gebhart/patrepeval huggingface dataset:
Resource for the Development of Biomedical Accelerator Mass Spectrometry (AMS) Final Report (2020)

The NIH Research Resource for Biomedical AMS was originally funded at Lawrence Livermore National Laboratory in 1999 to develop and apply the technology of accelerator mass spectrometry (AMS) in broad- based biomedical research. The Resource’s niche is to fill needs for ultra high sensitivity quantitation when isotope-labeled agents are used. The Research Resource’s Technology Research and Development (TR&D) efforts will focus on the needs of the biomedical research community in the context of seven Driving Biomedical Projects (DBPs) that will drive the Center’s technical capabilities through three core TR&Ds. We will expand our present capabilities by developing a fully integrated HPLC AMS to increase our capabilities for metabolic measurements, we will develop methods to understand cellular processes and we will develop and validate methods for the application of AMS in human studies, which is a growing area of demand by collaborators and service users. In addition, we will continue to support new and ongoing collaborative and service projects that require the capabilities of the Resource. The Center will continue to train researchers in the use of the AMS capabilities being developed, and the results of all efforts will be widely disseminated to advance progress in biomedical research. Towards these goals, our specific aims are to:1.) Increase the value and information content of AMS measurements by combining molecular speciation with quantitation of defined macromolecular isolates. Specifically, develop and validate methods for macromolecule labeling, characterization and quantitation.2.) Develop and validate methods and strategies to enable AMS to become more broadly used in human studies. Specifically, demonstrate robust methods for conducting pharmacokinetic/pharmacodynamics studies in humans and model systems.3.) Increase the accessibility of AMS to the Biomedical research community and the throughput of AMS through direct coupling to separatory instruments.4.) Provide high throughput 14C BioAMS analysis for collaborative and service clients.
Subsequence time series (STS) clustering techniques for meaningful pattern discovery (2006)

Subsequence time-series (STS) clustering is one way of finding significant patterns in time series. A window of size w is shifted over the series to produce a w dimensional sequence and clustering is applied. Recently, it has been demonstrated that subsequence time-series (STS) clustering often produces meaningless results. We demonstrate the problem on a synthetic dataset in a number of scenarios and provide a deeper insight to the sources of the issue. More specifically, we examine the effect of trivial matches, and the proliferation of patterns under a sliding window. Although STS clustering generates meaningless cluster averages, we show that cluster cores can be used to discover real patterns. We also demonstrate the effectiveness of using a high number of clusters. First approach is using a moderately high number where the results are visually inspected. Second approach is a two stage clustering method where a very high number of clusters are generated in the first stage. Then a minimum shift distance is used to align and cluster patterns. The original patterns in our synthetic dataset are successfully recovered using this novel method.
Antiandrogen Withdrawal Syndrome With Nilutamide (1997)

No AccessJournal of UrologyClinical Urology: Case Report1 Apr 1997Antiandrogen Withdrawal Syndrome With Nilutamide Leonard G. Gomella, Mohamed Ismail, and Faith E. Nathan Leonard G. GomellaLeonard G. Gomella , Mohamed IsmailMohamed Ismail , and Faith E. NathanFaith E. Nathan View All Author Informationhttps://doi.org/10.1016/S0022-5347(01)64984-XAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Antiandrogen Withdrawal Syndrome With Nilutamide." The Journal of Urology, 157(4), p. 1366 References 1 : Hormone and antihormone withdrawal: implications for the management of androgen-independent prostate cancer. Urology1996; 47: 61. Google Scholar 2 : Focus on nilutamide: a non-steroidal antiandrogen for the treatment of advanced prostate cancer. Formulary1996; 31: 105. Google Scholar 3 : Characterization of patients with androgen-independent prostatic carcinoma whose serum prostate specific antigen decreased following flutamide withdrawal. J. Urol.1996; 155: 620. Link, Google Scholar From the Department of Urology and Division of Neoplastic Disease, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania© 1997 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 157Issue 4April 1997Page: 1366 Advertisement Copyright & Permissions© 1997 by American Urological Association, Inc.MetricsAuthor Information Leonard G. Gomella More articles by this author Mohamed Ismail More articles by this author Faith E. Nathan More articles by this author Expand All Advertisement PDF downloadLoading ...
Progress in synthesis and characterization at the single particle level of aggregation induced emission nano-objects inside microfluidic devices (2019)

