gebhart/patrepeval huggingface dataset:
Characterization of genetic intratumor heterogeneity in colorectal cancer and matching patient‐derived spheroid cultures (2017)

Patient-derived in vitro cultures of colorectal cancer (CRC) may help guide treatment strategies prior to patient treatment. However, most previous studies have been performed on a single biopsy per tumor. The purpose of this study was to analyze multiple spatially distinct biopsies from CRCs and see how well intratumor heterogeneity (ITH) was recapitulated in matching patient-derived spheroids. Three to five biopsies were collected from six CRC tumors. Each biopsy was split in two; one half was used for spheroid culturing, while the other half was used for DNA and RNA purification. For two patients, lymph node metastases were analyzed. Somatic mutations were called from whole exome sequencing data. Each tumor contained mutations shared across all biopsies and spheroids, including major CRC drivers such as APC, KRAS, and TP53. At the same time, all tumors exhibited ITH on both mutation and copy number level. The concordance between biopsies and spheroids ranged between 40 and 70% for coding mutations. For three patients, the biopsy and spheroid from matching areas clustered together, meaning that the spheroid resembled the area of origin more than the other areas. However, all biopsies and spheroids contained private mutations. Therefore, multiple cultures from spatially distinct sites of the tumor increase the insight into the genetic profile of the entire tumor. Molecular subtypes were called from RNA sequencing data. When based on transcripts from both cancer and noncancerous cells, the subtypes were largely independent of sampling site. In contrast, subtyping based on cancer cell transcripts alone was dependent on sample site and genetic ITH. In conclusion, all examined CRC tumors showed genetic ITH. Spheroid cultures partly reflected this ITH, and having multiple cultures from distinct tumor sites improved the representation of the genetic tumor subclones. This should be taken into account when establishing patient-derived models for drug screening.
Stereoselective Functionalization of Dithiolanes and Dithianes: The First Example of an Axial Trapping (2002)

2-Silyl-1,3-dithiolanes and dithianes can be easily functionalized under fluoride ion conditions. The functionalization occurs stereoselectively, the products bearing the incoming groups in the position formerly occupied by the silyl moiety. These results lead to the first example of dithiolane and dithiane axial trapping.
Supplementary Table 1 and Figure 1 from DNA Methylation Changes after 5-Aza-2′-Deoxycytidine Therapy in Patients with Leukemia (2023)

Supplementary Table 1 and Figure 1 from DNA Methylation Changes after 5-Aza-2′-Deoxycytidine Therapy in Patients with Leukemia
ChemInform Abstract: Carbocyclic Analogues of Nucleosides. Part 4. Preparation of Enantiomerically Pure Analogues of Purine Nucleosides for the Synthesis of Sulfone‐Linked Oligonucleotide Analogues. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Achieving fast and exact hazard-free logic minimization of extended burst-mode gC finite state machines (2000)

This paper presents a new approach to two-level hazard-free logic minimization in the context of extended burst-mode finite state machine synthesis targeting generalized C-elements (gC). No currently available minimizers for literal-exact two-level hazard-free logic minimization of extended burst-mode gC controllers can handle large circuits without synthesis times ranging up over thousands of seconds. Even existing heuristic approaches take too much time when iterative exploration over a large design space is required and do not yield minimum results. The logic minimization approach presented in this paper is based on state graph exploration in conjunction with single-cube cover algorithms, an approach that has not been considered for minimization of extended burst-mode finite state machines previously. Our algorithm achieves very fast logic minimization by introducing compacted state graphs and cover tables and an efficient single-cube cover algorithm for single-output minimization. Our exact logic minimizer finds minimal number of literal solutions to all currently available benchmarks, in less than one second on a 333 MHz microprocessor -- more than three orders of magnitude faster than existing literal exact methods, and over an order of magnitude faster than existing heuristic methods for the largest benchmarks. This includes a benchmark that has never been possible to solve exactly in number of literals before.
ChemInform Abstract: A GENERAL METHOD FOR THE PREPARATION OF N‐MONOSUBSTITUTED‐3‐ISOTHIAZOLAMINES (1978)

Abstract Aus den Isothjazolen (I) erhält man über die Isothiazoliumsalze (II) mit Ammoniak unter Umlagerung die 3‐Amino‐isothiazole (III).
Cardiac-restricted Expression of the Carboxyl-terminal Fragment of GRK3 Uncovers Distinct Functions of GRK3 in Regulation of Cardiac Contractility and Growth (2007)

