gebhart/patrepeval huggingface dataset:
Structural and Mechanistic Studies on the Inhibition of the Hypoxia-inducible Transcription Factor Hydroxylases by Tricarboxylic Acid Cycle Intermediates (2006)

In humans both the levels and activity of the alpha-subunit of the hypoxia-inducible transcription factor (HIF-alpha) are regulated by its post-translation hydroxylation as catalyzed by iron- and 2-oxoglutarate (2OG)-dependent prolyl and asparaginyl hydroxylases (PHD1-3 and factor-inhibiting HIF (FIH), respectively). One consequence of hypoxia is the accumulation of tricarboxylic acid cycle intermediates (TCAIs). In vitro assays were used to assess non-2OG TCAIs as inhibitors of purified PHD2 and FIH. Under the assay conditions, no significant FIH inhibition was observed by the TCAIs or pyruvate, but fumarate, succinate, and isocitrate inhibited PHD2. Mass spectrometric analyses under nondenaturing conditions were used to investigate the binding of TCAIs to PHD2 and supported the solution studies. X-ray crystal structures of FIH in complex with Fe(II) and fumarate or succinate revealed similar binding modes for each in the 2OG co-substrate binding site. The in vitro results suggest that the cellular inhibition of PHD2, but probably not FIH, by fumarate and succinate may play a role in the Warburg effect providing that appropriate relative concentrations of the components are achieved under physiological conditions.
Fluorescence-Activated Cell Sorting Analysis of Mitochondrial Content, Membrane Potential, and Matrix Oxidant Burden in Human Lymphoblastoid Cell Lines (2011)

Fluorescence-activated cell sorting (FACS) permits specific biologic parameters of cellular populations to be quantified in a high-throughput fashion based on their unique fluorescent properties. Relative quantitation of mitochondrial-localized dyes in human cells using FACS analysis allows sensitive analysis of a variety of mitochondrial parameters including mitochondrial content, mitochondrial membrane potential, and matrix oxidant burden. Here, we describe protocols that utilize FACS analysis of human lymphoblastoid cell lines (LCL) for relative quantitation of mitochondrial-localized fluorescent dye intensity. The specific dyes described include MitoTracker Green FM to assess mitochondrial content, tetramethylrhodamine ethyl ester (TMRE) to assess mitochondrial membrane potential, and MitoSOX Red to assess mitochondrial matrix oxidant burden. Representative results of FACS-based mitochondrial analyses demonstrate the variability of these three basic mitochondrial parameters in LCLs from healthy individuals, as well as the sensitivity of applying FACS analysis of LCLs to study the effects of pharmacologic induction and scavenging of oxidant stress.
Development and Validation of an Administrative Codes Algorithm to Identify Abdominal Surgery and Bowel Obstruction in Patients With Inflammatory Bowel Disease (2021)

CPT and ICD codes for abdominal surgery and obstructive complications can be accurately utilized in IBD patients in VA.
Yeast-Derived Formulations Are Differentially Fermented by the Canine and Feline Microbiome As Assessed in a Novel <i>In Vitro</i> Colonic Fermentation Model (2020)

The current study evaluated the effect of five yeast-derived formulations (T1-T5) on microbial metabolism and composition of the canine and feline gut microbiota using a novel <i>in vitro</i> colonic incubation approach. This novel <i>in vitro</i> model allowed for growth of the entire spectrum of dog- and cat-derived bacteria from the inoculum, thus offering an excellent platform to evaluate effects of nutritional interventions on the gut microbiota. Further, yeast-derived ingredients differentially increased production of acetate, propionate, butyrate, ammonium, and branched short-chain fatty acids, with T5 and T1 consistently stimulating propionate and butyrate, respectively. 16S-targeted Illumina sequencing coupled with flow cytometry provided unprecedented high-resolution quantitative insights in canine and feline microbiota modulation by yeast-derived ingredients, revealing that effects on propionate production were related to Prevotellaceae, Tannerellaceae, Bacteroidaceae, and Veillonellaceae members, while effects on butyrate production were related to Erysipelotrichaceae, Lachnospiraceae, Ruminococcaceae, and Fusobacteriaceae. Overall, these findings strengthen the health-promoting potential of yeast-derived ingredients.
Health Effects of Residents Exposed to <i>Stachybotrys</i> in Water-damaged Houses in Finland (2010)

