gebhart/patrepeval huggingface dataset:
Genomic Survey of Pathogenicity Determinants and VNTR Markers in the Cassava Bacterial Pathogen Xanthomonas axonopodis pv. Manihotis Strain CIO151 (2013)

Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
Enhanced detection of oral dysplasia by structured illumination fluorescence lifetime imaging microscopy (2021)

We demonstrate that structured illumination microscopy has the potential to enhance fluorescence lifetime imaging microscopy (FLIM) as an early detection method for oral squamous cell carcinoma. FLIM can be used to monitor or detect changes in the fluorescence lifetime of metabolic cofactors (e.g. NADH and FAD) associated with the onset of carcinogenesis. However, out of focus fluorescence often interferes with this lifetime measurement. Structured illumination fluorescence lifetime imaging (SI-FLIM) addresses this by providing depth-resolved lifetime measurements, and applied to oral mucosa, can localize the collected signal to the epithelium. In this study, the hamster model of oral carcinogenesis was used to evaluate SI-FLIM in premalignant and malignant oral mucosa. Cheek pouches were imaged in vivo and correlated to histopathological diagnoses. The potential of NADH fluorescence signal and lifetime, as measured by widefield FLIM and SI-FLIM, to differentiate dysplasia (pre-malignancy) from normal tissue was evaluated. ROC analysis was carried out with the task of discriminating between normal tissue and mild dysplasia, when changes in fluorescence characteristics are localized to the epithelium only. The results demonstrate that SI-FLIM (AUC = 0.83) is a significantly better (p-value = 0.031) marker for mild dysplasia when compared to widefield FLIM (AUC = 0.63).
WE-D-BRA-04: Online 3D EPID-Based Dose Verification for Optimum Patient Safety (2015)

PURPOSE: To develop an online 3D dose verification tool based on EPID transit dosimetry to ensure optimum patient safety in radiotherapy treatments. METHODS: A new software package was developed which processes EPID portal images online using a back-projection algorithm for the 3D dose reconstruction. The package processes portal images faster than the acquisition rate of the portal imager (∼ 2.5 fps). After a portal image is acquired, the software seeks for "hot spots" in the reconstructed 3D dose distribution. A hot spot is in this study defined as a 4 cm(3) cube where the average cumulative reconstructed dose exceeds the average total planned dose by at least 20% and 50 cGy. If a hot spot is detected, an alert is generated resulting in a linac halt. The software has been tested by irradiating an Alderson phantom after introducing various types of serious delivery errors. RESULTS: In our first experiment the Alderson phantom was irradiated with two arcs from a 6 MV VMAT H&amp;N treatment having a large leaf position error or a large monitor unit error. For both arcs and both errors the linac was halted before dose delivery was completed. When no error was introduced, the linac was not halted. The complete processing of a single portal frame, including hot spot detection, takes about 220 ms on a dual hexacore Intel Xeon 25 X5650 CPU at 2.66 GHz. CONCLUSION: A prototype online 3D dose verification tool using portal imaging has been developed and successfully tested for various kinds of gross delivery errors. The detection of hot spots was proven to be effective for the timely detection of these errors. Current work is focused on hot spot detection criteria for various treatment sites and the introduction of a clinical pilot program with online verification of hypo-fractionated (lung) treatments.
Caffeic Acid Protects Hydrogen Peroxide Induced Cell Damage in WI-38 Human Lung Fibroblast Cells (2006)

Cytoprotective effect of caffeic acid (3,4-dihydroxy cinnamic acid) on human lung fibroblast (WI-38) cells against hydrogen peroxide induced damage was investigated. Caffeic acid was found to scavenge intracellular reactive oxygen species, and 1,1-diphenyl-2-picrylhydrazyl radical, and thus prevented lipid peroxidation. The caffeic acid protected cell damage of WI-38 cells exposed to hydrogen peroxide (H(2)O(2)), via the activation of extracellular signal regulated kinase protein. Caffeic acid increased the activity of catalase and its protein expression. Hence, from the present study, it is suggestive that caffeic acid protects WI-38 cells against H2O2 damage by enhancing the cellular antioxidant activity.
Hospitalization and Definitive Radiotherapy in Lung Cancer: Incidence, Risk Factors and Survival Impact (2020)

