offering action items: a comprehensive alerting system. (1996)

We developed and evaluated a system to automatically identify serious clinical conditions in inpatients. The system notifies the patient's covering physician via his pager that an alert is present and offers potential therapies for the patient's condition (action items) at the time he views the alert information. Over a 6 month period, physicians responded to 1214 (70.2%) of 1730 alerts for which they were paged; they responded to 1002 (82.5% of the 1214) in less than 15 minutes. They said they would take action in 71.5% of the alerts, and they placed an order directly from the alert display screen in 39.4%. Further study is needed to determine if this alerting system improves processes or outcomes of care.
Oligonucleotides Tethered to a Short Polyguanylic Acid Stretch Are Targeted to Macrophages: Enhanced Antiviral Activity of a Vesicular Stomatitis Virus-Specific Antisense Oligonucleotide (1999)

The poor membrane permeability of oligonucleotides is one of the major problems of antisense technology. Here we report the construction of designer oligonucleotides for targeted delivery to macrophages. The oligonucleotides tethered to a 10-mer poly(G) sequence at their 3' ends were recognized by scavenger receptors on macrophages and were taken up about 8- to 10-fold as efficiently as those oligonucleotides that either lacked a poly(G) tail or that contained a 10-mer poly(C) tail instead of the poly(G) tail. The enhanced uptake of poly(G) constructs was inhibited in the presence of poly(G) and other known ligands of the scavenger receptor. The bioefficacy of poly(G)-mediated targeting of antisense oligonucleotides (ANS) was demonstrated by using vesicular stomatitis virus (VSV) as a model system. The ability of ANS directed against the translation initiation site of N protein mRNA of VSV to inhibit virus replication was assessed. The ANS with the 10-mer poly(G) sequences (ANS-G) brought about significant inhibition of VSV replication in J774E cells (a murine monocyte/macrophage cell line) and Chinese hamster ovary (CHO) cell transfectants expressing scavenger receptors. The ANS lacking a 10-mer poly(G) stretch were ineffective. The inhibition of VSV replication due to ANS-G was completely abrogated in the presence of 10-mer poly(G), indicating that the antisense effect of the ANS-G molecule was a consequence of scavenger receptor-mediated enhanced uptake. Importantly, antisense molecules linked exclusively by natural phosphodiester bonds were as bioeffective as those synthesized with a mixed backbone of phosphodiester and phosphorothioate. Taken together, these results suggest that macrophage-directed designer ANS against infective agents may simply be obtained by adding a short stretch of guanylic acid sequence to the desired specific ANS during solid-phase synthesis. This nucleic acid-based strategy, which utilizes homogeneous preparation of ANS, may find applications in directed manipulation of macrophage metabolism for a variety of purposes as well as in therapy of a broad spectrum of macrophage-related disorders amenable to the antisense approach.
FLT3 and Acute Myelogenous Leukemia: Biology, Clinical Significance and Therapeutic Applications (2005)

Acute myelogenous leukemia (AML) is a difficult disease to treat, and better treatments are needed. Molecular targeted therapy represents a novel therapeutic approach. The FLT3 tyrosine kinase receptor is mutated in approximately one-fourth to one-third of patients with AML. Normally, binding of FLT3 ligand to the FLT3 receptor leads to phosphorylation of tyrosine residues and activation of the receptor. This in turn leads to induction of intracellular signaling pathways essential to regulation of cell proliferation and apoptosis. Two classes of FLT3 activating mutations have been identified in AML patients: internal tandem duplications (ITDS) and point mutations in the activating loop of the kinase domain. Both mutations result in constitutive FLT3 tyrosine kinase activity and lead to transformation of hematopoietic cell lines in vivo and in vitro. FLT3 ITDs are also an independent poor prognostic factor for overall survival and disease free survival in patients with AML. Therefore, targeting FLT3 mutations represents a potential therapeutic target for AML. This review will discuss the biology and clinical significance of FLT3 and FLT3 mutations in cell growth and signaling. In addition, I will discuss some of the novel FLT3 inhibitors which are entering clinical trials for AML.
Transforming growth factor-beta stimulates wound healing and modulates extracellular matrix gene expression in pig skin. I. Excisional wound model. (1990)