This paper describes the medical examination of 26 residents living in Finnish houses with indoor air problems and Stachybotrys contamination. Environmental samples were obtained from patients at the Clinic for Indoor Air Health Problems where special attention was paid to the presence of possible health effects caused by moulds, especially by Stachybotrys chartarum. S. chartarum was isolated and identified in samples collected from the homes or work places of 26 patients admitted for respiratory illness. Most of the isolated S. chartarum strains showed slight toxicity when tested in a cell culture but only two were found to produce satratoxins G and H. Diverse spectra of non-specific symptoms were reported by the 26 patients and irritation of the upper airways and eyes were the most common. Lymphocytosis was found in the bronchoalveolar lavage fluid in 6 of the 10 patients who underwent bronchofibreoscopy. IgG antibodies against S. chartarum were determined in the serum of 20 patients and increased levels were found in 10 of them. The symptoms or the severity of the illnesses were not associated with the IgG level. Patients were followed-up for 1—5 years, with a few patients experiencing persistent health effects such as severe eye irritation. We conclude that some of the symptoms may be caused by Stachybotrys exposure but a causal relationship could not be shown. Lymphocytosis was found in bronchial lavage in half of the patients examined by bronchoscopy suggesting that immunoactivation in lungs may quite often occur from exposure to water-damaged microbes.
Maximally Flat and Least-Square Co-Design of Variable Fractional Delay Filters for Wideband Software-Defined Radio (2018)

This paper describes improvements in a Farrow-structured variable fractional delay (FD) Lagrange filter for all-pass FD interpolation. The main idea is to integrate the truncated sinc into the Farrow structure of a Lagrange filter, in order that a superior FD approximation in the least-square sense can be achieved. Its primary advantages are the lower level of mean-square-error (MSE) over the whole FD range and the reduced implementation cost. Extra design parameters are introduced for making the trade-off between MSE and maximal flatness under different design requirements. Design examples are included, illustrating an MSE reduction of [Formula: see text] compared to a classical Farrow-structured Lagrange interpolator while the implementation cost is reduced. This improved variable FD interpolation system is suitable for many applications, such as sample rate conversion, digital beamforming and timing synchronization in wideband software-defined radio (SDR) communications.
Feasibility of robot‐assisted submandibular gland resection via retroauricular approach: Preliminary results (2012)

Robot-assisted SMG resection was feasible without any significant complications and satisfactory cosmetic results. The safety and oncologic outcome of the procedure should be verified with larger number of patients and longer follow up period.
Field Application of Composite Post-Tensioning System (2014)

The Michigan Department of Transportation (MDOT) is working to develop design standards for transverse post-tensioning of box beams. When adjacent precast prestressed concrete box beams used for bridge structures are topped with a cast-in-place concrete deck, longitudinal cracking above the joints between the beams can lead to deterioration. Two field applications of box-beam bridges with transverse ties have been completed, one in Detroit, the other in Jackson, Michigan.
Performance Analysis of a Five-phase Synchronous Reluctance Motor Connected to Matrix Converter (2021)

This paper analyses the performance of a high reliability multiphase electric drive system. The drive system consists of a five-phase synchronous reluctance machine (SynRM) connected to a three to five-phase matrix converter (MC). In this system, there is no vulnerable electrolytic DC-link capacitors, which considered a point of failure in conventional electric drive systems. The indirect space vector modulation (SVM) is used to control the five-phase MC. Indirect SVM deals with the five-phase MC as a virtual two-stage converter consisting of a virtual DC link, a virtual rectifier stage and a virtual inverter stage. In addition, a modified closed loop field-oriented control based on the indirect SVM is proposed to control the five-phase SynRM. The performance of the drive system is analyzed at different operating conditions.
IL-21 Is a Key Regulator Coordinating Multiple Immune Responses in Chronic Allograft Rejection. (2014)