Aggregation Induced Emission (AIE) is a relatively young field of research that is radically changing the way we use fluorophores for "real-life" applications. In this novel photophysical phenomenon, chromogens that are not fluorescent in solution become highly emissive in the aggregate or solid state. Consequently, aggregation is no more a threat for fluorophore based application and priors test that relied on 'turn-off' mechanisms can now be transferred to more sensitive "turn-on" detection scheme. Here we will present new results obtained on a series of small AIEgen push-pull molecules whose emission span the visible spectrum. The aggregates are created and characterized inside microfluidic chips. This short paper will mainly focus on technical aspects of such measurements.
The Kinetic Order of an Interfacial Diels–Alder Reaction Depends on the Environment of the Immobilized Dienophile (2000)

Cyclic voltammetry has been used to study the kinetics of the Diels–Alder reaction of cyclopentadiene with quinone immobilized on a monolayer (see scheme). By monitoring the reduction in current as the redox-active quinone is converted into the redox-inactive adduct, the reaction was shown to proceed with a second-order rate constant when hydroxyl groups were incorporated into the monolayer (X=OH), but with a first-order rate constant when methyl groups were incorporated (X=CH3).
Effect of Machine Length on Swimming Properties of Spiral Magnetic Micro-Machine (2004)

In previous studies, we examined a magnetic micro-machine composed a magnet and spiral structure. As the magnet was magnetized in the diameter direction, the micro-machine rotated in synchronism with the rotating magnetic field. This time, we fabricated two types of spiral magnetic micro-machines. One had the magnet and the wire of the spiral structure (head type). The other had the wire of the spiral structure (spiral type). We examined the influence of the micro-machine length. As a result, we found that the swimming velocity of the head type micro-machine depended on the machine length. The swimming velocity of the spiral type micro-machine does not depend on the machine length.
Autonomic Remodeling (2015)

AF resulted in progressive autonomic remodeling, manifesting as nerve sprouting, sympathetic and vagal hyperinnervation. Autonomic remodeling may play an important role in sustaining AF in the first 24 hours.
Driving Status and the Inner Drive for Community Mobility and Participation: A Survey of People with Disabilities and Senior Citizens from Support Groups in New Delhi, India (2009)

This paper presents community mobility trends by driving status among people with disabilities and senior citizens in New Delhi, India. Key factors in the study include frequency leaving the home, using transportation, and traveling to common locations in the community. Study participants self-reported experiences as drivers or transportation users by questionnaire. Responses showed a limit to the frequency of transportation use among people with no driving experience as compared to people driving currently or in the past. Transportation mismatch, where people did not use a preferred mode of transportation, was reported by all groups. These findings suggest people are driven internally to keep engaged in society, and there is a need to support growth of international driver rehabilitation services for maximum participation.
ChemInform Abstract: Reticulated Pd(II)/Cu(I) Cyclodextrin Complexes as Recyclable Green Catalyst for Sonogashira Alkynylation. (2012)

Abstract A new green solid catalyst system consisting of Pd 2+ and Cu + nanoparticles supported on β‐cyclodextrin is developed and screened in Sonogashira coupling reactions of phenylacetylene and p‐iodoanisole in water or glycerol giving the desired products with excellent GC yields.
Molecular profiling of ER weakly-positive breast cancer. (2015)

