gebhart/patrepeval huggingface dataset:
0775 SLEEP STAGE ESTIMATION USING A NON-CONTACT BIOSENSOR (2017)

Polysomnography is a gold standard sleep evaluation mainly conducted in sleep labs. Repetitive evaluation of sleep quality at home could be useful in the management of insomnia especially when there is discrepancy between subjective and objective sleep. The aim of the study was to evaluate the characteristic of a non-contact sensor in identifying sleep stages. Fifteen patients who underwent diagnostic polysomnography (PSG) at the university sleep laboratory were recruited. Non-contact biosensor measuring heart rate, respiration and body movement was laid under a bed mattress. Sleep stages were scores based on a AAMS standard procedure for PSG, and sleep stage analysis for the non-contact device was made using a previously reported method (Harada et al., 2016). Pattern of hypnogram obtained from standard PSG and non-contact device was compared. The study was approved by the institutional review board and written informed consent was obtained. Recordings were successfully completed in all cases. On average, non-contact device obtained heart rate and respiration data in 89.2% and 70.6% of the recording time respectively. Non-contact device mostly identified the sleep architecture trend, but non-contact device tend to overestimate slow wave sleep, especially in patients with repetitive arousals or awakenings. Non-contact sensor equipped under the bed mattress was able to identify clinically useful sleep quality data. Some modification in the detection of respiration signal and the analysis argorhythm idetifying brief awakenings may be necesarry.
Routine Plasma-Based Genotyping to Comprehensively Detect Germline, Somatic, and Reversion BRCA Mutations among Patients with Advanced Solid Tumors (2020)

cfDNA NGS identified high rates of therapeutically relevant mutations without foreknowledge of germline or tissue-based testing results, including deleterious somatic <i>BRCA1/2</i> mutations missed by germline testing and reversion mutations that can have important treatment implications. Further research is needed to confirm clinical utility of these findings to guide precision medicine approaches for patients with advanced malignancies.
Synthesis and characterization of a fluorinated anionic aluminophosphate framework UT-6, and its high-temperature dehydrofluorination to AlPO4-CHA (1997)

The structure of an anionic aluminophosphate molecular sieve UT-6 has been determined by single-crystal X-ray diffraction and 19 F MAS NMR, 31 P CP MAS NMR and 27 Al MQ MAS spectroscopy. Large crystals were grown in a non-aqueous synthesis system when hydrogen fluoride was used in trace amounts. The title compound, [Al 3 P 3 O 12 F] - [C 5 H 5 NH] + ·0.15H 2 O, crystallizes in the triclinic space group P (no. 2), with Z=2, a=9.118(1), b=9.161(1), c=9.335(1) Å, α=85.98(1), β=77.45(1), γ=89.01(1)°, V=759.25(14) Å 3 , R 1 =0.0280 and wR 2 =0.0830. UT-6 is a small pore material that has a three-dimensional network of channels running through the structure. The structure is closely related to that of chabazite. In addition to alternating tetrahedral phosphorus and aluminium atoms connected by bridging oxygens, there are also isolated pairs of octahedral aluminiums in the four-membered rings of the UT-6 framework that share two bridging fluorine atoms. The resulting negative charge on the framework is balanced by pyridinium cations that reside in the chabazite cages. Upon thermal treatment of UT-6, pyridine molecules and HF are removed from the structure and the material transforms into rhombohedral AlPO 4 -CHA, as evidenced by in situ high-temperature powder X-ray diffraction, thermogravimetry and mass spectrometry. This represents the first solid-state transformation of an anionic aluminophosphate molecular sieve framework to an entirely neutral one.
Reviews in Pharmaceutical and Biomedical Analysis (2011)

Analytical chemistry is playing a critical role in many scientific disciplines and certainly pharmaceutical and biomedical sciences are among the most important. Just a quick glance in the international literature can easily prove this statement.
P3B-2 Clutter From Multiple Scattering and Aberration in a Nonlinear Medium (2007)

