gebhart/patrepeval huggingface dataset:
Ambiguities and completeness of SAS data analysis: investigations of apoferritin by SAXS/SANS EID and SEC-SAXS methods (2018)

The method of small angle scattering (SAS) is widely used in the field of biophysical research of proteins in aqueous solutions. Obtaining low-resolution structure of proteins is still a highly valuable method despite the advances in high-resolution methods such as X-ray diffraction, cryo-EM etc. SAS offers the unique possibility to obtain structural information under conditions close to those of functional assays, i.e. in solution, without different additives, in the mg/mL concentration range. SAS method has a long history, but there are still many uncertainties related to data treatment. We compared 1D SAS profiles of apoferritin obtained by X-ray diffraction (XRD) and SAS methods. It is shown that SAS curves for X-ray diffraction crystallographic structure of apoferritin differ more significantly than it might be expected due to the resolution of the SAS instrument. Extrapolation to infinite dilution (EID) method does not sufficiently exclude dimerization and oligomerization effects and therefore could not guarantee total absence of dimers account in the final SAS curve. In this study, we show that EID SAXS, EID SANS and SEC-SAXS methods give complementary results and when they are used all together, it allows obtaining the most accurate results and high confidence from SAS data analysis of proteins.
Assessment of Risk and Sero-Prevalence of Helicobacter pylori Colonization among Remote Orang Asli Tribes in Peninsula Malaysia (2016)

The epidemiology of Helicobacter pylori (H. pylori) infection is related to human poverty with marked differences between developing and developed countries. Socioeconomic factors and living standards are the main determinants of the age-dependent acquisition rate of H. pylori, and consequently its prevalence. The aim of this study was to assess the risk and sero-prevalence of H. pylori colonization among Orang Asli in Peninsula Malaysia. This cross-sectional study was conducted on Orang Asli subjects in seven isolated settlements spanning across all three major tribes (Negrito, Proto Malay and Senoi) in Malaysia. Socio-demographic characteristics of the subjects were obtained through interview. Subjects were tested for H. pylori colonization based on CagA and whole cell (WC) antigen serological assays. A total of 275 subjects participated in this study. Among these subjects, 115 (44.7%) were H. pylori sero-positive with highest sero-prevalence among Negrito (65.7%). Among subjects who were H. pylori sero-positive, CagA sero positivity was also significantly higher among Negrito. The highest proportion of respondents reported to be H. pylori sero-positive was from age group 30 years old and below (57.9%), males (56.2%), Negrito (48.6%) and live in bamboo house (92.3%). The highest proportion of respondents reported to be CagA sero-positive was from age group 30 years old and below (41.4%), males (35.6%) and Negrito (48.6%). The results of this study demonstrate that H. pylori colonization can be related to age, gender, tribes and house materials and CagA sero-positive stain closely associated with age, gender and tribes.
Yearly changes in cases of acute acquired comitant esotropia during a 12-year period (2023)

This study confirmed a significant increase in the number of patients with AACE in recent years. The excessive use of smartphones may be associated with the increase in AACE.
ChemInform Abstract: KATALYTISCHE HYDROGENOLYSE VON BENZYLIDEN‐VERBINDUNGEN, DIE ENTWEDER AN ZWEI SAUERSTOFFATOME, AN ZWEI STICKSTOFFATOME ODER SOWOHL AN EIN SAUERSTOFF‐ ALS AUCH AN EIN STICKSTOFFATOM GEBUNDEN SIND (1972)

Abstract Die katalytische Hydrierung der N,N′‐Benzylidendiamine (I) an Pd/Cmit Wasserstoff in Äthanol oder Benzol liefert überwiegend die tert. Amine (II) (74 ‐ 90% Ausbeute), während die außerdem mögliche Bildung von Toluol (neben zwei Molen sekundären Amins (II) ) nur in geringem Umfang stattfindet.
Abstract 544: Hypoxia response signaling is linked to TACE resistance in hepatocellular carcinoma (HCC) patients (2017)