525 Background: The estrogen receptor (ER) is a key predictive biomarker in the treatment of breast cancer. Luminal subtypes of breast cancer express ESR1, and are eligible for hormonal therapy. Standard laboratory assessment of ER status is currently immunohistochemistry (IHC)-based. Since the introduction of ER IHC, the threshold for positivity has decreased from 10% to ≥ 1% of tumor cells whilst methodological advances have increased the sensitivity of IHC detection. These trends have led to considerable uncertainty regarding the use of hormonal therapy in the setting of ER weakly-positive tumors. We report intrinsic subtype classification on a cohort of ER weakly-positive early stage cancers and discuss the implications on clinical treatment. Methods: Consecutive cases of untreated, surgically resected primary breast cancer were retrospectively identified from 4 tertiary care centres in British Columbia, Canada. All participating centres engage in routine external proficiency testing for breast biomarkers. Based upon the semiquantitative Allred score, combining staining intensity and percentage of tumor cells, ER-negative (Allred 0 and 2) and ER weakly-positive (Allred 3-5) cases were included. Gene expression profiling was performed using qRT-PCR. Intrinsic subtype prediction was made based upon the PAM50 gene expression signature. Results: 153 cases were included in the series; 62 cases originally diagnosed as ER weakly-positive and 91 ER-negative. Weak ER signal by IHC correlated poorly with ESR1 gene expression by qRT-PCR (R2 =0.2 [0.1-0.3, 95% CI]). Of the 62 cases originally assessed as ER weakly-positive, only 6 (10%) were confirmed as luminal subtype by gene expression profiling with the remaining cases showing basal-like or HER2-enriched subtypes (90%). In this highly enriched ER weakly-positive cohort, the positive predictive value of low-level ER staining for luminal subtype was extremely poor (8% [3%-18%, 95% CI]). Conclusions: Weak ER expression by IHC is a poor correlate of both luminal subtype and ESR1 expression in breast cancer. In the setting of highly sensitive and robust IHC methodology, cutoffs for ER status determination and subsequent systemic therapy may need to be revisited.
ChemInform Abstract: DINITROGEN AND CARBONYL COMPLEXES OF TUNGSTEN(I) AND MOLYBDENUM(I). THE NATURE OF ′MOCL(N2)(DPPE)2′ (1981)

Abstract Die Oxidation der trans‐W(0)‐Komplexe (I) mit Tetracyanethylen, Iod und wasserfreiem F eC13 führt zu den luftstabilen, kristallinen W(I)‐Komplexen (II).
Final data from the phase 2a single-arm trial of SurVaxM for newly diagnosed glioblastoma. (2022)

2037 Background: Newly diagnosed glioblastoma (nGBM) routinely treated with surgery, radiation, and temozolomide (TMZ), still result in early progression and near-universal lethality within 5 years. Tumor associated “survivin” is expressed in &gt;95% of nGBM and targetable by SurVaxM immunotherapy. Results from the recently completed multi-center phase 2a trial of SurVaxM in nGBM are presented. Methods: nGBM patients (pts) were enrolled at 5 trial sites. Eligibility criteria included: age ≥ 18, Karnofsky performance status ≥70, IHC confirmation of survivin expression, expression of HLA-A*02, A*03, A*11 or A*24 MHC-I alleles and residual contrast enhancement of ≤1 cm 3 by MRI within 72h post-resection. Pts received standard TMZ chemoradiation followed by initiation of 4 priming doses of SurVaxM (500 mcg in emulsion with Montanide ISA 51, every 2 weeks) with 100 mcg sargramostim. Maintenance doses of SurVaxM-Montanide plus sargramostim were thereafter administered every 12 weeks. Adjuvant TMZ was administered for at least 6 cycles, after at least the first dose of SurVaxM and beginning no sooner than 28 days after completion of chemoradiation. Pts were monitored by MRI every 8 weeks, and progression was assessed using modified RANO criteria. The primary endpoint was 70% progression free survival (PFS) at 6 mos. Primary analyses of median PFS (mPFS) and median overall survival (OS) were measured from first immunization. Safety, tolerability, and immune responsiveness were also determined. Results: 63 pts with nGBM were enrolled, comprised of 38 males and 25 females with a median age of 60 years. The cohort was consistent with the 4 commonly observed primary molecular GBM subtypes (classical, mesenchymal, neural and proneural). SurVaxM was well tolerated, with no serious adverse events. A strong positive correlation, accounting for censoring, was observed between PFS and OS of all pts (r = 0.79; 95% CI (0.66,0.87)). SurVaxM was immunogenic and produced survivin-specific CD8+ T-cells and antibody (IgG) titers in both methylated and unmethylated MGMT pts and both groups showed clinical benefit. Conclusions: SurVaxM appeared to be safe and well-tolerated in pts with nGBM. SurVaxM was effective at stimulating survivin-specific immune responses and the primary endpoint was met. SurVaxM represents a promising therapy for nGBM, including for those pts with unmethylated MGMT genes. For pts treated with SurVaxM, PFS may be an acceptable surrogate for OS. Clinical trial information: NCT02455557. [Table: see text]
The relationship between vertical cup–disc ratio and body mass index in a population of adult Saudi females (2018)