Aberration, clutter, and reverberation degrade the quality of ultrasonic images. When an acoustic pulse propagates through tissue these effects occur simultaneously and it is difficult to obtain independent estimates for the precise source of the point spread function broadening. The purpose of this paper is to characterize the sources of clutter and reverberation with a simulation of ultrasonic propagation through the abdomen. A full-wave equation that describes nonlinear propagation in a heterogeneous attenuating medium is solved numerically with finite differences in the time domain (FDTD). Three dimensional solutions of the equation are verified with water tank measurements of a commercial diagnostic ultrasound transducer and are shown to be in excellent agreement in terms of the fundamental and harmonic acoustic fields, and the power spectrum at the focus. The linear and nonlinear components of the algorithm are also verified independently. In the linear non-attenuating regime solutions match results from Field II, a well established software package used in transducer modeling, to within 0.3 dB. In addition to thermoviscous attenuation we present a numerical solution of the relaxation attenuation laws that allows modeling of arbitrary frequency dependent attenuation, such as that observed in tissue. A perfectly matched layer (PML) is implemented at the boundaries with a novel numerical implementation that allows the PML to be used with high order discretizations. A -78 dB reduction in the reflected amplitude is demonstrated. The numerical algorithm is used to simulate a focused ultrasonic pulse propagating through a histologically determined representation of the human abdomen. An ultrasound image is created in silicon using the same physical and algorithmic process used in an ultrasound scanner: a series of pulses are transmitted through heterogeneous scattering tissue and the received echoes are used in a delay-and-sum beamforming algorithm to generate a images. The resulting harmonic image exhibits characteristic improvement in lesion boundary definition and contrast when compared to the fundamental image. We demonstrate a mechanism of harmonic image quality improvement by showing that the harmonic point spread function is less sensitive to reverberation clutter.
Locating application data across service discovery domains (2001)

The bulk of proposed pervasive computing devices such as PDAs and cellular telephones operate as thin clients within a larger infrastructure. To access services within their local environment, these devices participate in a service discovery protocol which involves a master directory that registers all services available in the local environment. These directories typically are isolated from each other. Devices that move across service discovery domains have no access to information outside their current local domain. In this paper we propose an application-level protocol called VIA that enables data sharing among discovery domains. Each directory maintains a table of active links to other directories that share related information. A set of linked directories forms a data cluster that can be queried by devices for information. The data cluster is distributed, self-organizing, responsive to data mobility, and robust to failures. Using application-defined data schemas, clusters organize themselves into a hierarchy for efficient querying and network resource usage. Through analysis and simulation we describe the behavior of VIA under different workloads and show that the protocol overhead for both maintaining a cluster and handling failures grows slowly with the number of gateways.
A critical review of exposure and effect modelling approaches for ecological risk assessment of pesticides (2021)

Supplementary information linked to the paper in <em>Environmental Science and Pollution Research</em> entitled "A critical review of exposure and effect modelling approaches for ecological risk assessment of pesticides".
Encoding for the Blackwell Channel with Reinforced Belief Propagation (2007)

A key idea in coding for the broadcast channel (BC) is binning, in which the transmitter encode information by selecting a codeword from an appropriate bin (the messages are thus the bin indexes). This selection is normally done by solving an appropriate (possibly difficult) combinatorial problem. Recently it has been shown that binning for the Blackwell channel -a particular BC- can be done by iterative schemes based on Survey Propagation (SP). This method uses decimation for SP and suffers a complexity of O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). In this paper we propose a new variation of the Belief Propagation (BP) algorithm, named Reinforced BP algorithm, that turns BP into a solver. Our simulations show that this new algorithm has complexity O(n log n). Using this new algorithm together with a non-linear coding scheme, we can efficiently achieve rates close to the border of the capacity region of the Blackwell channel.
Ultrafast dynamics of nanorod-based plasmonic metamaterial and their excitonic hybrids (2013)

