gebhart/patrepeval huggingface dataset:
Dynamics of titanium ablation suppression induced by below-ablation-threshold femtosecond laser pulse irradiation (2021)

We have discovered that the pre-irradiation of a below-ablation-threshold femtosecond laser pulse (first pulse) suppressed titanium ablation rate by subsequent irradiation of another above-ablation-threshold femtosecond laser pulse (second pulse). To ablate titanium targets, we used linearly polarized femtosecond laser pulses (810nm wavelength, 45fs pulse duration, 10Hz repetition rate). Ablation suppression was transiently observed with the delay of several hundreds of picosecond. With these delays, the ablation rate with 10% below-ablation-threshold first-pulse pre-irradiation was suppressed to half of that without pre-irradiation. This result indicated that the below-ablation-threshold first-pulse preirradiation does not ablate the titanium target but changes the optical property of the surface. To understand the physics of the ablation suppression, we have developed and performed a new measurement to estimate the temporal changes of the effective laser penetration length (LPL) induced by the below-ablation-threshold first-pulse pre-irradiation. We developed a new description of the dependence of the ablation rate on the laser fluences and delay by considering the absorption and decay of the laser pulse energy in the target. We have demonstrated that below-ablation-threshold firstpulse pre-irradiation reduced LPL with the delay of several hundreds of picosecond. The result indicated that the preirradiation of a below-ablation-threshold first-pulse changed the titanium surface into a novel state with reduced LPL, which is not explained by simple heating of surface.
Computational studies of the binding profile of phosphoinositide PtdIns (3,4,5) P3 with the pleckstrin homology domain of an oomycete cellulose synthase (2016)

Saprolegnia monoica is a model organism to investigate Saprolegnia parasitica, an important oomycete which causes considerable loss in aquaculture every year. S. monoica contains cellulose synthases vital for oomycete growth. However, the molecular mechanism of the cellulose biosynthesis process in the oomycete growth is still poorly understood. Some cellulose synthases of S. monoica, such as SmCesA2, are found to contain a plecsktrin homology (PH) domain, which is a protein module widely found in nature and known to bind to phosphoinositides, a class of signaling compounds involved in many biological processes. Understanding the molecular interactions between the PH domain and phosphoinositides would help to unravel the cellulose biosynthesis process of oomycetes. In this work, the binding profile of PtdIns (3,4,5) P3, a typical phosphoinositide, with SmCesA2-PH was studied by molecular docking, molecular dynamics and metadynamics simulations. PtdIns (3,4,5) P3 is found to bind at a specific site located at β1, β2 and β1-β2 loop of SmCesA2-PH. The high affinity of PtdIns (3,4,5) P3 to SmCesA2-PH is contributed by the free phosphate groups, which have electrostatic and hydrogen-bond interactions with Lys88, Lys100 and Arg102 in the binding site.
Analysis of the Robustness and Discrimination for Video Fingerprints in Video Copy Detection (2013)

무분별한 복제 비디오를 막기 위하여 비디오 지문을 개발연구가 진행되고 있다. 이러한 비디오 지문들은 복제 비디오에서 발생되는 다양한 변화에 강인해야 하며 정확하게 구별될 수 있는 높은 분별력을 지녀야 한다. 일반적으로 비디오 지문들은 luminance(밝기), gradient(기울기), 그리고 DCT(주파수) 공간 등에서 주로 추출이 되고 있다. 그러나 아직 각 공간과 비디오 지문 사이에 실질적인 성능이 차이에 대한 연구가 부족하다. 따라서 본 논문에서는 각 공간에 따른 복제 비디오 검출 성능을 비교하기 위하여 강인함과 분별력에 기반한 복제 비디오 검출 실험을 진행하고 분석 하였다. 본 논문에서 동일한 패턴으로 각 공간에서 비디오 지문을 추출하고 각각 강인함과 분별력을 비교 한 후 최종적으로 복제 비디오 검출 실험을 진행하였다. 본 실험에서 DCT 공간에서 추출된 비디오 지문이 다른 공간보다 좀더 우수한 성능을 보여 주었는데 이는 해당 공간이 다른 비디오 지문들과 분별력이 가장 높았기 때문이다. In order to prevent illegal video copies, many video fingerprints have been developed. Video fingerprints should be robust from various video transformations and have high discriminative powers. In general, video fingerprints are generated from three feature spaces such as luminance, gradient, and DCT coefficients. However, there is a few study for the robustness and discrimination according to feature spaces. Thus, we analyzed the property of each feature space by video copy detion task with the robustness and the discrimination of video fingerprints. We generated three video fingerprints from these feature spaces using a same algorithm. In our test, a video fingerprint. based on DCT coefficient outperformed others because the discrimination of it was higher.
Skeletal Muscle Wasting in Chronic Heart Failure (2018)