Abstract Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and outcome is dismal, due to tumor heterogeneity and lack of effective treatment options for patients with later stage disease. Transcatheter arterial chemoembolization (TACE) is the gold standard of therapy for patients with intermediate to locally advanced tumors. TACE delivers a high dose of chemotherapy directly to the tumor via the hepatic artery, followed by an embolizing agent to restrict tumor blood supply. However, tumor hypoxia is linked to alterations in metabolism, such as increased glycolysis (the Warburg effect), and can lead to enhanced cell survival. Several randomized control trials (RCTs) showed a survival benefit with TACE, but only with strict patient selection criteria. In Asia, TACE is also commonly used as adjuvant therapy after surgical resection, yet RCTs evaluating adjuvant TACE have shown conflicting results, likely due to patient selection and stratification. We hypothesize that tumor gene expression is predictive of response following TACE, and that differential cellular metabolism resembling a hypoxic phenotype prior to treatment is responsible for TACE resistance. We retrospectively analyzed gene expression data in treatment-naive tumor tissue from a cohort of Chinese patients who received TACE. Using hierarchical clustering, followed by class comparison and survival risk prediction, we identified a 14-gene signature that is predictive of response vs. non-response to TACE, as measured by overall survival, independent of other clinical variables. We found that hypoxia- and glycolysis-related genes are enriched among differentially expressed genes in TACE Responders vs. Non-Responders, and that hypoxia master regulator HIF-1α and hypoxia target gene VEGF are significantly up-regulated in Non-Responders. We determined that a key glycolysis gene is up-regulated in Non-Responders, and conversely, two rate-limiting genes involved in gluconeogenesis, the pathway opposing glycolysis, are up-regulated in Responders. We also examined metabolomic data from the TACE cohort, and found an enrichment of glycolysis-related metabolites in Non-Responders, and gluconeogenesis-related metabolites in Responders. Further investigation will be required to connect altered glucose metabolism to TACE resistance and to determine driver genes linking hypoxia and metabolism, which, together with our 14-gene signature, may serve as a stratification tool to guide personalized treatment modalities for HCC patients. Citation Format: Valerie Fako, Joyce Lee, Tan-To Cheung, Irene O. Ng, Xin W. Wang. Hypoxia response signaling is linked to TACE resistance in hepatocellular carcinoma (HCC) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 544. doi:10.1158/1538-7445.AM2017-544
1H NMR study of cortex neurons and cerebellar granule cells on microcarriers and their PCA extracts: Lactate production under hypoxia (1992)

Lactate production of 6-day-old cerebral cortex neurons and 7-day-old cerebellar granule cells from mouse brain attached to cytodex 3 microcarriers was studied as a function of time, under hypoxic conditions using 1H NMR. Perchloric acid extracts of both cell types were prepared and 1H NMR spectra showed compounds characteristic for these neurons. In particular the granule cell extracts showed a large amount of glutamate as expected from biochemical experiments, whereas the cortex neurons showed a large amount of 4-aminobutyric acid.
A New Methodology for Predicting Fatigue Properties of Bearing Steels: From X-Ray Micro-Tomography and Ultrasonic Measurements to the Bearing Lives Distribution (2010)

Abstract This work aims at developing a new methodology for predicting the distribution of fatigue lives of bearings versus steel microstructure, namely, concentration, morphology, and properties of residual inclusions in steel. On the experimental side, X-ray micro-tomography and high frequency ultrasonic testing are used to provide the required inclusion characteristics. A physically based model is used to compute the number of cycles to crack nucleation and crack propagation up to the surface. For the statistics predictions, the inclusions and/or stringers are distributed randomly in the bearing steel according to the concentration of stringers provided by ultrasonic data. The distributions of the fatigue lives predicted by the model are compared successfully to the experimental distributions determined by fatigue tests performed on flat washer machines. Finally, it is shown that the model is able to predict the influence of the orientation of stringers on the fatigue lives.
Smooth YBa2Cu3O7−x thin films prepared by pulsed laser deposition in O2/Ar atmosphere (1994)