In this presentation we show that the recently discovered nonlocal optical behaviour of plasmonic nanorod metamaterials enables an enhanced, ultrafast, and nonlinear optical response of this hyperbolic structure. In particular, a large (80%) change of transmission through this subwavelength thick slab of metamaterial subjected to a low control light fluence of 7 mJ/cm2, is observed when the conditions of non-locality are satisfied. The picosecond temporal response of the system leads to switching frequencies in the terahertz range. [1] Coupling the metamaterial to a molecular aggregate supporting excitonic excitation, leads to an hybrid material with exciton-plasmon eigenstates. [2] Ultrafast spectroscopy reveals the dynamics of the hybrid metamaterial in both strong and weak coupling regimes, demonstrating drastic differences in both their temporal and spectral dynamic response.
Micromachined heat exchanger for a cryosurgical probe (2006)

This paper describes a lithography-based microfabrication process developed for a recuperative heat exchanger intended for use in a cryosurgical probe. The probe, which uses the Joule-Thomson (JT) cooling cycle, must achieve a temperature &lt; -50°C, with a freeze rate of 25-50°C/min. The heat exchanger must maintain high stream-to-stream thermal conductance while restricting parasitic stream-wise (axial) conduction losses. It has a footprint of 6x1.5cm2 and 2.5mm thickness, and is fabricated using a five-mask process. Rows of fins composed of high conductivity silicon are bonded onto a 100µm base plate composed of low conductivity Pyrex glass. The fabrication process involves anodic bonding, deep reactive ion dry etching, glass frit bonding, electrochemical drilling and several other steps, along with special features that compensate for manufacturing tolerances. The paper describes the fabrication challenges and how they constrain dimensional variables.
Message from the poster chairs (2014)

We are delighted to welcome you to ISMAR 2014, the 13th symposium on Mixed and Augmented Reality: Augment Everything Everywhere for Everyone. We consider posters to be one of the core elements of ISMAR. We expect them to spark exciting discussions and thus turn ISMAR into a true breeding ground for future directions of research, technical development and applications of augmented reality. Therefore, this year the posters were introduced as a truly separate submission track. The poster chairs now manage an independent reviewing process. The submission deadline was set after the paper decisions were sent to the authors. This timeline provides an opportunity for authors whose papers were rejected, but recommended for submitting their work as a poster. The distinction between papers and posters strengthens the focus of each respective submission track. While the paper review process aims on collecting mature results, the poster selection process now can uniquely focus on an unbiased selection of valuable poster material.
BFRF1 of Epstein-Barr Virus Is Essential for Efficient Primary Viral Envelopment and Egress (2005)

The molecular mechanisms that underlie maturation and egress of Epstein-Barr virus (EBV) virions are only partially characterized. We have recently shown that the BFRF1 gene, the EBV positional homolog of herpes simplex virus type 1 and pseudorabies virus UL34, is expressed early during EBV lytic replication and that it is found predominantly on the nuclear membrane (A. Farina, R. Santarelli, R. Gonnella, R. Bei, R. Muraro, G. Cardinali, S. Uccini, G. Ragona, L. Frati, A. Faggioni, and A. Angeloni, J. Virol. 74:3235-3244, 2000). These data suggest that the BFRF1 protein might be involved in viral primary envelopment. To precisely determine the function of this protein, we have constructed an EBV mutant devoid of the BFRF1 gene (BFRF1-KO). 293 cells carrying BFRF1-KO showed no differences in comparison with wild-type EBV in terms of DNA lytic replication or expression of late viral proteins upon induction of the lytic cycle. However, binding assays and infection experiments using cell lines or human cord blood lymphocytes showed a clear reduction in the viral mutant titers. Complementation experiments with BFRF1-KO and a BFRF1 expression vector restored viral titers to levels similar to those for the wild-type control, showing that the modifications that we introduced were limited to the BFRF1 gene. Electron microscopic observations showed that the reduction in viral titers was due to sequestration of EBV nucleocapsids in the nuclei of lytically induced cells. This suggests that BFRF1 is involved in transport of the maturing virion across the nuclear membrane. This hypothesis was further supported by the observation that BFRF1 is present in maturing intracellular virions but not in their extracellular counterparts. This implies that BFRF1 is a key protein for EBV maturation.
THE EFFECT OF MENGOVIRUS INFECTION ON THE ACTIVITY OF THE DNA-DEPENDENT RNA POLYMERASE OF L-CELLS (1962)