Patients suffering from chronic heart failure (CHF) show an increased prevalence (~20% in elderly CHF patients) of loss of muscle mass and muscle function (i.e. sarcopenia) compared with healthy elderly people. Sarcopenia, which can also occur in obese patients, is considered a strong predictor of frailty, disability, and mortality in older persons and is present in 5-13% of elderly persons aged 60-70 years and up to 50% of all octogenarians. In a CHF study, sarcopenia was associated with lower strength, reduced peak oxygen consumption (peak VO<sub>2</sub> , 1173 ± 433 vs. 1622 ± 456 mL/min), and lower exercise time (7.7 ± 3.8 vs. 10.22 ± 3.0 min, both P < 0.001). Unfortunately, there are only very limited therapy options. Currently, the main intervention remains resistance exercise. Specialized nutritional support may aid the effects of resistance training. Testosterone has significant positive effects on muscle mass and function, and low endogenous testosterone has been described as an independent risk factor in CHF in a study with 618 men (hazard ratio 0.929, P = 0.042). However, the use of testosterone is controversial because of possible side effects. Selective androgen receptor modulators have been developed to overcome these side effects but are not yet available on the market. Further investigational drugs include growth hormone, insulin-like growth factor 1, and several compounds that target the myostatin pathway. The continuing development of new treatment strategies and compounds for sarcopenia, muscle wasting regardless of CHF, and cardiac cachexia makes this a stimulating research area.
Faecalibacterium prausnitzii phylotypes in type two diabetic, obese, and lean control subjects (2016)

Faecalibacterium prausnitzii is one of the main butyrate producers in the healthy human gut. Information on its genetic diversity is lacking, although two genetic phylotypes have been differentiated. In the present study, F. prausnitzii phylotypes were examined in faeces of obese and type two diabetes with similar eating behaviour compared to a lean control group. The purpose of the study was to analyse if an excessive butyrate production induced by different F. prausnitzii phylotypes discriminates between obese developing type two diabetes or not. The faecal samples were analysed for the total abundance of F. prausnitzii 16S rRNA copies, fragment lengths polymorphism, high resolution melt curve analysis (HRM) and the butyryl-CoA:acetate CoA-transferase gene copies and melt curve variances. The diabetic group was found to differ significantly from the lean control group in the results of qPCR, butyryl-CoA:acetyate CoA-transferase gene melt curve, and HRM. F. prausnitzii phylotypes differed in obese with and without developed diabetes type two. Different phylotypes of F. prausnitzii may lead to differences in the inflammatory genesis in the host. F. prausnitzii phylotypes may have an influence on developing type two diabetes and might also act as starting points for prevention and therapy of obesity associated disease.
Characterizing Post-Acute Sequelae of SARS-CoV-2 Infection across Claims and Electronic Health Record Databases (2021)

Structured Abstract Importance Post-acute sequelae of SARS-CoV-2 infection (PASC) is emerging as a major public health issue. Objective We characterized the incidence of PASC, or related symptoms and diagnoses, for COVID-19 and influenza patients. Design Retrospective cohort study. Setting Our data sources were the IBM MarketScan Commercial Claims and Encounters (CCAE), Optum Electronic Health Record (EHR) and Columbia University Irving Medical Center (CUIMC) databases that were transformed to the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) and were part of the Observational Health Sciences and Informatics (OHDSI) network. Participants The COVID-19 cohort consisted of patients with a diagnosis of COVID-19 or positive lab test of SARS-CoV-2 after January 1st 2020 with a follow up period of at least 30 days. The influenza cohort consisted of patients with a diagnosis of influenza between October 1, 2018 and May 1, 2019 with a follow up period of at least 30 days. Intervention Infection with COVID-19 or influenza. Main Outcomes and Measures Post-acute sequelae of SARS-CoV-2 infection (PASC), or related diagnoses, for COVID-19 and influenza patients. Results In aggregate, we characterized the post-acute experience for over 440,000 patients who were diagnosed with COVID-19 or tested positive for SARS-COV-2. The long term sequelae that had a higher incidence in the COVID-19 compared to Influenza cohorts were altered smell or taste, myocarditis, acute kidney injury, dyspnea and alopecia. Additionally, the long term incidences of respiratory illness, musculoskeletal disease, and psychiatric disorders for the COVID-19 population were higher than expected. Conclusions and Relevance The long term sequelae of COVID-19 and influenza may be different. Further characterization of PASC on large scale observational healthcare databases is warranted.
[Mexiletine: electrophysiologic effects]. (1983)