Aims: IL-21 is critical for developing chronic autoimmune and anti-viral responses. However, its role in cardiac allograft rejection is unknown. Our recent work has shown that IL-21 signaling is critical for maintaining T-cell survival under IL-2 deprivation conditions (in press) and in sustaining autoimmune responses to islets (in preparation). We, thus hypothesize that IL-21 is necessary in promoting chronic allo-immune responses during cardiac allograft rejection. Methods: We performed heart transplants in IL21-/-, BATF-/-, and wild-type B6 mice recipients with or without transient therapy with an IL-21 receptor fusion protein (IL-21R.Fc). The donors of heart allografts were either fully-mismatched Balb/c mice or class-II mismatched Bm12 mice. Results: We showed that donor Bm12 heart allografts were protected from chronic rejection in IL21-/- mice (>100 days) but not control B6 mice (56.3 ± 22.9 days) (n=10; p<0.001). In contrast, both IL-21-/- and B6 mice acutely rejected fully mismatched Balb/c cardiac allografts (<12 days; n=6; p=NS). The protection from chronic rejection in IL-21-/- recipients was confirmed with reductions in pathological (GAD) scores, intimal thickening [figure 1], and vascular infiltration (B-cells, T-cells & macrophages). The IL21-/- recipients also displayed reduced anti-donor responses as well as significantly lower IFN-g (but not IL-2) production by alloreactive T-cells. Importantly, the smooth muscle actin (SMAC) staining showed loss of SMAC in the arterial smooth muscle bed and abnormal accumulation in cardiomyocytes of wild-type recipients, whereas in IL21-/- mice the SMAC was intact. Additionally, the central role of IL-21 signaling in chronic rejection was validated in BATF-/- as well as IL-21R.Fc treated B6 recipients of Bm12 heart allografts, showing protection from chronic rejection (>100 days). Conclusions: We show a novel role for IL-21 signaling in promoting multiple immune responses during chronic allograft rejection. We propose that IL-21 is a key regulator of chronic allo-responses and contributes to endothelial cells and/or vascular SMC damage.Figure: No Caption available.
Assays for the Rapid and Specific Identification of North American <i>Yersinia Pestis</i> and the Common Laboratory Strain CO92 (2008)

We present TaqMan-minor groove binding (MGB) assays for an SNP that separates the Yersinia pestis strain CO92 from all other strains and for another SNP that separates North American strains from all other global strains.
Aerobic Oxidation of 5‐(Hydroxymethyl)furfural Cyclic Acetal Enables Selective Furan‐2,5‐dicarboxylic Acid Formation with CeO<sub>2</sub>‐Supported Gold Catalyst (2018)

Abstract The utilization of 5‐(hydroxymethyl)furfural (HMF) for the large‐scale production of essential chemicals has been largely limited by the formation of solid humin as a byproduct, which prevents the operation of stepwise batch‐type and continuous flow‐type processes. The reaction of HMF with 1,3‐propanediol produces an HMF acetal derivative that exhibits excellent thermal stability. Aerobic oxidation of the HMF acetal with a CeO 2 ‐supported Au catalyst and Na 2 CO 3 in water gives a 90–95 % yield of furan 2,5‐dicarboxylic acid, an increasingly important commodity chemical for the biorenewables industry, from concentrated solutions (10–20 wt %) without humin formation. The six‐membered acetal ring suppresses thermal decomposition and self‐polymerization of HMF in concentrated solutions. Kinetic studies supported by DFT calculations identify two crucial steps in the reaction mechanism, that is, the partial hydrolysis of the acetal into 5‐formyl‐2‐furan carboxylic acid involving OH − and Lewis acid sites on CeO 2 , and subsequent oxidative dehydrogenation of the in situ generated hemiacetal involving Au nanoparticles. These results represent a significant advance over the current state of the art, overcoming an inherent limitation of the oxidation of HMF to an important monomer for biopolymer production.
Lipopolysaccharide from Gut‐Associated Lymphoid‐Tissue‐Resident <i>Alcaligenes faecalis</i>: Complete Structure Determination and Chemical Synthesis of Its Lipid A (2021)