G protein-coupled receptor kinase-2 and -3 (GRK2 and GRK3) in cardiac myocytes catalyze phosphorylation and desensitization of different G protein-coupled receptors through specificity controlled by their carboxyl-terminal pleckstrin homology domain. Although GRK2 has been extensively investigated, the function of cardiac GRK3 remains unknown. Thus, in this study cardiac function of GRK3 was investigated in transgenic (Tg) mice with cardiac-restricted expression of a competitive inhibitor of GRK3, i.e. the carboxyl-terminal plasma membrane targeting domain of GRK3 (GRK3ct). Cardiac myocytes from Tg-GRK3ct mice displayed significantly enhanced agonist-stimulated alpha(1)-adrenergic receptor-mediated activation of ERK1/2 versus cardiac myocytes from nontransgenic littermate control (NLC) mice consistent with inhibition of GRK3. Tg-GRK3ct mice did not display alterations of cardiac mass or left ventricular dimensions compared with NLC mice. Tail-cuff plethysmography of 3- and 9-month-old mice revealed elevated systolic blood pressure in Tg-GRK3ct mice versus control mice (3-month-old mice, 136.8 +/- 3.6 versus 118.3 +/- 4.7 mm Hg, p < 0.001), an observation confirmed by radiotelemetric recording of blood pressure of conscious, unrestrained mice. Simultaneous recording of left ventricular pressure and volume in vivo by miniaturized conductance micromanometry revealed increased systolic performance with significantly higher stroke volume and stroke work in Tg-GRK3ct mice than in NLC mice. This phenotype was corroborated in electrically paced ex vivo perfused working hearts. However, analysis of left ventricular function ex vivo as a function of increasing filling pressure disclosed significantly reduced (dP/dt)(min) and prolonged time constant of relaxation (tau) in Tg-GRK3ct hearts at elevated supraphysiological filling pressure compared with control hearts. Thus, inhibition of GRK3 apparently reduces tolerance to elevation of preload. In conclusion, inhibition of cardiac GRK3 causes hypertension because of hyperkinetic myocardium and increased cardiac output relying at least partially on cardiac myocyte alpha(1)-adrenergic receptor hyper-responsiveness. The reduced tolerance to elevation of preload may cause impaired ability to withstand pathophysiological mechanisms of heart failure.
새로운 비전통적 나노리소그라피 공정 (2003)

본 총설에서는 나노 형상 및 나노 구조체의 제작에 있어서 기존의 노광 공정을 이용하는 대신, 물리적 접촉법을 통해서 형상을 구현하는 비전통적 패터닝 방법을 소개하였다. 이에 기존 노광 공정의 비용 및 기술적 문제를 극복하는 대안으로써 나노 각인 리소그라피법과 연성 리소그라피법을 제시하였다. 이들 공정은 주형을 이용하여 반복적으로 형상을 구현함으로써 경제적인 공정을 구현하면서도, 곡면상에의 형상 구현까지도 가능한 기술적 장점을 가지고 있다. 더 나아가, 이들 공정의 단점을 보완함과 동시에 산업적 이용가치를 높인 공정으로써 상은 각인 리소그라피법 및 연성 성형법을 제시하였다. 이를 통해 간단한 공정만으로도 복잡한 구조나 3차원 구조의 나노 형상을 자유로이 제조할 수 있었다.
Digital tanlock loop architecture with no delay (2011)

This article proposes a new architecture for a digital tanlock loop which eliminates the time-delay block. The (rad) phase shift relationship between the two channels, which is generated by the delay block in the conventional time-delay digital tanlock loop (TDTL), is preserved using two quadrature sampling signals for the loop channels. The proposed system outperformed the original TDTL architecture, when both systems were tested with frequency shift keying input signal. The new system demonstrated better linearity and acquisition speed as well as improved noise performance compared with the original TDTL architecture. Furthermore, the removal of the time-delay block enables all processing to be digitally performed, which reduces the implementation complexity. Both the original TDTL and the new architecture without the delay block were modelled and simulated using MATLAB/Simulink. Implementation issues, including complexity and relation to simulation of both architectures, are also addressed.
Prevention of Infections Associated With Combat-Related Burn Injuries (2011)