A complete electrophysiological evaluation has been performed before and after the intravenous administration of Mexiletine (M.) (3 mg/Kg/B.W. in 5 minutes) in 28 patients (pts) (6 pts with normal conduction system, 4 pts with sick sinus syndrome, 5 pts with intranodal AV block, 13 pts with bundle branch block, of which 4 with pathological HV and 1 with intrahisian conduction defect). With the exception of a shortening of QTc interval in all the pts, the drug did not significantly affect any other electrophysiological parameters. In the patient with intrahisian conduction defect, M. prolonged the H1 - H2 interval. A statistically significant increase of heart rate has been also observed in a second group of 8 pts with normal sinus function, in whom M. administration was preceded by Atropine (I.V. bolus 0,04 mg/Kg/B.W.). This finding seems to exclude a vagolytic effect of M. The conclusions derived from our experience and pertinent literature are the following: M. is not useful in the treatment of supraventricular arrhythmias because it has negligible effects on atrial and AV nodal conduction; the drug may be safely employed in the treatment of ventricular arrhythmias in pts with atrial and/or AV nodal conduction defects; special caution must be employed when the drug is utilized in pts with sick sinus syndrome and/or with marked intraventricular conduction defects.
Layered software-the next step for switching systems in the intelligent network (1990)

An effort has been made to determine how fast new services can be introduced and how the service programming capability will be brought into the hands of the service providers in the intelligent network. It is suggested that the answer to such questions can be found in a layered software structure, which will give switching systems the flexibility that the era of intelligent networks requires. This new structure makes it possible to implement a bona fide intelligent network platform, where service programs are unbundled from access and transport technologies. The new software structure also provides a more powerful service programming interface.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mismatch Repair Protein Deficiency/Microsatellite Instability Is Rare in Cholangiocarcinomas and Associated With Distinctive Morphologies (2019)

Solid, mucinous, or signet-ring appearance of a cholangiocarcinoma should prompt MMR testing for immunotherapy options but should not necessarily raise concern about Lynch syndrome.
Biochemical Lesion in Dilantin-Induced Erythroid Aplasia (1967)

Abstract Clinical and biochemical studies are reported in a patient who developed pure red cell aplasia after 2 years therapy with Dilantin but in whom aplasia could subsequently be induced with 4-5 Gm. of the drug. Recovery occurred regularly when the drug was discontinued. The administration of 1500 ml. of patient’s plasma obtained during the aplastic phase to a normal volunteer with Dilantin had no effect on the recipient’s reticulocyte count, number of nucleated red cells in his bone marrow, or Fe59 clearance. Attempts to demonstrate binding of gamma globulin to the patient’s nucleated red cells in the presence of Dilantin by immunofluorescence technic were unsuccessful. Dilantin, in a concentration of 20 µg./ml. in vitro, caused significant inhibition of the uptake of C14 formate, glycine, adenine, orotic acid, and uridine into DNA but not into RNA of patient’s bone marrow studied when fully recovered. There was no effect on the uptake of deoxyuridine or thymidine. The Dilantin effect was specific to the erythroid cells as shown by radioautographic studies and by the absence of inhibition when these cells were absent from the bone marrow. Vitamin B12 and folinic aci dgiven to the patient in large doses did not reverse the hematologic effects of Dilantin. The daily intravenous administration of all four deoxyribonucleosides, deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine had a suggestive, but not clear-cut, effect. In an effort to examine a possible relationship of the pure red cell aplasia in this patient to riboflavin metabolism, the patient was started simultaneously on Dilantin and riboflavin. Dilantin was now without effect. However, the patient remains refractory to Dilantin a year after riboflavin was discontinued. It is concluded that Dilantin exerted its toxic effect in this patient by specifically inhibiting DNA synthesis in erythroid cells probably at the step of deoxyribotide formation. The role of riboflavin in the development of resistance to the toxic effect of Dilantin in this patient remains uncertain.
Neuronal calcium sensor 1 (NCS1) dependent modulation of neuronal morphology and development (2021)