Alcaligenes faecalis is the predominant Gram-negative bacterium inhabiting gut-associated lymphoid tissues, Peyer's patches. We previously reported that an A. faecalis lipopolysaccharide (LPS) acted as a weak agonist for Toll-like receptor 4 (TLR4)/myeloid differentiation factor-2 (MD-2) receptor as well as a potent inducer of IgA without excessive inflammation, thus suggesting that A. faecalis LPS might be used as a safe adjuvant. In this study, we characterized the structure of both the lipooligosaccharide (LOS) and LPS from A. faecalis. We synthesized three lipid A molecules with different degrees of acylation by an efficient route involving the simultaneous introduction of 1- and 4'-phosphates. Hexaacylated A. faecalis lipid A showed moderate agonistic activity towards TLR4-mediated signaling and the ability to elicit a discrete interleukin-6 release in human cell lines and mice. It was thus found to be the active principle of the LOS/LPS and a promising vaccine adjuvant candidate.
The conservative management of Paget's disease of the breast with radiotherapy Presented in part at the 38th Annual Meeting of the American Society for Therapeutic Radiology and Oncology, Los Angeles, California, October 27-30, 1996. (1997)

BACKGROUND The purpose of this study was to evaluate the feasibility of breast-conserving therapy involving limited surgery and definitive radiotherapy as a treatment for Paget's disease, and to determine the disease free and overall survival associated with this approach. METHODS The authors retrospectively reviewed the charts of all patients treated during the period 1980-1994 for Paget's disease of the breast who did not present with a palpable mass or mammographic density. Through a collaborative review, 30 cases were identified. A biopsy confirming the presence of typical Paget's cells was performed on all patients. All patients received external beam radiotherapy to the breast, with a median dose of 50 gray (Gy). Ninety-seven percent received a boost to the remaining nipple or tumor bed, with a median dose to the tumor bed of 61.5 Gy. RESULTS The median follow-up for surviving patients was 62 months. Three patients (10%) developed a recurrence in the breast as the only site of first failure, and 2 additional patients (7%) experienced failure in the breast as a component of first failure. The median time to local failure was 69 months. The 5- and 8-year actuarial estimates of local failure as the only site of first failure were 9% (95% confidence interval [CI], 0-20%) and 16% (95% CI, 0-31%), respectively. Of the 5 patients with local failures, 3 were among 22 patients (14%) who underwent complete resection of the nipple or nipple-areola complex, compared with 2 failures among 6 patients (33%) after partial resection ( P = 0.29). There were no failures among 2 patients who had a biopsy only. Four of 5 local failures were salvaged by mastectomy, and 3 of these patients were free of disease after a median follow-up of 52 months. The 5- and 8-year estimates of disease free survival for the overall series were both 95% (95% CI, 87-100%); cause specific overall survival was 100% at 8 years. CONCLUSIONS Breast-conserving therapy involving complete resection of the nipple-areola complex followed by definitive radiotherapy is a viable alternative to mastectomy in the treatment of Paget's disease. High rates of disease free and cause specific survival, in addition to adequate local control, justify consideration of a conservative approach. Cancer 1997; 80:1065-72. © 1997 American Cancer Society.
User decision support system for on-site tourism navigation on smartphone (2020)

In recent years, there has been a growing interest in travel applications that provide on-site personalized tourist spot recommendations. While they are generally useful, most of the available apps are focused on helping tourists make decisions only on the next spot to visit. This may cause that the tourists miss attractive spots to visit in the future. Due to the lack of awareness on the spots to go afterwards, they are unable to visit the spots they wanted to visit later, hence their overall tourism satisfaction decreases. In this study, we introduce an on-site tourism recommendation system, ISO-Tour, which can be used on the spot during the tour and allows users to consider multiple spots to visit next taking into account the trade-off between satisfaction of the next spot and that of the subsequent spots visited in the future.
Towards Cognitive Automation of Data Science (2015)

A Data Scientist typically performs a number of tedious and time-consuming steps to derive insight from a raw data set. The process usually starts with data ingestion, cleaning, and transformation (e.g. outlier removal, missing value imputation), then proceeds to model building, and finally a presentation of predictions that align with the end-users objectives and preferences. It is a long, complex, and sometimes artful process requiring substantial time and effort, especially because of the combinatorial explosion in choices of algorithms (and platforms), their parameters, and their compositions. Tools that can help automate steps in this process have the potential to accelerate the time-to-delivery of useful results, expand the reach of data science to non-experts, and offer a more systematic exploration of the available options. This work presents a step towards this goal.
Hydrodynamic instability measurements in DT-layered ICF capsules using the layered-HGR platform (2016)