Purpose: The vertical cup–disc (C/D) ratio is useful clinically in optic-disc assessment in glaucoma suspects and diagnosing glaucomas and is thought to also be influenced by many ocular and systemic factors. The body mass index (BMI) is said to be an important parameter which influences vertical C/D ratio and different studies have shown different correlation between these two variables. The aim of the study was to assess the relationship of vertical C/D ratio with BMI in a population of Saudi adult females. Methods: One hundred and one female participants in the age group 18 to 40 years were included in a cross-sectional study after obtaining information regarding demographic data, ocular/systemic diseases, and surgeries by an oral interview. The BMI was calculated as ratio of body weight divided by the square of the body height. C/D ratio was recorded with direct ophthalmoscopic examination and examination with 90-D (Volk) lens. Analysis of variance was used to examine the BMI on vertical C/D ratio. A P-value <0.05 was considered to be statistically significant with confidence interval of 95%. Results: The mean BMI was 22.7 (±4.49) and the mean C/D ratio was 0.22 (±0.14). No significant relationship between increasing vertical C/D ratio and BMI P-value 0.154 was found. Conclusion: This study, conducted as a pilot study to investigate the relationship between C/D ratio and BMI in a young female Saudi population, found no significant relationship between vertical C/D ratio and BMI. This relationship is important as it helps to rule out effect of BMI on C/D ratio parameters in this population.
Resource Allocation in Mobility-Aware Federated Learning Networks: A Deep Reinforcement Learning Approach (2020)

Federated learning allows mobile devices, i.e., workers, to use their local data to collaboratively train a global model required by the model owner. Federated learning thus addresses the privacy issues of traditional machine learning. However, federated learning faces the energy constraints of the workers and the high network resource cost due to the fact that a number of global model transmissions may be required to achieve the target accuracy. To address the energy constraint, a power beacon can be used that recharges energy to the workers. However, the model owner may need to pay an energy cost to the power beacon for the energy recharge. To address the high network resource cost, the model owner can use a WiFi channel, called default channel, for the global model transmissions. However, communication interruptions may occur due to the instability of the default channel quality. For this, special channels such as LTE channels can be used, but this incurs channel cost. As such, the problem of the model owner is to decide amounts of energy recharged to the workers and to choose channels used to transmit its global model to the workers to maximize the number of global model transmissions while minimizing the energy and channel costs. This is challenging for the model owner under the uncertainty of the channel, energy and mobility states of the workers. In this paper, we thus propose to employ the Deep Q-Network (DQN) that enables the model owner to find the optimal decisions on the energy and the channels without any a priori network knowledge. Simulation results show that the proposed DQN always achieves better performance compared to the conventional algorithms.
P1‐348: Longitudinal [11C]PIB PET study in healthy elderly persons, patients with mild cognitive impairment, and Alzheimer's disease (2011)