Mengovirus is a small RNA virus, approximately 27 mµ in diameter, containing&#13;\nonly RNA and protein, according to the analyses of Faulkner et al. on the closely&#13;\nrelated encephalomyocarditis (EMC) virus. It is a member of the Columbia SK&#13;\ngroup of viruses which we have been studying in detail in recent years.&#13;\n
Neurotrophins and their receptors in rat peripheral trigeminal system during maxillary nerve growth (1993)

We examined the expression of the neurotrophins (NTFs) and their receptor mRNAs in the rat trigeminal ganglion and the first branchial arch before and at the time of maxillary nerve growth. The maxillary nerve appears first at embryonic day (E)10 and reaches the epithelium of the first branchial arch at E12, as revealed by anti-L1 immunohistochemistry. In situ hybridization demonstrates, that at E10-E11, neurotrophin-3 (NT-3) mRNA is expressed mainly in the mesenchyme, but neurotrophin-4 (NT-4) mRNA in the epithelium of the first branchial arch. NGF and brain-derived neurotrophic factor (BDNF) mRNAs start to be expressed in the distal part of the first brachial arch shortly before its innervation by the maxillary nerve. Trigeminal ganglia strongly express the mRNA of trkA at E10 and thereafter. The expression of mRNAs for low-affinity neurotrophin receptor (LANR), trkB, and trkC in trigeminal ganglia is weak at E10, but increases by E11-E12. NT-3, NT-4, and more prominently BDNF, induce neurite outgrowth from explant cultures of the E10 trigeminal ganglia but no neurites are induced by NGF, despite the expression of trkA. By E12, the neuritogenic potency of NGF also appears. The expression of NT-3 and NT-4 and their receptors in the trigeminal system prior to target field innervation suggests that these NTFs have also other functions than being the target-derived trophic factors.
PORTUGUESE REAL‐LIFE EXPERIENCE WITH IBRUTINIB OUTSIDE CLINICAL TRIALS – A MULTICENTER ANALYSIS (2017)

Introduction: Bruton's tyrosine kinase inhibitor, ibrutinib, was recently approved for treatment-naïve, relapsed/refractory and del(17p)/TP53 mutated chronic lymphocytic leukemia (CLL). Discrepancies between clinical trials and routine healthcare are commonly observed in hematology–oncology. We aimed to evaluate the real-world clinical characteristics and drug-related toxicities of patients with CLL treated with ibrutinib in Portugal. Methods: We conducted a multicenter (13 institutions) retrospective observational study of 70 patients diagnosed with CLL that began treatment with ibrutinib between May 2014 and January 2017. We evaluated patient characteristics, biological features of the disease, previous therapy, toxicities, and overall survival (OS). All patients received ibrutinib as a single agent, all but 5 at an initial dose of 420 mg daily. Clinical data were analyzed using IBM® SPSS® Statistics version 22.0. Results: Median age of the cohort was 68 years (IQR: 63–74); 41 patients (58.6%) were male. Median CIRS score was 4 (2–6); ECOG performance status score was 0–1 in 90.5% and 2–4 in 9.5% of evaluable patients; 65.7% were staged as Rai III/IV and 61.4% as Binet C; 54.4% had del(17p) and 11.9% del(11q); 15.7% were treatment naïve; median number of previous lines of therapy for CLL was 2 (1–3); 50% were previously treated with fludarabine and 74.3% with rituximab-containing regimens. Median duration of Ibrutinib treatment was 7.7 months (3–15.5); median follow-up was 8.7 months (4–18.3). Adverse events (AEs) were identified in 87.1% of patients; 51.4% had severe AEs (SAEs – CTCAE grade ≥ 3). The most frequent AE was infection, in 41.4% of patients (69% SAEs), followed by thrombocytopenia (40%–21.4% of which SAEs), neutropenia (35.7%–48% of which SAEs), anemia (28.6%), diarrhea (25.7%), bleeding (21.4%–40% of which SAEs), and arthralgia (20%). AEs led to ibrutinib dose reduction in 18.6% and temporary suspension in 31.4% of patients. Discontinuation-free survival at median follow-up was 82.9%. Ibrutinib was discontinued in 16 patients (22.9%): 5 due to progression, 2 prior to allogeneic hematopoietic stem cell transplantation, 1 due to loss of follow-up, and the remaining 8 because of AEs (50% infectious). OS at median follow-up was 82.9%. 14 patients died, 6 due to disease progression, 5 due to infection, 2 due to hemorrhage, and 1 of sudden death. ECOG 2-4 was significantly associated with an increased risk of death (log-rank p-value 0.013; HR 4.06, 95% CI: 1.22–13.5). OS wasn't significantly different in patients with and without del(17p). Keywords: chronic lymphocytic leukemia (CLL); ibrutinib.
Biosynthesis of chick type VI collagen. II. Processing and secretion in fibroblasts and smooth muscle cells. (1987)