We report on pulsed laser deposition of YBa2Cu3O7−x in a diluted O2/Ar gas resulting in thin epitaxial films which are almost outgrowth-free. Films were deposited on SrTiO3 or MgO substrates around 800 °C at a total chamber pressure of 1.0 mbar, varying the argon partial pressure from 0 to 0.6 mbar. The density of boulders and outgrowths usual for laser deposited films varies strongly with Ar pressure: the outgrowth density is reduced from 1.4×107 to 4.5×105 cm−2 with increasing Ar partial pressure, maintaining a critical temperature Tc,zero≊90 K and a transport critical current density Jc(77 K)≥106 A/cm2 by extended oxygenation time during cool down.
Sodium Alginate Oligosaccharides Attenuate Hypertension in Spontaneously Hypertensive Rats Fed a Low-Salt Diet (2012)

We investigated the effects of sodium alginate oligosaccharides (alginate) on the development of spontaneous hypertension in rats. Spontaneous hypertensive rats were treated with alginate for 7 weeks. Systolic blood pressure (SBP) and cardiovascular and kidney damage were assessed. Systolic blood pressure increased in SHRs and this elevation was attenuated with alginate treatment. The heart weight tended to decline. Alginate did not change plasma cholesterol levels or urinary sodium excretions. The slightly higher urinary protein excretion in SHRs was not changed with the treatment; however, morphologic glomerular damage was significantly attenuated. Sodium alginate oligosaccharide attenuates spontaneous hypertension in SHRs, and may help prevent early-stage kidney injury.
Increased RTV in ADHD: A Novel Approach to Detect Inattention [Florida International University] (2019)

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder and the second most common mental condition in U.S. children, affecting more than 6.1 million individuals between the ages of 2-17 years. Defined by two behavioral features - inattention and hyperactivity - identifying and studying ADHD, especially related periods of inattention, a defining feature, poses an important limitation. Recent studies have identified elevated reaction time variability (RTV) as a reliable feature of ADHD, that may be related to periods of inattention. However, the neural mechanisms behind RTV, and thereby inattention, are not well understood. The default mode network (DMN) is a functional brain system responsible for internally-directed mental processes, that is active when not engaged in cognitively demanding externally directed tasks. Activation of the DMN during active states, thus, could disrupt externally directed behavior and related neurobiological mechanisms – perhaps acting as an internal distraction. We predicted that activation in the DMN during an externally directed task will be elevated during periods of increased RTV. Further, we anticipated DMN activation to precede abnormally slow responses. We used blood-oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) while participants with and without ADHD performed a standard sustained attention to response (SART) task. We then examined the activation of the DMN during episodes of aberrant RTV, defined as reaction times more than two standard deviations from the preceding measure of variability, to ascertain the nature of the aforementioned association. The neurobiological mechanisms that are related to the attention-deficit in ADHD must be better understood to aid in diagnosis and treatment. This study aims to be the first to provide comprehensive evidence of the neural underpinnings behind increased RTV and thereby inattention in individuals with ADHD. The current system to diagnose ADHD in children is based on potentially subjective behavioral observations by parents and teachers. Identifying increased RTV as a behavioral marker of ADHD with a well-characterized neurobiological mechanism may enable a more effective and objective method of diagnosis, resulting in more successful treatment outcomes and decreased costs of care for families of children with the disorder.
Antihypertensive Properties of a Pea Protein Hydrolysate during Short‐ and Long‐Term Oral Administration to Spontaneously Hypertensive Rats (2016)