Abstract Background: Unplanned hospitalization during cancer treatment is costly, can disrupt treatment, and affect patient quality of life. However, incidence and risks factors for hospitalization during lung cancer radiotherapy are not well characterized. Methods: Patients treated with definitive intent radiation (≥45 Gy) for lung cancer between 2008 and 2018 at a tertiary academic institution were identified. In addition to patient, tumor, and treatment related characteristics, specific baseline frailty markers (Charlson comorbidity index, ECOG, patient reported weight loss, BMI, hemoglobin, creatinine, albumin) were recorded. All cancer-related hospitalizations during or within 30 days of completing radiation were identified. Associations between baseline variables and any hospitalization, number of hospitalizations, and overall survival were identified using multivariable linear regression and multivariable Cox proportional-hazards models, respectively. Results: Of 270 patients included: median age was 66.6 years (31-88), 50.4% of patients were male (n=136), 62% were Caucasian (n=168). Cancer-related hospitalization incidence was 17% (n=47), of which 21% of patients hospitalized (n=10/47) had &gt;1 hospitalization. On multivariable analysis, each 1 g/dL baseline drop in albumin was associated with a 2.4 times higher risk of any hospitalization (95% confidence interval (CI) 1.2-5.0, P =0.01), and baseline hemoglobin ≤10 was associated with, on average, 2.7 more hospitalizations than having pre-treatment hemoglobin &gt;10 (95% CI 1.3-5.4, P =0.01). After controlling for baseline variables, cancer-related hospitalization was associated with 1.8 times increased risk of all-cause death (95% CI: 1.02-3.1, P =0.04).Conclusions: Our data show baseline factors can predict those who may be at increased risk for hospitalization, which was independently associated with increased mortality. Taken together, these data support the need for developing further studies aimed at early and aggressive interventions to decrease hospitalizations during treatment.
Bimetallic Janus nanostructures via programmed shell growth (2013)

We report the synthesis of compositionally asymmetric, core-Janus shell plasmonic nanostructures comprised of Au and Ag. Kinetic control was employed to achieve asymmetric shell growth on Au nanoparticles acting as cores. Subsequent differential surface functionalization of these nanostructures enabled programmed shell growth resulting in core-Janus shell nanostructures. UV/vis extinction spectra reveal that the localized surface plasmon resonance of the nanostructures depends on the composition and distribution of the components, providing additional handles to tune the optical properties of metal nanostructures. The core-Janus shell nanostructures demonstrated here are highly Raman-active making them attractive candidates for Raman-based biosensing and bioimaging applications.
[Sarcoidosis simulating a pulmonary veno-occlusive disease]. (1991)

We report the case of a man of 43 years old presenting with sarcoidosis which produced pulmonary hypertension and respiratory failure without radiological evidence of interstitial fibrosis. In spite of treatment with steroids and corticosteroids (1 mg/kg) there was progression over 2 1/2 years to respiratory failure and irreversible right heart failure and the death of the patient. At autopsy the pulmonary veins were obliterated by non caseating granulomas and there were minimal fibrotic parenchymal lesions. To our knowledge this is only the second case of sarcoidosis resulting in a veno occlusive pulmonary disorder.
To Pack or Not to Pack: A Generalized Packing Analysis and Transformation (2023)

Packing is an essential loop optimization for handcrafting a high-performance General Matrix Multiplication (GEMM). Packing copies a non-contiguous block of data to a contiguous block to reduce the number of TLB entries required to access it, avoiding expensive TLB misses. When copying data, packing can rearrange elements of the block to decrease the stride between consecutive accesses, improving spatial locality. Until now the use of packing has been limited to handcrafted GEMM implementations and to auto-tuning techniques. Existing loop optimizers, such as Polly and Pluto, either only apply packing to GEMM computations (Polly), or not at all (Pluto). This work proposes GPAT, a generalized packing analysis and code transformation that applies packing, when beneficial, to a generic input loop nest. GPAT is implemented in the Affine dialect of MLIR and evaluated on Polybench/C. GPAT applies packing to benchmarks beyond GEMM and obtains significant speedup compared to current loop optimizers that do not apply packing.
Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain: The Acute to Chronic Pain Signatures (A2CPS) Study Protocol (2022)

Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or "omics," quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
Epigenetic Therapy for Solid Tumors: from Bench Science to Clinical Trials (2015)

The cancer epigenome is characterized by global DNA methylation and chromatin changes, such as the hypermethylation of specific CpG island promoters. Epigenetic agents like DNA methyltransferase or histone deacetylase inhibitors induce phenotype changes by reactivation of epigenetically silenced tumor suppressor genes. Despite initial promise in hematologic malignancies, epigenetic agents have not shown significant efficacy as monotherapy against solid tumors. Recent trials showed that epigenetic agents exert favorable modifier effects when combined with chemotherapy, hormonal therapy, or other epigenetic agents. Due to the novel nature of their mechanism, it is important to reconsider the optimal patient selection, drug regimen, study design, and outcome measures when pursuing future trials in order to discover the full potential of this new therapeutic modality.
Enrichment of PI3K-AKT–mTOR Pathway Activation in Hepatic Metastases from Breast Cancer (2017)