Calcium (Ca<sup>2+</sup> ) signaling is critical for neuronal functioning and requires the concerted interplay of numerous Ca<sup>2+</sup> -binding proteins, including neuronal calcium sensor 1 (NCS1). Although an important role of NCS1 in neuronal processes and in neurodevelopmental and neurodegenerative diseases has been established, the underlying mechanisms remain enigmatic. Here, we systematically investigated the functions of NCS1 in the brain. Using Golgi-Cox staining, we observed a reduction in dendritic complexity and spine density in the prefrontal cortex and the dorsal hippocampus of Ncs1<sup>-/-</sup> mice, which may underlie concomitantly observed deficits in memory acquisition. Subsequent RNA sequencing of Ncs1<sup>-/-</sup> and Ncs1<sup>+/+</sup> mouse brain tissues revealed that NCS1 modulates gene expression related to neuronal morphology and development. Investigation of developmental databases further supported a molecular role of NCS1 during brain development by identifying temporal gene expression patterns. Collectively, this study provides insights into NCS1-dependent signaling and lays the foundation for a better understanding of NCS1-associated diseases.
Architecture Aware Programming on Multi-Core Systems (2011)

In order to improve the processor performance, the response of the industry has been to increase the number of cores on the die. One salient feature of multi-core architectures is that they have a varying degree of sharing of caches at different levels. With the advent of multi-core architectures, we are facing the problem that is new to parallel computing, namely, the management of hierarchical caches. Data locality features need to be considered in order to reduce the variance in the performance for different data sizes. In this paper, we propose a programming approach for the algorithms running on shared memory multi-core systems by using blocking, which is a well-known optimization technique coupled with parallel programming paradigm, OpenMP. We have chosen the sizes of various problems based on the architectural parameters of the system like cache level, cache size, cache line size. We studied the cache optimization scheme on commonly used linear algebra applications – matrix multiplication (MM), Gauss-Elimination (GE) and LU Decomposition (LUD) algorithm.
Transverse optical patterns for ultra‐low‐light‐level all‐optical switching (2009)

Abstract We review recent theoretical and experimental efforts toward developing an all‐optical switch based on transverse optical patterns. Transverse optical patterns are formed when counterpropagating laser beams interact with a nonlinear medium. A perturbation, in the form of a weak switch beam injected into the nonlinear medium, controls the orientation of the generated patterns. Each state of the pattern orientation is associated with a state of the switch. That is, information is stored in the orientation state. A realization of this switch using a warm rubidium vapor shows that it can be actuated by as few as 600 ± 40 photons with a response time of 5 µs. Models of nonlinear optical interactions in semiconductor quantum wells and microresonators suggest these systems are also suitable for use as fast all‐optical switches using this same conceptual design, albeit at higher switching powers.
LOGISMOS-B: Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces for the Brain (2014)

Automated reconstruction of the cortical surface is one of the most challenging problems in the analysis of human brain magnetic resonance imaging (MRI). A desirable segmentation must be both spatially and topologically accurate, as well as robust and computationally efficient. We propose a novel algorithm, LOGISMOS-B, based on probabilistic tissue classification, generalized gradient vector flows and the LOGISMOS graph segmentation framework. Quantitative results on MRI datasets from both healthy subjects and multiple sclerosis patients using a total of 16,800 manually placed landmarks illustrate the excellent performance of our algorithm with respect to spatial accuracy. Remarkably, the average signed error was only 0.084 mm for the white matter and 0.008 mm for the gray matter, even in the presence of multiple sclerosis lesions. Statistical comparison shows that LOGISMOS-B produces a significantly more accurate cortical reconstruction than FreeSurfer, the current state-of-the-art approach (p << 0.001). Furthermore, LOGISMOS-B enjoys a run time that is less than a third of that of FreeSurfer, which is both substantial, considering the latter takes 10 h/subject on average, and a statistically significant speedup.
Figure S4 from Multikinase Inhibitors Induce Cutaneous Toxicity through OAT6-Mediated Uptake and MAP3K7-Driven Cell Death (2023)

&lt;p&gt;Sorafenib-induced keratinocyte toxicity in vivo.&lt;/p&gt;
Continuous PM-10 Measurements Using the Tapered Element Oscillating Microbalance (1991)