The effect of transforming growth factor-beta 1 (TGF-beta 1) on matrix gene expression has been investigated during the process of wound repair, where the formation of new connective tissue represents a critical step in restoring tissue integrity. Split-thickness excisional wounds in the pig were studied by in situ hybridization in order to obtain subjective findings on the activity and location of cells involved in matrix gene expression after the administration of recombinant TGF-beta 1. Data focus on the stimulatory role of this growth factor in granulation tissue formation, on the enhanced mRNA content of collagen types I and III, fibronectin, TGF-beta 1 itself, and on the reduction in stromelysin mRNA, suggesting that increased matrix formation measured after treatment with TGF-beta 1 is due to fibroplasia regulated by the abundance of mRNAs for several different structural, matrix proteins as well as inhibition of proteolytic phenomena elicited by metalloproteinases. These studies reveal elastin mRNA early in the repair process, and elastin mRNA expression is enhanced by administration of TGF-beta 1. Moreover, we show that TGF-beta 1 was auto-stimulating in wounds, accounting, at least in part, for the persistent effects of single doses of this multipotential cytokine.
Hepatocyte nuclear factor 3 beta contains two transcriptional activation domains, one of which is novel and conserved with the Drosophila fork head protein. (1992)

The hepatocyte nuclear factor 3 (HNF-3) gene family is composed of three proteins (alpha, beta, and gamma) that are transcription factors involved in the coordinate expression of several liver genes. All three proteins share strong homology in their DNA binding domains (region I) and are able to recognize the same DNA sequence. They also possess two similar stretches of amino acids at the carboxyl terminus (regions II and III) and a fourth segment of homology at the amino terminus (region IV). Furthermore, the HNF-3 proteins demonstrate homology with the Drosophila homeotic gene fork head in regions I, II, and III, suggesting that HNF-3 may be its mammalian homolog. In order to define HNF-3 beta protein domains involved in transcriptional activation, we have used a reporter gene, whose transcription is dependent on HNF-3 binding, for hepatoma cell cotransfection assays with expression vectors that produced different truncated HNF-3 beta proteins. A position-independent activation domain which contained conserved regions II and III was identified at the carboxyl terminus of the HNF-3 beta protein (amino acids 361 to 458). Moreover, site-directed mutations that altered the sequences within regions II and III demonstrated their importance to transactivation. The region II-III domain does not possess amino acid sequences in common with other transcription factors and may define a novel activation motif. HNF-3 beta amino-terminal sequences defined by conserved region IV also contributed to transactivation, but region IV activity required the participation of the region II-III domain. Region IV is abundant in serine amino acids and contains two putative casein kinase I phosphorylation sites, a feature similar to protein motifs described for the transcription factors Pit-1/GHF-1 and HNF-1.
Air Quality Model Evaluation Data for Organics. 4. C2−C36 Non-Aromatic Hydrocarbons (1997)

The concentrations of 143 non-aromatic hydrocarbons are quantified in 36 samples (32 urban and 4 background) collected during a severe Los Angeles area photochemical smog episode. Gas phase, semivolatile, and particle phase organic compounds are viewed simultaneously across the carbon number range from C2 to C36. Compound classes studied include the n-alkanes, branched alkanes, n-alkenes, branched alkenes, diolefins, alkynes, saturated cyclic hydrocarbons, unsaturated cyclic hydrocarbons, biogenic hydrocarbons, petroleum biomarkers, and the unresolved complex mixture contained within the semivolatile and particle phase organics samples. The abundance of the n-alkanes falls almost exponentially with increasing n-alkane carbon number, and the distribution of the n-alkanes between the gas and particle phases follows vapor/particle partitioning theory. The concentrations of individual low molecular weight alkenes decline during transport across the urban area in about the order expected given their initial rates of reaction with the hydroxyl radical. Petroleum biomarker concentrations that act as tracers for particulate organics emitted from vehicle exhaust have declined substantially between 1982 and 1993, reflecting the increased penetration of catalyst-equipped cars into the vehicle fleet. The most pronounced change in vapor phase non-aromatic hydrocarbons concentrations between 1987 and 1993 is a reduction in the concentration of the lightest blending components of gasoline (e.g., butanes), reflecting new regula tions that limit the Reid vapor pressure of gasoline.
Fluorescence Resonance Energy Transfer Reveals Interleukin (IL)-1-dependent Aggregation of IL-1 Type I Receptors That Correlates with Receptor Activation (1995)

