gebhart/patrepeval huggingface dataset:
Global expression profiling of <i>Bacillus subtilis</i> cells during industrial‐close fed‐batch fermentations with different nitrogen sources (2005)

A detailed gene expression analysis of industrial-close Bacillus subtilis fed-batch fermentation processes with casamino acids as the only nitrogen source and with a reduced casamino acid concentration but supplemented by ammonia was carried out. Although glutamine and arginine are supposed to be the preferred nitrogen sources of B. subtilis, we demonstrate that a combined feeding of ammonia and casamino acids supports cell growth under fed-batch fermentation conditions. The transcriptome and proteome analyses revealed that the additional feeding of ammonia in combination with a reduced amino acid concentration results in a significantly lower expression level of the glnAR or tnrA genes, coding for proteins, which are mainly involved in the nitrogen metabolism of B. subtilis. However, the mRNA levels of the genes of the ilvBHC-leuABD and hom-thrCB operons were significantly increased, indicating a valine, leucine, isoleucine, and threonine limitation under these fermentation conditions. In contrast, during the fermentation with casamino acids as the only nitrogen source, several genes, which play a crucial role in nitrogen metabolism of B. subtilis (e.g., glnAR, nasCDE, nrgAB, and ureABC), were up-regulated, indicating a nitrogen limitation under these conditions. Furthermore, increased expression of genes, which are involved in motility and chemotaxis (e.g., hag, fliT) and in acetoin metabolism (e.g., acoABCL), was determined during the fermentation with the mixed nitrogen source of casamino acids and ammonia, indicating a carbon limitation under these fermentation conditions. Under high cell density and slow growth rate conditions a weak up-regulation of autolysis genes could be observed as well as the induction of a number of genes involved in motility, chemotaxis and general stress response. Results of this study allowed the selection of marker genes, which could be used for the monitoring of B. subtilis fermentation processes. The data suggest for example acoA as a marker gene for glucose limitation or glnA as an indicator for nitrogen limitation.
Adaptive Boosting Based Personalized Glucose Monitoring System (PGMS) for Non-Invasive Blood Glucose Prediction with Improved Accuracy (2020)

In this paper, we present an architecture of a personalized glucose monitoring system (PGMS). PGMS consists of both invasive and non-invasive sensors on a single device. Initially, blood glucose is measured invasively and non-invasively, to train the machine learning models. Then, paired data and corresponding errors are divided scientifically into six different clusters based on blood glucose ranges as per the patient's diabetic conditions. Each cluster is trained to build the unique error prediction model using an adaptive boosting (AdaBoost) algorithm. Later, these error prediction models undergo personalized calibration based on the patient's characteristics. Once, the errors in predicted non-invasive values are within the acceptable error range, the device gets personalized for a patient to measure the blood glucose non-invasively. We verify PGMS on two different datasets. Performance analysis shows that the mean absolute relative difference (MARD) is reduced exceptionally to 7.3% and 7.1% for predicted values as compared to 25.4% and 18.4% for measured non-invasive glucose values. The Clarke error grid analysis (CEGA) plot for non-invasive predicted values shows 97% data in Zone A and 3% data in Zone B for dataset 1. Moreover, for dataset 2 results echoed with 98% and 2% in Zones A and B, respectively.
Cardiovascular disease related circulating biomarkers and cancer incidence and mortality: is there an association? (2021)

We observed several significant associations between circulating CVD biomarkers and cancer, supporting the idea that shared biological pathways underlie both diseases. Further investigations of specific mechanisms that lead to both CVD and cancer are warranted.
Gut Microbiome Analysis In Adult Tropical Gars ( <i>Atractosteus tropicus</i> ) (2019)