<b>Purpose:</b> Little is known about the molecular signatures associated with specific metastatic sites in breast cancer. Using comprehensive multi-omic molecular profiling, we assessed whether alterations or activation of the PI3K-AKT-mTOR pathway is associated with specific sites of breast cancer metastasis.<b>Experimental Design:</b> Next-generation sequencing-based whole-exome sequencing was coupled with reverse-phase protein microarray (RPPA) functional signaling network analysis to explore the PI3K-AKT-mTOR axis in 32 pretreated breast cancer metastases. RPPA-based signaling data were further validated in an independent cohort of 154 metastatic lesions from breast cancer and 101 unmatched primary breast tumors. The proportion of cases with PI3K-AKT-mTOR genomic alterations or signaling network activation were compared between hepatic and nonhepatic lesions.<b>Results:</b><i>PIK3CA</i> mutation and activation of AKT (S473) and p70S6K (T389) were detected more frequently among liver metastases than nonhepatic lesions (<i>P</i> < 0.01, <i>P</i> = 0.056, and <i>P</i> = 0.053, respectively). However, <i>PIK3CA</i> mutations alone were insufficient in predicting protein activation (<i>P</i> = 0.32 and <i>P</i> = 0.19 for activated AKT and p70S6K, respectively). RPPA analysis of an independent cohort of 154 tumors confirmed the relationship between pathway activation and hepatic metastasis [AKT (S473), mTOR (S2448), and 4EBP1 (S65); <i>P</i> < 0.01, <i>P</i> = 0.02, and <i>P</i> = 0.01, respectively]. Similar results were also seen between liver metastases and primary breast tumors [AKT (S473) <i>P</i> < 0.01, mTOR (S2448) <i>P</i> < 0.01, 4EBP1 (S65) <i>P</i> = 0.01]. This signature was lost when primary tumors were compared with all metastatic sites combined.<b>Conclusions:</b> Breast cancer patients with liver metastasis may represent a molecularly homogenized cohort with increased incidence of <i>PIK3CA</i> mutations and activation of the PI3K-AKT-mTOR signaling network. <i>Clin Cancer Res; 23(16); 4919-28. ©2017 AACR</i>.
Vancomycin Adsorption during in vitro Model of Hemoperfusion with Mini-Module of HA380 Cartridge (2022)

HA380 adsorbs significant amounts of vancomycin. Adjusting the achieved results with the experimental mini-module to a full-scale cartridge, a total of 25 g of antibiotic can be removed. This might have affected outcome results in clinical trials. This suggests prescribing administration to critically ill patients requiring hemoperfusion, immediately after or in the inter-session time window. In case of administration during hemoperfusion, adequate adjustment and plasma level monitoring is strongly recommended.
Ionizing radiation delivered by specific antibody is therapeutic against a fungal infection (2003)

There is an urgent need for new antimicrobial therapies to combat drug resistance, new pathogens, and the relative inefficacy of current therapy in compromised hosts. Ionizing radiation can kill microorganisms quickly and efficiently, but this modality has not been exploited as a therapeutic antimicrobial strategy. We have developed methods to target ionizing radiation to a fungal cell by labeling a specific mAb with the therapeutic radioisotopes Rhenium-188 and Bismuth-213. Radiolabeled antibody killed cells of human pathogenic fungus Cryptococcus neoformans in vitro, thus converting an antibody with no inherent antifungal activity into a microbicidal molecule. Administration of radiolabeled antibody to mice with C. neoformans infection delivered 213Bi and 188Re to the sites of infection, reduced their organ fungal burden, and significantly prolonged their survival without apparent toxicity. This study establishes the principle that targeted radiation can be used for the therapy of an infectious disease, and suggests that it may have wide applicability as an antimicrobial strategy.
Comparison of low-temperature-sensitive liposome encapsulated docetaxel and doxorubicin in a murine model of prostate cancer. (2011)