Burns are a very real component of combat-related injuries, and infections are the leading cause of mortality in burn casualties. The prevention of infection in the burn casualty transitioning from the battlefield to definitive care provided at the burn center is critical in reducing overall morbidity and mortality. This review highlights evidence-based medicine recommendations using military and civilian data to provide the most comprehensive, up-to-date management strategies for initial care of burned combat casualties. Areas of emphasis include antimicrobial prophylaxis, debridement of devitalized tissue, topical antimicrobial therapy, and optimal time to wound coverage. This evidence-based medicine review was produced to support the Guidelines for the Prevention of Infections Associated With Combat-Related Injuries: 2011 Update contained in this supplement of Journal of Trauma.
Development of flaw evaluation and acceptance procedures for flaw indications in the cooling water system at the Savannah River Site K Reactor (1993)

This paper describes the methodology used in determining the criteria for acceptance of inspection indications in the K-Reactor Cooling Water System at the Savannah River Plant. These criteria have been developed in a manner consistent with the development of similar criteria in the ASME Code Section 11 for commercial light water reactors, but with a realistic treatment of the operating conditions in the cooling water system. The technical basis for the development of these criteria called {open_quotes}Acceptance Standards{close_quotes} is contained in this paper. A second portion of this paper contains the methodology used in the construction of flaw evaluation charts which have been developed for each specific line size in the cooling water system. The charts provide the results of detailed fracture mechanics calculations which have been completed to determine the largest flaw which can be accepted in the cooling water system without repair. These charts are designed for use in conjunction with inservice inspections of the cooling water system, and only require inspection results to determine acceptability.
Mildly oxidized LDL induces an increased apolipoprotein J/paraoxonase ratio. (1997)

We have examined the effects of mildly oxidized LDL and atherosclerosis on the levels of two proteins associated with HDL; apolipoprotein J (apoJ), and paraoxonase (PON). On an atherogenic diet, PON activity decreased by 52%, and apoJ levels increased 2.8-fold in fatty streak susceptible mice, C57BL/6J (BL/6), but not in fatty streak resistant mice, C3H/HeJ (C3H). Plasma PON activity was also significantly decreased, and apoJ levels were markedly increased in apolipoprotein E knockout mice on the chow diet, resulting in a 9.2-fold increase in the apoJ/PON ratio as compared to controls. Furthermore, a dramatic increase in the apoJ/PON ratio (over 100-fold) was observed in LDL receptor knockout mice when they were fed a 0.15%-cholesterol-enriched diet. Injection of mildly oxidized LDL (but not native LDL) into BL/6 mice (but not in C3H mice) on a chow diet resulted in a 59% decrease in PON activity (P < 0.01) and a 3.6-fold increase in apoJ levels (P < 0.01). When an acute phase reaction was induced in rabbits, or the rabbits were placed on an atherogenic diet, hepatic mRNA for apoJ was increased by 2.7-fold and 2.8-fold, respectively. Treatment of HepG2 cells in culture with mildly oxidized LDL (but not native LDL) resulted in reduced mRNA levels for PON (3.0-fold decrease) and increased mRNA levels for apoJ (2.0-fold increase). In normolipidemic patients with angiographically documented coronary artery disease who did not have diabetes and were not on lipid-lowering medication (n = 14), the total cholesterol/HDL cholesterol ratio was 3.1+/-0.9 as compared to 2.9+/-0.4 in the controls (n = 19). This difference was not statistically significant. In contrast, the apoJ/PON ratio was 3.0+/-0.4 in the patients compared to 0.72+/-0.2 in the controls (P < 0.009). In a subset of these normolipidemic patients (n = 5), the PON activity was low (48+/-6.6 versus 98+/-17 U/ml for controls; P < 0.009), despite similar normal HDL levels, and the HDL from these patients failed to protect against LDL oxidation in co-cultures of human artery wall cells. We conclude that: (a) mildly oxidized LDL can induce an increased apoJ/PON ratio, and (b) the apoJ/PON ratio may prove to be a better predictor of atherosclerosis than the total cholesterol/HDL cholesterol ratio.
Geometry of binding of the benzamidine‐ and arginine‐based inhibitors <i>N</i><sup>α</sup>‐(2‐naphthyl‐sulphonyl‐glycyl)‐<scp>dl</scp>‐<i>p</i>‐amidinophenylalanyl‐piperidine (NAPAP) and (2<i>R</i>,4<i>R</i>)‐4‐methyl‐1‐[<i>N</i><sup>α</sup>‐(3‐methyl‐1,2,3,4‐tetrahydro‐8‐quinolinesulphonyl)‐<scp>l</scp>‐arginyl]‐2‐piperidine carboxylic acid (MQPA) to human α‐thrombin (1990)