Abstract Tropical gar ( Atractosteus tropicus ), is freshwater and estuarine fish that has inhabited the Earth since the Mesozoic era, undergoing limited physiological variation ever since. This omnivorous fish is endemic to southern Mexico and part of Central America. Besides its recognized cultural and scientific relevance, the species has seen remarkable growth in its economic impact due to pisciculture. Previous studies have highlighted the role of microbial communities in fish, particularly those in the gut microbiome, in maintaining their host homeostasis or disease. In this study, we present the first report of the whole taxonomic composition of microbial communities in gut contents of adults’ A. tropicus , by sex (female/male) and origin (wild/cultivated). Using culture-independent techniques, we extracted metagenomic DNA that was used for high throughput 16S rDNA profiling by amplifying the V4 – V5 hypervariable regions of the bacterial gene. A total of 364,735 total paired-end reads were obtained on an Illumina MiSeq sequencing platform, belonging to 508 identified genera, with the most and least abundant are Cetobacterium, Edwardsiella, Serratia, Clostridium sensu stricto, Paludibacter and Campylobacter, Snodgrassella, Albirhodobacter, Lentilitoribacter , respectively. We detected that, by sex and origin, Proteobacteria, Fusobacteria, Firmicutes and Bacteroidetes phyla are the core gut microbiome of the adults’ A. tropicus . We discover the Deinococcus-Thermus phylum sequence, wildtype males only, with extremophile capacity in another freshwater fish. We also identified the species Lactococcus lactis strains CAU929 and CAU6600, Cp6 and CAU9951, Cetobacterium strain H69, Aeromonas hydrophila strains P5 and WR-5-3-2, Aeromonas sobria strain CP DC28 and Aeromonas hydrophila with probiotic potential in aquaculture within the three dominant phyla, especially in wild-type organisms.
Abstract 2365: Pharmacogenomic Application Of The Haptoglobin Genotype To Identify Individuals With Diabetes Mellitus Who Benefit From Vitamin E Supplementation: A Prospective Randomized, Double-blind, Placebo Controlled Trial (2007)

Background. Large clinical trials of antioxidant therapy with vitamin E have failed to demonstrate a decrease in cardiovascular events. However, these studies did not address possible benefit to subgroups with increased oxidative stress. Haptoglobin (Hp), a major anti-oxidant protein, is a determinant of cardiovascular events in patients with diabetes mellitus (DM). The Hp gene is polymorphic with two common alleles, 1 and 2. The Hp 2 allelic protein product provides inferior anti-oxidant protection as compared to the Hp 1 allelic product. In a retrospective analysis of HOPE participants with DM and the Hp 2–2 genotype, vitamin E significantly reduced the incidence of myocardial infarction and cardiovascular death. We sought to validate this observation in a prospective trial. Methods and Results. 984 DM individuals with the Hp 2–2 genotype were randomized and treated with either natural source vitamin E (400IU/day) or placebo. The primary composite outcome was non-fatal myocardial infarction, stroke and cardiovascular death. The study was intended to last 4 years with initial evaluation of endpoints scheduled 12 months after enrollment of the first patient. At the initial evaluation, the primary composite outcome was significantly reduced in patients receiving vitamin E compared to placebo (1.0% vs. 3.8%, p=0.004). This was predominately due to a significant decrease in the incidence of non-fatal myocardial infarction (0.2% vs. 2.1%, p=0.004) and led to early termination of the study. Conclusions . Vitamin E supplementation appears to reduce cardiovascular events in individuals with DM and the Hp 2–2 genotype. (ClinicalTrials.gov number NCT00220831 ).
DocParser: End-to-end OCR-free Information Extraction from Visually Rich Documents (2023)

Information Extraction from visually rich documents is a challenging task that has gained a lot of attention in recent years due to its importance in several document-control based applications and its widespread commercial value. The majority of the research work conducted on this topic to date follow a two-step pipeline. First, they read the text using an off-the-shelf Optical Character Recognition (OCR) engine, then, they extract the fields of interest from the obtained text. The main drawback of these approaches is their dependence on an external OCR system, which can negatively impact both performance and computational speed. Recent OCR-free methods were proposed to address the previous issues. Inspired by their promising results, we propose in this paper an OCR-free end-to-end information extraction model named DocParser. It differs from prior end-to-end approaches by its ability to better extract discriminative character features. DocParser achieves state-of-the-art results on various datasets, while still being faster than previous works.
Closed loop adaptive system with Hartmann wavefront sensor for CO&lt;inf&gt;2&lt;/inf&gt; laser radiation correction (2014)

Summary form only given: In this paper we consider the design and realization of wide aperture adaptive system to correct for high power CW CO2 laser radiation. Two new approaches for development of the wavefront sensors to measure 10 μ laser radiation are considered.
Glycyrrhizin, inhibitor of high mobility group box-1, attenuates monocrotaline-induced pulmonary hypertension and vascular remodeling in rats. (2014)