The biosynthesis of type VI collagen was studied in "matrix-free" chick embryo smooth muscle cells and fibroblasts. Omission of ascorbate from the culture affected to a great extent the secretion in fibroblasts but had a very minor effect on smooth muscle cells. Quantitative analysis of the secretion process in continuous time course and in pulse-chase experiments confirmed that fibroblasts and smooth muscle cells secreted type VI collagen with the same chain composition but with different kinetics: after 4 h of chase more than 60% of the labeled type VI collagen was present in the culture medium of fibroblasts, whereas at the same time interval less than 25% was secreted by smooth muscle cells. The different kinetics depends on intrinsic properties of the cells, since it was detected also in adherent cells. However, even in fibroblasts, secretion of type VI collagen was much slower than secretion of fibronectin, of which more than 50% was already in the cell medium after 1 h of chase. Treatment of the cells with inhibitors of hydroxylation and glycosylation caused a shift in mobility that revealed a size heterogeneity in the Mr = 260,000 subunit. No evidence of processing was observed in chick cells for any of the subunits that were synthesized and secreted uncleaved. In addition, after several days of chase the Mr of the subunits of type VI collagen isolated from the matrix remained unchanged, thus excluding that in the chick even a partial or incomplete processing takes place.
Moving obstacle segmentation using MMW radar and image sequence (2008)

Sensor fusion of millimeter-wave (MMW) radar and a camera is beneficial for advanced driver assistance functions such as obstacle avoidance and StopG the motion segmentation technique is applied toward the tracks that drop in the region. Note that an obstacle's position detected by MMW radar is remarkably rough because MMW radar has low directional resolution. Nevertheless, the position contributes to rapid and robust estimation for satisfactory image boundaries. We demonstrate the validity of the proposed method through experiments using sensors that are mounted on a vehicle.
Precision of Raman Spectroscopy Measurements in Detection of Microcalcifications in Breast Needle Biopsies (2012)

Microcalcifications are an early mammographic sign of breast cancer and a target for stereotactic breast needle biopsy. We developed Raman spectroscopy decision algorithms to detect breast microcalcifications, based on fit coefficients (FC) derived by modeling tissue Raman spectra as a linear combination of the Raman spectra of 9 chemical and morphologic components of breast tissue. However, little or no information is available on the precision of such measurements and its effect on the ability of Raman spectroscopy to make predictions for breast microcalcification detection. Here we report the precision, that is, the closeness of agreement between replicate Raman spectral measurements--and the model FC derived from them--obtained ex vivo from fresh breast biopsies from patients undergoing stereotactic breast needle biopsy, using a compact clinical Raman system. The coefficients of variation of the model FC averaged 0.03 for normal breast tissue sites, 0.12 for breast lesions without, and 0.22 for breast lesions with microcalcifications. Imprecision in the FC resulted in diagnostic discordance among replicates only for line-sitters, that is, tissue sites with FC values near the decision line or plane. The source of this imprecision and their implications for the use of Raman spectroscopy for guidance of stereotactic breast biopsies for microcalcifications are also discussed. In summary, we conclude that the precision of Raman spectroscopy measurements in breast tissue obtained using our compact clinical system is more than adequate to make accurate and repeatable predictions of microcalcifications in breast tissue using decision algorithms based on model FC. This provides strong evidence of the potential of Raman spectroscopy guidance of stereotactic breast needle biopsies for microcalcifications.