31 Background: Low-temperature-sensitive liposomes (LTSLs) release their encapsulated drug into targeted tissue when activated by a source of hyperthermia. The efficacy of an LTSL formulation of docetaxel (DOC) or doxorubicin (DOX) was compared against prostate cancer in a xenograft mouse model. Methods: Under an approved IACUC protocol, Luciferase transfected human prostate PC-3M-luciferase cells were inoculated (3x10 6 cells) subcutaneously in the right hind leg of 8 wk old female athymic nude mice. When tumors reached a volume of 200–300 mm 3 , mice were randomized to receive one intravenous injection of saline, Stealth liposomal DOX (5 mg/kg), LTSL DOX (5 mg/kg), or LTSL DOC (15 mg/kg), with or without hyperthermia treatment (LTSL DOX and LTSL DOC were supplied by Celsion Corp., Columbia MD). Mice undergoing hyperthermia treatment were anesthetized and stabilized in a holder that allowed for only the leg with tumor to be heated to 41–42°C that triggered LTSL drug release. Mice were monitored daily for tumor volume and body weight. Study end-points included growth of tumor to 5x the initial treatment volume or monitoring of survival for 60 days. Results: The LTSL DOC delayed tumor growth longer (&gt; 14 days) than DOX (0 day) and LTSL DOX (1 day) with hyperthermia (P&lt;0.05). Mice treated with LTSL DOC and hyperthermia survived longest (60 days) compared to all other mice (range 6–8 days, P&lt;0.05). LTSL in the setting of hyperthermia demonstrated complete regression of tumor in 57% of mice. Conclusions: LTSL DOC with hyperthermia delayed tumor growth more than all other treatments. Survival studies suggest LTSL DOC is a more effective temperature sensitive delivery system against PC-3M prostate tumors. No significant financial relationships to disclose.
Use of multiparametric MRI to alter management pathways: Treatment patterns of prostate cancer in the targeted biopsy era. (2015)

56 Background: As the use of multiparametric MRI (mpMRI) to diagnose prostate cancer (PCa) becomes established, better knowledge of treatment patterns is needed to counsel patients. Prior studies have shown 40-55% undergo Radical Prostatectomy (RP), while only 6% prefer Active Surveillance (AS), and that stratification by risk does not greatly alter treatment pathways. We aim to delineate the distribution of PCa treatment modalities in the MRI/US fusion-guided prostate biopsy (FB) era. Methods: A retrospective review was performed of all patients who underwent FB at the NIH from 2010 to present. Demographics, Gleason scores, MRI Suspicion scores and treatment outcomes were recorded. Patients were stratified according to D’Amico Risk Criteria, and outcomes were coded into four categories: AS; RP; Radiation (XRT, Brachytherapy); and Other (Systemic or Focal therapy). Results: 839 men were reviewed. Mean age was 62.6 years old and mean PSA was 9.7 ng/mL. Total cancer detection rate was 70% (n = 589). Of FB positive men, 474 had treatment information available. Overall 225 (47.5%) entered AS, 158 (33.3%) underwent RP, 61 (12.9%) received XRT, and 30 (6.3%) received other intervention. Subgroup analysis by MRI suspicion score (Table) showed 47.4% frequency of RP in the high vs. 30.9% and 19.4% for moderate and low suspicion groups, respectively. Analysis by D’Amico Risk (Table) showed 86% of low risk men chose AS vs. 0% of high risk men. Conversely 9.7% of low, 44.5% of intermediate and 55.7% of high risk men underwent RP. Conclusions: FB was associated with a higher rate of AS choice as a treatment modality for low risk disease. However most patients with clinically significant PCa still chose RP as their treatment. FB is an additional tool that allows the urologist to better counsel patients and provides individualized treatment for PCa. [Table: see text]
ChemInform Abstract: CHEMIE DER NITRENIUMIONEN 26. MITT. NACHBARGRUPPENBETEILIGUNG MITTELS DES BRUECKENKOPF‐STICKSTOFFS IN VERBRUECKTEN POLYCYCLISCHEN SYST. (1972)

Abstract Es werden die kinetischen Daten der Methanolyse von 1 wie z.B. des Chlorids (Ia) sowie der Hydrolyse des Esters sprechenden Daten derstickstofffreien Derivate (Ib) und ( Die höheren Geschwindigkeiten für die Azaver durch das N ‐Aza‐bicyclo‐heptanen (IIa) mit den ent‐ IIb) verglichen.
On ensembles of low-density parity-check codes: asymptotic distance distributions (2002)

We derive expressions for the average distance distributions in several ensembles of regular low-density parity-check codes (LDPC). Among these ensembles are the standard one defined by matrices having given column and row sums, ensembles defined by matrices with given column sums or given row sums, and an ensemble defined by bipartite graphs.
Internal Carotid Artery Pseudoaneurysms: Treatment with the Wallgraft Endoprosthesis (2003)

The thin-walled fabric of the Wallgraft appears capable of completely excluding the pseudoaneurysm, resulting in decreased aneurysm size over time.