Background: High mobility group box-1 (HMGB1), a proinflammatory cytokine, plays a pivotal role in tissue remodeling and angiogenesis, both of which are crucial for the pathogenesis of pulmonary arterial hypertension. In this study, we explored the relationship between HMGB1 and pulmonary hypertension and whether glycyrrhizin, an inhibitor of HMGB1, attenuates disease progression in an animal model of pulmonary hypertension induced by monocrotaline sodium (MCT). Methods: After inducing pulmonary hypertension through a single subcutaneous injection of MCT (60 mg/kg) to Sprague–Dawley rats, we administered daily intraperitoneal injections of either glycyrrhizin (GLY, 50 mg/kg), an inhibitor of HMGB1, or saline (control) for either 4 or 6 weeks. Results: Expression levels of HMGB1 in serum increased from the second week after MCT injection and remained elevated throughout the experiment periods. Lung tissue levels of HMGB1 assessed by immunohistochemical staining at 4 weeks after MCT injection also increased. Chronic inhibition of HMGB1 by GLY treatment reduced the MCT-induced increase in right ventricular (RV) systolic pressure, RV hypertrophy (ratio of RV to [left ventricle+septum]), and pulmonary inflammation. MCT-induced muscularization of the pulmonary artery was also attenuated in the GLY-treated group. As assessed 6 weeks after MCT injection, the GLY-treated group exhibited increased survival (90% [18 of 20]) when compared with the control group (60% [12 of 20]; p =0.0027). Conclusions: Glycyrrhizin, an inhibitor of HMGB1, attenuates pulmonary hypertension progression and pulmonary vascular remodeling in the MCT-induced pulmonary hypertension rat model. Further studies are needed to confirm the potential of HMGB1 as a novel therapeutic target for pulmonary hypertension.
B7 blockade prevents activation-induced cell death of thymocytes (1997)

Although both B7 and its counter-receptor CD28 are expressed in the thymus, the role of B7 in thymic selection is not clear. We investigated the role of B7 in intrathymic deletion of antigen-specific T cells using a TCR transgenic model specific for antigen ovalbumin (OVA) and H-2Ad. Intraperitoneal injection of OVA induced apoptosis of thymocytes and drastic reduction of thymocyte numbers. This was significantly inhibited by co-injection of CTLA-4-Ig which blocks B7 co-stimulation. Deletion of T cells in the thymus following i.p. injection of OVA was associated with T cell pre-activation as demonstrated by T cell proliferation and cytokine production. Injection of CTLA-4-Ig blocked all these activation events and rescued thymocytes from activation-induced cell death. These results demonstrate that B7 is required for the activation-induced cell death of MHC class II-restricted thymocytes in vivo.
Cabrol perfusion graft (2000)

FIG. 1 Aortogram in left lateral projection. Figure shows the prosthetic aortic root and the Cabrol perfusion graft. No aortic regurgitation is seen. The black arrow indicates the perfusion graft and the white arrow the critical stenosis involving the anastomosis of the perfusion graft to the left main coronary artery.
Abstract 230: AT2 Receptor Agonist, Compound 21, Attenuates Pulmonary Hypertension and Associated Cardiac Pathophysiology via the Vasoprotective ACE2/Ang-(1-7)/Mas axis (2012)

Pulmonary hypertension (PH) is a devastating disease affecting the lung vasculature. Recently, we determined that increased activation of the ACE2/Ang-(1-7)/Mas axis attenuates much of the associated pathophysiology. In other models of cardiovascular disease, the beneficial effects seen with ACE2/Ang-(1-7)/Mas activation are similar to those seen by AT2 receptor (AT2R) activation. We hypothesize that activation of the AT2R, via selective agonist Compound 21 (C21), will be an effective treatment against PH. SD rats were injected with 50mg/kg of monocrotaline (MCT) at 8 weeks of age, to induce PH. Control animals were given saline. Two weeks post MCT injection, when right ventricular systolic pressures (RVSP) were significantly elevated (MCT 48.3±8.8; Control 32.0 ±2.4 mmHg), animals received 0.03mg/kg/day C21 ip (MCT+C21) or vehicle for 2 weeks. Two weeks later, RV hemodynamic parameters were measured and tissues collected. Treatment with C21 significantly reduced PH and associated cardiac pathophysiologies. The mechanism by which C21 attenuates PH may be the restored balance between the RAS vasodeleterious and vasoprotective arms. Relative quantitation of lung mRNA expression showed C21 treatment normalized the ACE/ACE2 and AT1R/AT2R ratios, and increased Mas receptors. C21 also attenuated the increase in pro-inflammatory cytokines TGF-β, TNF-α, and Il-1b. The increased expression of the vasoprotective axis and resulting decrease in inflammatory cytokines may account for reduced PH and associated cardiopathophysiology. The increases in ACE2/Mas receptor expression may indicate an underlying connection between the AT2R and the vasoprotective axis of the RAS.
Strong Resistance Against<i>Rice grassy stunt virus</i>Is Induced in Transgenic Rice Plants Expressing Double-Stranded RNA of the Viral Genes for Nucleocapsid or Movement Proteins as Targets for RNA Interference (2012)