Abstract not provided
Memory Tests Distinguish Between Patients with Focal Temporal and Extratemporal Lobe Epilepsy (1996)

We examined the ability of preoperative memory performance to distinguish between patients who had been diagnosed as having left (LTLE, n = 31), right (RTLE, n = 37), and extra-(ETLE, n = 17) temporal lobe focal epilepsy. All patients eventually underwent surgical resections. Analyses indicated that the ETLE group performed better than the RTLE group on nonverbal memory measures and better than the LTLE group on verbal memory measures. Discriminant function analyses indicated that use of a combination of measures that assess different aspects of memory were of significant value in distinguishing between patients with focal TLE and ETLE. This approach, as compared the use of single measures, improved classification rates of all three groups. The best single predictor of group membership, an index of verbal learning, yielded a 47% overall correct classification rate, with sensitivities ranging from 25 to 59%, and performed at worse than chance levels in classifying RTLE patients. A multivariate approach, which included an index of verbal and nonverbal learning, incidental nonverbal memory, and consolidation of organized and rote verbal material, yielded a 65% correct classification rate, with sensitivities ranging from 57 to 75%. This compares favorably with the other noninvasive techniques for lateralizing epileptogenic lesions.
Identification of serum MicroRNAs as diagnostic biomarkers for influenza H7N9 infection (2016)

MicroRNAs (miRNAs) have been reported to play an important role in influenza virus-host interactions. To gain more insight into the contribution of miRNAs to the host immune response, the miRNA expression profiles in the sera of H7N9-infected patients and healthy controls were analyzed using miRNA microarray. Among the ninety-four miRNAs that were significantly differentially expressed in H7N9 serum samples when compared with that of healthy controls, fifty-three miRNAs were up-regulated and forty-one down-regulated. Five serum miRNA candidates (hsa-miR-197-5p, hsa-miR-320a, hsa-miR-320d, hsa-miR-320e, and hsa-miR-765) were further verified by RT-qPCR. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the potential use of these miRNAs for the H7N9 infection diagnosis from the serum samples. In silico analyses indicate that most the target genes of these miRNAs are implicated in cell invasion, inflammatory response and apoptosis. Our results indicate that these miRNA biomarkers from serum samples can be used for influenza diagnosis.
Active Flow Control of Single and Dual Supersonic Impinging Jets using Microjets (2021)

View Video Presentation: https://doi.org/10.2514/6.2021-1637.vid An impinging jet produces a highly unsteady flowfield which produces high noise levels in the near-field, harmful structural vibrations, and significant lift-loss in applications such as Short Take-Off and Vertical Landing (STOVL) aircraft. Furthermore, the presence of multiple impinging jets leads to the generation of a fountain flow which further adds complexity to the flowfield. An understanding of the flowfield and implementation of an effective flow control technique is necessary to reduce these adverse effects for better design of STOVL aircraft. In the present study, flowfields of single supersonic round jet (Mach 1.5) and dual impinging jets are explored. The dual impinging jets consist of the supersonic jet and a sonic jet. A microjet flow control technique is applied to mitigate flow unsteadiness, in part by effecting the shear layer instability of the jet issuing from the supersonic nozzle. The effectiveness of the microjet flow control method is investigated with the help of schlieren visualization technique, near-field acoustic measurements, and unsteady surface pressure measurements. Proper Orthogonal Decomposition (POD) technique is applied to the time-resolved schlieren data sets in order to capture dominant modes of shear layer instabilities and acoustic waves. The passive and active influence of the microjet hardware is examined over a range of impingement distances (2.25D – 10D) with a fine resolution (D/16) to obtain detailed resonance characteristics. For single and dual impinging jets, relative to their respective baselines, the microjet control on dual impinging jets shows better near-field noise attenuation of over-all sound pressure level within short impingement distances (H/D < 4.5).