The natural course of amyloid deposition in the human brain has not been established. We measured change in brain amyloid deposition over time in healthy elderly persons, patients with mild cognitive impairment (MCI), and Alzheimer's disease (AD) using [11C]PIB PET. Eleven healthy volunteers (HV, 67 ± 6 years; MMSE scores: 28.4 ± 1.6), 10 patients with MCI (76 ± 5 years; MMSE scores: 26.9± 1.4), and 8 patients with AD (69 ± 8 years of age; MMSE scores: 20.6 ± 4.0) participated in this study. The subjects were studied twice at the baseline and the follow-up study with a mean interval of 2 years. Following intravenous injection of [11C]PIB (about 370 MBq), 19 sequential PET scans were performed for a period of 90 min. PET images were co-registered to MRI in each subject. Volume of interests were placed manually on bilateral frontal, temporal, parietal, anterior and posterior cingulate cortices, and cerebellar cortex on MRI, and these VOIs were transferred to co-registered PET images. The distribution volume ratio (DVR) of each target VOI to cerebellar cortical VOI was calculated in non-invasive Logan plot. Cortical DVR was calculated as a mean DVR value in bilateral frontal, temporal, parietal, anterior and posterior cingulated cortices. Cortical DVR was higher in AD group (Baseline: 1.73±0.18, Follow-up:1.82±0.13) than MCI group (1.21±0.24, 1.26±0.28) and HVs (1.09±0.09, 1.13±0.06) both in the baseline study and follow up study (p < 0.001). Cortical DVR was elevated by 1.8%/ year (0.48 unit) in the whole subjects including AD and MCI patients and HVs (p < 0.02, paired t-test). There was no difference in increase of cortical DVR among AD and MCI groups and HVs. Our result is in accord with the previous longitudinal [11C]PIB PET study in HVs, MCI, and AD [1], and suggest a constant slow rate of amyloid deposition in elderly persons, MCI and AD patients. [1] Jack CR, et al. Brain 2009:132;1355-1365.
Regulation of the cAMP Level in the Yeast Saccharomyces cerevisiae: the Glucose-induced cAMP Signal Is Not Mediated by a Transient Drop in the Intracellular pH (1987)

Addition of glucose to derepressed cells of the yeast Saccharomyces cerevisiae is known to cause a rapid, transient increase in the cAMP level, which lasts for 1-2 min and induces a cAMP-dependent protein phosphorylation cascade. The glucose-induced cAMP signal cannot be explained solely on the basis of an increased ATP level. Transient membrane depolarization and transient intracellular acidification have been suggested as possible triggers for the cAMP peak. Addition of glucose to cells in which the plasma membrane had been depolarized still produced the increase in the cAMP level excluding membrane depolarization as the possible trigger. Using in vivo 31P NMR-spectroscopy we followed phosphate metabolism and the time course of the drop in the intracellular pH after addition of glucose with a time resolution of 15 s. Under aerobic conditions the initial pH and ATP level were high. On addition of glucose, they both showed a rapid, transient drop, which lasted for about 30 s. Under anaerobic conditions, the initial pH and ATP level were low and on addition of glucose they both increased relatively slowly compared to aerobic conditions. Several conditions were found in which the pH drop which occurs under aerobic conditions could be blocked completely without effect on the cAMP signal or without completely preventing it: addition of NH4Cl together with glucose at high extracellular pH and addition of a low concentration of glucose before a high concentration. Also, when glucose was added twice to the same cells no consistent relationship was observed between the pH drop and the cAMP peak. These results appear to exclude transient intracellular acidification as the trigger for the cAMP signal. Hence, we conclude that the effect of glucose cannot be explained on the basis of effects known to be caused by the membrane depolarizing compounds which cause increases in the cAMP level. A new, more specific kind of interaction appears to be involved.
Acute pacing-induced cardiomyopathy (2016)

Introduction: Pacing-induced cardiomyopathy (PICM) is defined as a 10% reduction in the left ventricular ejection fraction over several months to a year after pacemaker implantation, resulting in an ejection fraction of less than 50%. Nonetheless, other causes of cardiomyopathy should be excluded to diagnose patients with this condition. Case Report: A 59-year-old male presented with a third-degree heart block and underwent pacemaker implantation with right ventricular pacing. Subsequently, he manifested with an acute heart failure exacerbation and a reduced ejection fraction within two months of pacemaker implantation. Consequently, he underwent further workup to exclude causes of dilated cardiomyopathy such as acute coronary syndrome, sarcoidosis, hemochromatosis, granulomatosis with polyangiitis, and eosinophilic myocarditis. His left heart catheterization showed worsening in his ejection fraction without any significant coronary stenosis. He had an endomyocardial biopsy, which showed fibroblast proliferation and fibrosis with no evidence of any infiltrative cardiomyopathy. This patient was diagnosed with pacing-induced cardiomyopathy because other causes of cardiomyopathy were ruled out. Thus, his cardiac pacemaker device was upgraded to Biventricular pacing device with implantable cardioverter defibrillator. Conclusion: This report describes a patient with a severe acute form of pacing-induced cardiomyopathy and discusses the prevention and therapy of this condition.