The X-ray crystal structure of the trypsin complex formed with N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-piper idine (NAPAP) was determined with X-ray data to 0.18-nm resolution and crystallographically refined. NAPAP binds into the active site of trypsin in a quite compact form: the p-amidinophenylalanine moiety of the D-stereoisomer binds into the specificity pocket; the glycyl group is hydrogen bonded with Gly216; the naphthyl group stands perpendicular to the indole moiety of Trp215; the piperidine ring is tightly packed between this naphthyl moiety and His57; in consequence the carboxy-terminal amido bond of NAPAP is located in such a way that it is not susceptible to the active-site Ser195. NAPAP and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) [Matzusaki, T., Sasaki, C., Okumura, C. & Umeyama (1989) J. Biochem. (Tokyo) 105, 949-952] were transferred in their trypsin-binding conformations to human alpha-thrombin [Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R. & Hofsteenge, J. (1989) EMBO J. 8. 3467 - 3475] and energy minimized. Both synthetic inhibitors fit perfectly into the much more restricted active site of thrombin. The accommodation of the S-aryl moieties in the 'aryl-binding site' and of the piperidine rings in the S2 subsite of thrombin are particularly favorable. The preference of thrombin for distinctly substituted piperidine derivatives and its generally higher (compared with trypsin) affinity for benzamidine and arginine-based inhibitors can be accounted for by these thrombin inhibitor models.
Mutactimycin AP, a New Mutactimycin Isolated from an Actinobacteria from the Atacama Desert (2022)

Bacteria belonging to the phylum <i>Actinobacteria</i> are a very good source of antibiotics, and indeed dominate the current clinical antibiotic space. This paper reports Mutactimycin AP, a new compound belonging to an anthracycline-type family of antibiotics, isolated from a <i>Saccharothrix sp.</i> This actinobacterial strain was isolated from the rhizosphere of lupine plants growing in the extreme hyper-arid Atacama Desert. Structural characterization was carried out using electrospray ionization-mass spectrometry (ESI-MS) and NMR spectroscopy in combination with molecular modelling. The compound was tested against the ESKAPE pathogens, where it showed activity against MRSA and five strains associated with bovine mastitis, where it showed activity against <i>Enterococcus pseudoavium</i> and <i>Staphylycoccus Aureus subsp. Aureus</i>.
Sleep Architecture in Term and Preterm Infants Beyond the Neonatal Period: The Influence of Gestational Age, Steroids, and Ventilatory Support (2005)

With few exceptions, asymptomatic premature infants do not exhibit significant delays in sleep architecture compared with term infants at comparable postmenstrual age. The preterm infant with an early gestational age and morbidity exhibited delayed sleep architecture.
Validity of Predicting VO2max Using Linear Regression of HR and VO2 From a Multi-stage, Submaximal Treadmill Test (2004)

0603 PURPOSE: The purpose of this study was to determine the validity of predicting VO2max using linear regression of heart rate and oxygen consumption obtained during a submaximal treadmill test with multiple stages. METHODS: A total of 40 (20 males, 20 females) Low Risk (ACSM GETP 6th Ed.) subjects (28.9 ± 7.1 years, Height = 170.2 ± 11.3 cm, Weight = 68.4 ± 12.5 kg, Body Fat = 16.6 ± 5.3%, BMI = 23.5 ± 2.6 kg/m2) completed 2 maximal and 1 submaximal treadmill tests. The treadmill test had a 4 minute warmup stage followed by 2 minute stages that increased in workload by approximately 1.5 METs. Oxygen consumption was measured during each test, and measured VO2max was determined using standard criteria from the 2 max tests (CV = 3.8%). Predicted VO2max was determined by linear regression of heart rate from ECG and VO2 using age-predicted maximum heart rate. VO2max was predicted for each individual using all HR and VO2 pairs and by eliminating heart rates below 100, 110, and 120 bpm, respectively. The accuracy of predicting VO2max using measured HRmax was also determined. The relationship of predicted VO2max to measured VO2max was determined with Pearson's Product Moment Correlation. RESULTS: Mean measured VO2max was 2.785 ± 0.680 L/min, and the most accurate prediction of VO2maxoccurred when heart rates below 110 bpm were excluded from the linear regression and measured HRmax was used (Mean VO2max = 2.681 ± 0.691 L/min, R = 0.931, SEE = 0.252 L/min). Use of age-predicted HRmax with heart rates below 110 bpm excluded also resulted in highly accurate predictions of VO2max (Mean VO2max = 2.767 ± 0.744 L/min, R = 0.922, SEE = 0.266 L/min). CONCLUSIONS: The results of this study demonstrate that a very strong positive correlation exists between measured VO2max and VO2max predicted using linear regression of HR and VO2 and age-predicted HR, and support the use of a submaximal treadmill test and linear regression to accurately predict maximal oxygen consumption in low risk adults.
Figure S7 from Colony-Stimulating Factor 1 Receptor (CSF1R) Activates AKT/mTOR Signaling and Promotes T-Cell Lymphoma Viability (2023)