This study investigated short-term (24 h) and long-term (5 wk) systolic blood pressure (SBP)-lowering effects in spontaneously hypertensive rats (SHR) of a 5 kDa membrane pea protein hydrolysate permeate (PPH-5) produced through thermoase hydrolysis of pea protein isolate (PPI). Amino acid analysis showed that the PPH-5 had lower contents of sulfur-containing amino acids than the PPI. Size-exclusion chromatography indicated mainly low molecular weight (<10 kDa) peptides in PPH-5 but not in the PPI. The PPH-5 had renin and angiotensin converting enzyme inhibition IC50 values of 0.57 and 0.10 mg/mL (P < 0.05), respectively, and consisted mainly of peptides with 2 to 6 amino acids. Mass spectrometry analysis revealed mainly hydrophilic tetrapeptide sequences. After a single oral administration (100 mg/kg body weight) to SHR, the unheated PPI showed weakest (P < 0.05) SBP-lowering effect with a -4 mm Hg maximum when compared to -25 mm Hg for heat-treated PPI and -36 mm Hg for PPH-5. Incorporation of the PPH-5 as 0.5% or 1% (w/w) casein substitute in the SHR diet produced maximum SBP reductions of -22 or -26 mm Hg (P < 0.05), respectively after 3 wk. In comparison, the unhydrolyzed PPI produced a maximum SBP reduction of -17 mm Hg also after 3 wk. Potency of the pea products decreased in the 4th and 5th wk, though SBP values of the treated rats were still lower than the untreated control. We conclude that the antihypertensive potency of PPH-5 may have been due to the presence of easily absorbed hydrophilic peptides.
Fundamentals and experimental studies in essential oil extraction by instant autovaporisation using the instant controlled pressure drop DIC technology (2009)

International audience
Table S8 from Genomic and Epigenomic Signatures in Ovarian Cancer Associated with Resensitization to Platinum Drugs (2023)

&lt;p&gt;Table S8. deconvolution_results&lt;/p&gt;
Thermal barrier coatings for gas turbine and diesel engines (1989)

The present state of development of thin thermal barrier coatings for aircraft gas turbine engines and thick thermal barrier coatings for truck diesel engines is assessed. Although current thermal barrier coatings are flying in certain gas turbine engines, additional advances will be needed for future engines. Thick thermal barrier coatings for truck diesel engines have advanced to the point where they are being seriously considered for the next generation of engine. Since coatings for truck engines is a young field of inquiry, continued research and development efforts will be required to help bring this technology to commercialization.
Guided Variational Autoencoder for Speech Enhancement with a Supervised Classifier (2021)

Recently, variational autoencoders have been successfully used to learn a probabilistic prior over speech signals, which is then used to perform speech enhancement. However, variational autoencoders are trained on clean speech only, which results in a limited ability of extracting the speech signal from noisy speech compared to supervised approaches. In this paper, we propose to guide the variational autoencoder with a supervised classifier separately trained on noisy speech. The estimated label is a high-level categorical variable describing the speech signal (e.g. speech activity) allowing for a more informed latent distribution compared to the standard variational autoencoder. We evaluate our method with different types of labels on real recordings of different noisy environments. Provided that the label better informs the latent distribution and that the classifier achieves good performance, the proposed approach outperforms the standard variational autoencoder and a conventional neural network- based supervised approach.
Reduced insulin-like growth factor binding protein-1 (IGFBP-1) levels correlate with increased cardiovascular risk in non-insulin dependent diabetes mellitus (NIDDM) (1996)

IGF-I and -II levels are altered in patients with atherogenic lipid profiles and may contribute to the development of macrovascular disease in NIDDM. We examined cardiovascular risk factors, IGF-I, IGF-II and IGFBP-1 in 74 NIDDM patients analysed as a whole group and according to treatment type. IGF-I was not significantly associated with cardiovascular risk factors but IGF-II levels correlated positively with total and LDL cholesterol most markedly in the diet treated group (0.72, p
Varying intensity of postremission therapy in acute myeloid leukemia (1992)