The goal of continuous ambient participate monitoring has been realized through the use of tapered element oscillating microbalance technology. This technology measures particle mass inertially as the mass deposits on a filter. As such, it is a direct mass measurement and eliminates the mass uncertainties inherent in indirect methods represented by optical or beta adsorption instrumentation. A description of the tapered element oscillating microbalance PM-10 measurement technique is given. Tests have been conducted on tapered element oscillating microbalance PM-10 monitors both in the United States and Europe. Test results presented include comparisons to samplers designated as EPA reference methods.
Detection of sputum eicosanoids in cystic fibrosis and in normal saliva by bioassay and radioimmunoassay. (1987)

We have measured arachidonic acid (AA) metabolites, leukotrienes (LTs) and prostanoids (Ps), in sputum of patients with cystic fibrosis (CF) and in normal saliva using bioassay and radioimmunoassay (RIA). Almost three times as much LTB4 is present in CF extracts compared with slow reacting substances (SRSs). Leukotrienes were not detected in normal saliva. In CF sputum there is a three-fold increase in the level of the vasodilator prostanoid prostaglandin E2 (PGE2) and the stable metabolite of prostacyclin, 6-oxo PGF1 alpha compared with the vasoconstrictor prostaglandin F2 alpha (PGF2 alpha) and thromboxane B2 (TxB2), a hydrolysis product of thromboxane A2. Experiments with BW755c (25 micrograms ml-1, n = 3) indicated that the majority of this activity was not produced during the extraction procedure. The detection of LTs and Ps in sputum of CF patients shows that these substances are present at biologically active concentrations and may contribute to the pathophysiology of this disease.
A Cyclic CCK8 Analogue Selective for the Cholecystokinin Type A Receptor: Design, Synthesis, NMR Structure and Binding Measurements (2003)

A cyclic CCK8 analogue, cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 (Dpr=L-2,3-diaminopropionic acid), has been designed on the basis of the NMR structure of the bimolecular complex between the N-terminal fragment of the CCK(A) receptor and its natural ligand CCK8. The conformational features of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 have been determined by NMR spectroscopy in aqueous solution and in water containing DPC-d(38) micelles (DPC=dodecylphosphocholine). The structure of the cyclic peptide in aqueous solution is found to be in a relaxed conformation, with the backbone and Dpr29 side chain atoms making a planar ring and the N-terminal tripeptide extending approximately along the plane of this ring. In DPC/water, the cyclic peptide adopts a "boat-shaped" conformation, which is more compact than that found in aqueous solution. The cyclic constraint between the Dpr29 side chain and the CCK8 carboxyl terminus (Lys34) introduces a restriction in the backbone conformational freedom. However, the interaction of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 with the micelles still plays an important role in the stabilisation of the bioactive conformation. A careful comparison of the NMR structure of the cyclic peptide in a DPC micelle aqueous solution with the structure of the rationally designed model underlines that the turn-like conformation in the Trp30-Met31 region is preserved, such that the Trp30 and Met31 side chains can adopt the proper spatial orientation to interact with the CCK(A) receptor. The binding properties of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 to the N-terminal receptor fragment have been investigated by fluorescence spectroscopy in a micellar environment. Estimates of the apparent dissociation constant, K(d), were in the range of 70-150 nM, with a mean value of 120+/-27 nM. Preliminary nuclear medicine studies on cell lines transfected with the CCK(A) receptor indicate that the sulfated-Tyr derivative of cyclo(29,34)[Dpr(29),Lys(34)]-CCK8 displaces the natural ligand with an IC(50) value of 15 microM.
Fast Lattice-Free Keyword Filtering for Accelerated Spoken Term Detection (2020)

We present a novel set of keyword detection techniques to accelerate spoken term detection for known queries with minimal loss in accuracy. Using only ASR frame-level acoustic posteriors we can train multiple models to effectively detect non-target segments for which we need not perform full lattice decoding. We estimate phone n-gram soft counts for each segment in a single pass over the frame-level output. From this we can efficiently detect a fixed set of keywords with both linear and DNN-based classifiers. Furthermore we can train the linear classifiers on a small number of labeled examples. Experiments on the PSC and VAST English subset of NIST's 2019 OpenSAT evaluation demonstrate we can filter out half of the test audio segments while only increasing the keyword miss rate by under 3%.