&lt;p&gt;Proposed model for oncogenic activity of CSF1R.&lt;/p&gt;
Multiple Techniques for Size Determination of Generalized Modules for Membrane Antigens from <i>Salmonella typhimurium</i> and <i>Salmonella enteritidis</i> (2017)

In the last years, outer membrane vesicles have attracted a lot of attention for the development of vaccines against bacterial pathogens. Extracellular vesicles can be obtained in high yields by genetic mutations, resulting in generalized modules for membrane antigens (GMMA). Methods to check the quality, consistency of production, and stability of GMMA vaccines are of fundamental importance. In this context, analytical methods for size distribution determination and verifying the integrity and possible aggregation of GMMA particles are strongly needed. Herein, GMMA particle size distribution has been evaluated by means of three different techniques. Dynamic light scattering (DLS), multiangle light scattering (MALS) coupled with high-performance liquid chromatography-size exclusion chromatography (SEC), and nanoparticle tracking analysis (NTA) have been compared to characterize GMMA from different mutants of <i>Salmonella typhimurium</i> and <i>Salmonella enteritidis</i> strains. We found that the presence of O-antigen chains on GMMA determined higher <i>Z</i>-average diameters by DLS compared to size estimation by MALS and that the hydrodynamic diameter increased with the number of O-antigen chains per GMMA particle. In the case of SEC-MALS, the size of the whole population better reflects the size of the most abundant particles, whereas DLS diameter is more influenced by the presence of larger particles in the sample. SEC-MALS and NTA are preferable to DLS for the analysis of bimodal samples, as they better distinguish populations of different size. MALS coupled to a size exclusion chromatography module also allows checking the purity of GMMA preparations, allowing determination of generally occurring contaminants such as soluble proteins and DNA. NTA permits real-time visualization with simultaneous tracking and counting of individual particles, but it is deeply dependent on the choice of data analysis parameters. All of the three techniques have provided complementary information leading to a more complete characterization of GMMA particles.
The sum rules for the spin dependent structure functions corresponding to the moment at $n=0$ (2007)

Sum rules for the spin dependent structure functions corresponding to the moment at $n=0$ derived from the current algebra based on the canonical quantization on the null-plane are reviewed.
Electrocardiogram Measurement and Emotion Estimation of Working Dogs (2022)

Physiological measurements of dogs' emotional states during human-animal interactions are essential for understanding the underlying biological relationship. Heart rate measured by electrocardiogram (ECG) can be used for the physiological measurement of emotional state. Soft disposable electrodes, which can be purchased commercially and reduce the risk of an injury on hitting objects, are used to measure the heart rate during working dogs' exercise. However, the heart rate measurements using soft disposable electrodes in M-X lead layout are unstable due to the detachment of electrodes during intensive movement. In addition, the collection of accurately labeled ECG data, which reflects the emotion of the working dog during exercise, is a key issue to conduct reliable estimation and visualization of the working dog's emotional states. In this paper, we propose an innerwear that fixes soft disposable electrodes in M-X lead layout on a dog's body for measuring the heart rates of exercising dogs, even during intense movement. We experimentally tested the proposed method using seven dogs. Our proposed system reduced the time required to attach soft disposable electrodes by more than two-thirds and enabled the measurement of >97% of the heartbeats in exercising dogs. We also proposed a method for collecting ECG data with reliable positive/negative emotional labels of search and rescue (SAR) dogs. A combination of the collected data with the emotion estimation algorithm proposed in previous studies estimated SAR dogs' positive/negative emotions at 97.9% accuracy. The transition of the two SAR dogs' emotions during drills was visualized using the collected data.
ChemInform Abstract: In situ Investigations of Catalysts and Catalytic Reaction Mechanisms. Part 1. General Introduction and Applications of in situ MAS NMR Spectroscopy (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.