Fluorescence resonance energy transfer (FRET) was used to investigate whether interleukin-1 (IL-1) causes the aggregation of IL-1 type I receptors (IL-1 RI) at the cell surface. For these experiments, a noncompetitive anti-IL1 RI monoclonal antibody, M5, was labeled separately with a donor probe, fluorescein isothiocyanate, or with an acceptor carbocyanine probe, Cy3. Donor-labeled M5 and acceptor-labeled M5 were simultaneously bound to transfected mouse IL-1 RI on either C-127 mouse mammary carcinoma cells or on Chinese hamster ovary (CHO)-K1 cells, and the ratio of acceptor emission at 590 nm to donor emission at 525 nm (excitation at 488 and 514 nm) was monitored with flow cytometry as an indicator of FRET. Addition of a saturating concentration of human IL-1 alpha at 22 degrees C causes a time-dependent increase in FRET for both cell lines that indicates IL-1-dependent self-association of IL-1 RI. Binding of the IL-1 receptor antagonist at 22 degrees C causes little or no FRET for both cell lines, indicating a correlation between receptor aggregation and the ability of the ligand to stimulate a functional response. When donor-labeled and acceptor-labeled Fab fragments of M5 are used to monitor FRET, IL-1 alpha causes efficient energy transfer in the CHO-K1 cells at 22 degrees C, but not at 4 degrees C. In contrast, IL-1 alpha causes much less FRET at 22 degrees C in C-127 cells when the M5 Fab fragments are used instead of the intact bivalent M5. In a striking parallel, IL-1 alpha-dependent activation of prostaglandin E2 production depends on the bivalent M5 antibody in the C-127 cells, but is independent of this monoclonal antibody in the CHO-K1 cells. These results provide a strong correlation between the ability of IL-1 to cause the aggregation of IL-1 RI and the stimulation of a functional response.
In vivo biodegradability and biocompatibility of porcine type I atelocollagen newly crosslinked by oxidized glycogen. (2007)

Oxidized glycogen is used as a collagen crosslinker to prepare materials with defined crosslinking rates. Thus, films are prepared from native or denatured porcine type I atelocollagen crosslinked with three crosslinking levels defined by the ratios between the aldehyde groups of the glycogen and the amino groups of the collagen. The remaining free aldehyde groups and the imine bonds formed in the reaction are subsequently reduced or not. All the materials are subjected to in vivo biocompatibility and biodegradability evaluations by subcutaneous implantation in mice, while immunogenicity is evaluated by rabbit immunizations. As a result, cellular reactions on the implantation site are more important with nonreduced materials, and biodegradability is correlated to the structural integrity of the collagen molecule, the crosslinking rate and the reduction state of the material. No immunological reaction or calcification is detected in our in vivo experimental model. This new method for collagen crosslinking using oxidized glycogen as a crosslinking agent enables the obtention of reproducible and biocompatible materials with a large scale of biodegradability, starting from 28 days to more than 7 months.
On the bus arbitration for MPEG 2 video decoder (2002)

A bus arbitration scheme for the MPEG-2 video decoder VLSI developed by NCTU is proposed in this paper. Compared to the traditional pure stochastic bus scheduling scheme, the internal buffer requirement and bus arbitration overheads are reduced due to the deterministic nature of this strategy. This bus arbitration scheme has been verified using a Verilog simulator and will be implemented in the NCTU MPEG-2 decoder.
Volume‐pressure properties of the upper airway in normal subjects and patients with obstructive sleep apnoea (1999)

The aim of this study was to examine the volume-pressure (V-P) characteristics of isolated upper airways in normal subjects and patients with obstructive sleep apnoea (OSA) and to ascertain whether an increase in upper airway muscle activity affects these characteristics. We studied upper airway pressure changes during volume changes by inflation and deflation of air volumes of 5, 10, 15 and 20 mL without and with submental electrical stimulation, during voluntary closing of the glottis, in seven normal subjects and 13 OSA patients. Volume-pressure properties of the upper airway were assessed by elastance (Euaw) which was obtained from the slope of the regression line of the V-P relationships. Euaw in OSA patients was 0.52 +/- 0.08 cmH2O/mL, which was greater than in normal subjects (0.26 +/- 0.06 cmH2O/mL). Submental stimulation increased Euaw in both OSA patients and normal subjects (0.70 +/- 0.11 cmH2O/mL and 0.41 +/- 0.11 cmH2O/mL, respectively). These results suggest that upper airways of OSA patients during wakefulness are less collapsible than those of normal subjects, and that, in both groups, submental stimulation may stiffen the upper airway.