Rice grassy stunt virus (RGSV), a member of the genus Tenuivirus, causes significant economic losses in rice production in South, Southeast, and East Asian countries. Growing resistant varieties is the most efficient method to control RGSV; however, suitable resistance genes have not yet been found in natural rice resources. One of the most promising methods to confer resistance against RGSV is the use of RNA interference (RNAi). It is important to target viral genes that play important roles in viral infection and proliferation at an early stage of viral replication. Our recent findings obtained from an RNAi experiment with Rice stripe virus (RSV), a tenuivirus, revealed that the genes for nucleocapsid and movement proteins were appropriate targets for RNAi to confer resistance against RSV. In this study, we transformed rice plants by introducing an RNAi construct of the RGSV genes for the nucelocapsid protein pC5 or movement protein pC6. All progenies from self-fertilized transgenic plants had strong resistance against RGSV infection and did not allow the proliferation of RGSV. Thus, our strategy to target genes for nucleocapsid and movement proteins for conferring viral resistance might be applicable to the plant viruses in the genus Tenuivirus.
Growth Hormone Internalization in Mitochondria Decreases Respiratory Chain Activity (2009)

Growth hormone (GH) is a signaling molecule regulating cell proliferation, differentiation and metabolism via activation of specific cell surface receptors and subsequent triggering of signal transduction pathways. This is associated with GH/GH receptor internalization and accumulation of GH in several subcellular compartments, including mitochondria. To assess the functional relevance of such mitochondrial accumulation, we first confirmed the occurrence of mitochondrial GH uptake ex vivo as early as 10 min after (125)I-GH injection to the rats. We next showed that intact (125)I-GH accumulates in mitochondrial fractions in vitro in a specific, rapid and saturable manner with an apparent affinity (K(d)) of 1.44 nM. At the electron-microscopic level, immunoreactive GH density within mitochondria increased after in vitro hormone incubation, without any modification of the sub-mitochondrial distribution pattern. The presence of GH in the inter-membrane space and at the inner membrane seen by electron microscopy was confirmed by SDS-PAGE and autoradiography after mitochondrial fractioning thus suggesting the involvement of GH in the respiration control. To test this hypothesis further, we performed polarographic and spectrophotometric assays on isolated mitochondria. These assays pointed to a direct, selective and dose-dependent effect of GH on the inhibition of succinate dehydrogenase and cytochrome C oxidase activities. The latter inhibition was in contrast with indirect, GH receptor-initiated stimulation of cytochrome C oxidase activity observed in GH-treated whole BRL cells transfected to express this receptor. Altogether, these data show that GH is specifically imported in mitochondria, where it operates a direct metabolic effect, independently of cell surface receptors and signal transduction.
Estradiol and phorbol ester cause phosphorylation of serine 118 in the human estrogen receptor. (1995)

Serine 118 is definitively identified as a major site of phosphorylation in the human estrogen receptor expressed in COS-1 cells treated with estradiol or phorbol ester. At least 30% of the estrogen receptor appears to be phosphorylated on serine 118 after treatment with estradiol or phorbol ester. Human estrogen receptor was expressed in COS-1 cells and labeled in vivo with [32P]orthophosphate in the presence of estradiol or phorbol ester. Immunopurified receptor was digested with cyanogen bromide. The most heavily labeled peptide (7 kilodaltons) was identified as amino acids 110-174 by microsequencing. Manual Edman degradation released a major portion of the 32P-label in the peptide at serine 118. A mutant with serine 118 replaced by alanine (S118A) had 80% less 32P-label in the 7 kilodalton peptide. Estrogen receptor labeled in vivo with [32P]-orthophosphate in the presence of estradiol or phorbol ester migrates electrophoretically as a doublet. The major difference between the bands is phosphorylation of serine 118 in the upshifted band. The mutant S118A does not show an upshifted band. Labeling of the estrogen receptor with [35S]methionine indicates that > or = 30% of the receptor is upshifted and suggests that > or = 30% of the receptor is phosphorylated on serine 118.
Malnutrition and risk of procedural complication in patients with atrial fibrillation undergoing catheter ablation (2021)