The Eastern Cooperative Oncology Group (ECOG) conducted a randomized trial in patients less than or equal to 65 years old (median, 44 years) to determine whether increasing the intensity of postremission therapy in acute myeloid leukemia (AML) would improve the outcome. After uniform induction therapy, patients in complete remission (CR) who were less than 41 years old and who had a histocompatible sibling underwent allogeneic bone marrow transplantation (alloBMT) (54 patients). The remainder of patients in CR were randomized to receive either 2 years of continuous outpatient maintenance therapy with cytarabine and 6-thioguanine (83 patients) or a single course of inpatient consolidation therapy consisting of 6 days of high-dose cytarabine plus 3 days of amsacrine (87 patients). The median duration of follow-up is now 4 years, and patients are included in the analyses of outcome regardless of whether they relapsed before starting the intended treatment. Four-year event-free survival (EFS) was 27% +/- 10% for consolidation therapy versus 16% +/- 8% for maintenance therapy (P = .068) and 28% +/- 11% versus 15% +/- 9% (P = .047) in patients less than 60 years old. The outcome for patients receiving alloBMT was compared with the subset of patients less than 41 years old who received consolidation therapy (N = 29) or maintenance therapy (N = 21). Four-year EFS was 42% +/- 13% for alloBMT, 30% +/- 17% for consolidation therapy, and 14% +/- 15% for maintenance therapy. AlloBMT had a significantly better EFS (P = .013) than maintenance therapy, but was not different from consolidation therapy. In patients less than 41 years old, 4-year survival after alloBMT (42% +/- 14%) did not differ from consolidation therapy (43% +/- 18%), but both were significantly better than maintenance therapy (19% +/- 17%), P = .047 and .043, respectively. The mortality rate for maintenance therapy was 0%, consolidation therapy, 21%; and alloBMT, 36%. Consolidation therapy caused an especially high mortality rate in the patients greater than or equal to 60 years old (8 of 14 or 57%). The toxicity of combined high-dose cytarabine and amsacrine is unacceptable, especially in older patients, and alternative approaches to consolidation therapy such as high-dose cytarabine alone need to be tested. In AML, a single course of consolidation therapy or alloBMT after initial CR produces better results than lengthy maintenance therapy. Although EFS and survival of alloBMT and consolidation therapy do not differ significantly, a larger number of patients need to be studied before concluding that they are equivalent.
Tau, amyloid, and cascading network failure across the Alzheimer's disease spectrum (2017)

Functionally related brain regions are selectively vulnerable to Alzheimer's disease pathophysiology. However, molecular markers of this pathophysiology (i.e., beta-amyloid and tau aggregates) have discrepant spatial and temporal patterns of progression within these selectively vulnerable brain regions. Existing reductionist pathophysiologic models cannot account for these large-scale spatiotemporal inconsistencies. Within the framework of the recently proposed cascading network failure model of Alzheimer's disease, however, these large-scale patterns are to be expected. This model postulates the following: 1) a tau-associated, circumscribed network disruption occurs in brain regions specific to a given phenotype in clinically normal individuals; 2) this disruption can trigger phenotype independent, stereotypic, and amyloid-associated compensatory brain network changes indexed by changes in the default mode network; 3) amyloid deposition marks a saturation of functional compensation and portends an acceleration of the inciting phenotype specific, and tau-associated, network failure. With the advent of in vivo molecular imaging of tau pathology, combined with amyloid and functional network imaging, it is now possible to investigate the relationship between functional brain networks, tau, and amyloid across the disease spectrum within these selectively vulnerable brain regions. In a large cohort (n = 218) spanning the Alzheimer's disease spectrum from young, amyloid negative, cognitively normal subjects to Alzheimer's disease dementia, we found several distinct spatial patterns of tau deposition, including 'Braak-like' and 'non-Braak-like', across functionally related brain regions. Rather than arising focally and spreading sequentially, elevated tau signal seems to occur system-wide based on inferences made from multiple cross-sectional analyses we conducted looking at regional patterns of tau signal. Younger age-of-disease-onset was associated with 'non-Braak-like' patterns of tau, suggesting an association with atypical clinical phenotypes. As predicted by the cascading network failure model of Alzheimer's disease, we found that amyloid is a partial mediator of the relationship between functional network failure and tau deposition in functionally connected brain regions. This study implicates large-scale brain networks in the pathophysiology of tau deposition and offers support to models incorporating large-scale network physiology into disease models linking tau and amyloid, such as the cascading network failure model of Alzheimer's disease.