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Ministry of Health and Welfare of Korea Ministry of Science, ICT &amp; Future Planning of Korea Background Malnutrition is common in the elderly, even in developed countries, and increases mortality. Purpose To investigate the prevalence and prognostic value of malnutrition among patients with atrial fibrillation (AF) which is a type of metabolic disease. Methods We included 3,239 patients (age 58.5 ± 10.8 years, 73.2% male, 67.7% paroxysmal type) undergoing de novo AF catheter ablation (AFCA) between 2009 and 2020. Nutritional status was assessed using controlling nutritional status (CONUT) score. The associations between malnutrition and the risk of AFCA complications or long-term rhythm outcome were evaluated by multivariable logistic regression. Results Among 3,239 patients, 1,005 (31.0%) patients had malnutrition; 991 (30.6%) with mild (CONUT scores 2-4) and 14 (0.4%) with moderate-to-severe (CONUT scores ≥5) malnutrition. Overall complication rates after AFCA were 3.3% in normal nutrition, 4.2% in mild malnutrition, and 21.4% in moderate to severe malnutrition, respectively (P for trend = 0.031). Major complication rates were 1.9%, 2.6%, and 14.3% in normal nutrition, mild malnutrition, and moderate to severe malnutrition (P for trend = 0.042). After multivariable adjustment, moderate-to-severe malnutrition status was associated with increased risks of overall (OR 8.215 [2.199-30.691], P = 0.002) and major (OR 7.392 [1.568-34.837], P = 0.011) complications compared with normal nutrition. However, CONUT score did not affect the long-term rhythm outcome during the mean follow-up of 40 (interquartile range 18-74) months (log-rank P = 0.760). Conclusion Malnutrition is common in patients undergoing AFCA. Those with moderate-to-severe malnutrition status were at substantially higher risk of complications after AFCA. Abstract Figure. Overall and major complication rates
Evidence for the role of PPAR‐β/δ in the development of spinal cord injury (2010)

Evidence suggests a biological role for peroxisome proliferator activated receptor (PPAR)‐β/δ in the pathogenesis of a number of diseases. The aim of the present study was to evaluate the contribution of PPAR‐β/δ in the secondary damage following experimental spinal cord injury (SCI) in mice. Spinal cord trauma was induced by the application of vascular clips to the dura via a four‐level T5–T8 laminectomy. SCI resulted in severe trauma characterized by oedema, neutrophil infiltration, production of inflammatory mediators, tissue damage, and apoptosis. The high affinity PPAR‐β/δ agonist GW0742 (0.3 mg/kg, i.p.) 1 and 6 h after the SCI significantly reduced: (1) the degree of spinal cord inflammation and tissue injury, (2) neutrophil infiltration, (3) nitrotyrosine formation, (4) pro‐inflammmaory cytokines, (5) NF‐κB activation, (6) iNOS expression and (6) apoptosis (TUNEL staining, FasL, Bax and Bcl‐2 expression). Moreover, GW0742 significantly ameliorated the recovery of locomotory function (evaluated by motor score). In order to elucidate whether the protective effects of GW0742 are related to activation of the PPAR‐β/δ, we investigated the function of PPAR‐β/δ antagonist, GSK0660, on the protective effects of GW0742. GSK0660 (1 mg/kg i.p. 30 min prior to GW0742)significantly blunted the protective effect of the PPAR‐β/δ agonist. Our results demonstrate that GW0742 treatment reduces the development of inflammation and tissue injury associated with spinal cord trauma.
Poly-Silicon Wet Removal for Replacement Gate Integration Scheme: Impact of Process Parameters on the Removal Rate (2012)

We report in this work some process optimization effort in performing poly silicon removal for replacement gate process integration. Successful wet poly silicon removal after dummy gate patterning is not only conditioned by suitable process conditions during wet removal but is also impacted by process steps prior to gate removal A thorough evaluation of the impact on poly removal from dopants or contaminants introduced in the poly silicon by previous processing is done, resulting in an optimized integration flow with successful poly removal. This work also shows that use of diluted TMAH chemistry instead of diluted ammonia in performing poly silicon removal provides better ability in removing poly silicon especially in narrow gate structures.
Golden Rice and Beyond (2001)

Ingo Potrykus

Professor Emeritus, ETH Zurich, Switzerland; Member of Academia Europaea; and Recipient of the International Society for Plant Molecular Biology 2000 Kumho Science International Award

The term “golden rice” was coined by a Thai businessman who is active in initiatives aimed at