gebhart/patrepeval huggingface dataset:
Infrastructure for collaborative science and societal applications in the Columbia River estuary (2015)

Abstract To meet societal needs, modern estuarine science needs to be interdisciplinary and collaborative, combine discovery with hypotheses testing, and be responsive to issues facing both regional and global stakeholders. Such an approach is best conducted with the benefit of data-rich environments, where information from sensors and models is openly accessible within convenient timeframes. Here, we introduce the operational infrastructure of one such data-rich environment, a collaboratory created to support (a) interdisciplinary research in the Columbia River estuary by the multi-institutional team of investigators of the Science and Technology Center for Coastal Margin Observation &amp; Prediction and (b) the integration of scientific knowledge into regional decision making. Core components of the operational infrastructure are an observation network, a modeling system and a cyber-infrastructure, each of which is described. The observation network is anchored on an extensive array of long-term stations, many of them interdisciplinary, and is complemented by on-demand deployment of temporary stations and mobile platforms, often in coordinated field campaigns. The modeling system is based on finiteelement unstructured-grid codes and includes operational and process-oriented simulations of circulation, sediments and ecosystem processes. The flow of information is managed through a dedicated cyber-infrastructure, conversant with regional and national observing systems.
Metastatic Ovarian Tumor Masquerading as Atypical Pneumonia. (2016)

Krukenberg tumor is a malignancy in the ovary from a primary lesion in the gastrointestinal tract and a metastatic signet ring cell adenocarcinoma to the ovary. Stomach is the most common primary site, but other organs can serve as a primary site. The lymphatic system is the most likely route for metastasis. CA 125 levels can be used for screening for early detection of ovarian metastasis as well as for monitoring the course of disease. The prognosis of Krukenberg tumor is poor and no curative treatment is currently available.
Comparison of the Structural and Physical Properties of Human Hair Eumelanin Following Enzymatic or Acid/Base Extraction (2003)

Eumelanin was isolated from a sample of black, Indonesian human hair using three different published procedures: two different acid/base extractions and an enzymatic extraction. The morphology and spectroscopic properties of the isolated pigments differ significantly. The acid/base procedures both yield an amorphous material, while enzymatic extraction yields ellipsoidal melanosomes. Amino acid analysis shows that there is protein associated with the isolated pigments, accounting for 52, 40 and 14% of the total mass for the two acid/base extractions and the enzymatic extraction, respectively. The amino acid compositions do not correlate with those of keratin or tyrosinase. Metal elemental analysis shows that the acid/base extraction removes a majority of many metal ions bound to the pigment. Chemical degradation analysis by KMnO4/H+ and H2O2/OH- indicates significant differences between the pigments isolated by acid/base and enzymatic extraction. After correction for the protein mass in the two pigments, the lower yields of both pyrrole-2,3,5-tricarboxylic acid and pyrrole-2,3-dicarboxylic acid, eumelanin degradation products, indicate acid/base extraction modifies the chemical structure of the melanin, consistent with the result of Soluene solubilization assay. While the optical absorption spectra of the bulk pigments are similar, the spectra of the molecular weight less than 1000 mass fractions differ significantly. The data clearly indicate that pigment obtained from human hair by acid/base extraction contains significant protein, exhibits destruction of the melanosome, and possesses altered molecular structure. The acid/base extracted hair melanin is not representative of the natural material and is a poor model system for studying the physical and biological properties of melanins. The enzymatically extracted hair melanin, on the contrary, retains the morphology of intact melanosomes and is an excellent source of human melanin.
Pharmacologic inhibition of cyclin-dependent kinase 4/6 activity arrests proliferation in myoblasts and rhabdomyosarcoma-derived cells (2006)

Myoblast cell cycle exit and differentiation are mediated in part by down-regulation of cyclin D1 and associated cyclin-dependent kinase (Cdk) activity. Because rhabdomyosarcoma may represent a malignant tumor composed of myoblast-like cells failing to exit the cell cycle and differentiate, we considered whether excess Cdk activity might contribute to this biology. Cyclin D-dependent Cdk4 and Cdk6 were expressed in most of a panel of six human rhabdomyosarcoma-derived cell lines. Cdk4 was expressed in 73% of alveolar and embryonal rhabdomyosarcoma tumors evaluated using a human tissue microarray. When challenged to differentiate by mitogen deprivation in vitro, mouse C2C12 myoblasts arrested in G(1) phase of the cell cycle, whereas four in the panel of rhabdomyosarcoma cell lines failed to do so. C2C12 myoblasts maintained in mitogen-rich media and exposed to a Cdk4/Cdk6 inhibitor PD 0332991 accumulated in G(1) cell cycle phase. Similar treatment of rhabdomyosarcoma cell lines caused G(1) arrest and prevented cell accumulation in vitro, and it delayed growth of rhabdomyosarcoma xenografts in vivo. Consistent with a role for Cdk4/Cdk6 activity as a regulator of myogenic differentiation, we observed that PD 0332991 exposure promoted morphologic changes and enhanced the expression of muscle-specific proteins in cultured myoblasts and in the Rh30 cell line. Our findings support the concept that pharmacologic inhibition of Cdk4/Cdk6 may represent a useful therapeutic strategy to control cell proliferation and possibly promote myogenic differentiation in rhabdomyosarcoma.
Nitrogen and hydrogen defect equilibria in Ca12Al14O33: a combined experimental and computational study (2012)

The defect structure of mayenite is investigated by Density Functional Theory (DFT) defect calculations; in situ electrical conductivity measurements in NH3 atmosphere at high temperature; and X-ray photoelectron spectroscopy (XPS) and gas phase mass spectrometry (GP-MS) of NH3 treated specimens. The computational results suggest that nitrogen is primarily incorporated substitutionally on oxygen sites as NH−2 and N3−. The concentration of nitrogen was estimated to be within the same order of magnitude by XPS, GP-MS and DFT, yielding a stoichiometry close to Ca12Al14O31.5N0.5:(NH2)0.5O0.5 which corresponds well with that obtained by Boysen et al. from similarly treated samples. Out diffusion of nitrogen was found to occur around 700 °C in Ar by XPS, GP-MS and conductivity measurements, also in accordance with Boysen et al. The conductivity measurements showed that NH3 treatment had a significant effect on the defect structure of the material which became evident only after replacing the NH3 atmosphere with Ar: the conductivity increased abruptly due to a temporary non-equilibrium reduction of the material as nitrogen diffuses out while the lack of a sufficiently large source of oxygen in the surrounding atmosphere prevents the specimen from re-oxidizing. Further, based on the computational results and the pH2 dependency on conductivity after NH3 treatment, we propose dissolution of hydride ions from H2 in the reduced and highly conductive post-NH3 state.
O2‐15‐03: DIFFERENTIAL RISK FACTORS FOR PROGRESSION TO MCI/DEMENTIA BY AMYLOID‐BETA STATUS (2018)

Preclinical AD is characterized by elevated levels of cortical amyloid-beta (Aβ+), even in the absence of cognitive impairment. These cognitively normal (CN) individuals are at higher risk for clinical progression to MCI/dementia, making Aβ+ a valuable prognostic marker. However, some clinical progression is observed in Aβ-. This may be due to higher Aβ load that remains within normal limits, or due to non-AD disease processes. This study hypothesizes that differential risk factors for progression to MCI/dementia will be observed between the Aβ groups; higher relative Aβ will increase risk for Aβ+, but not for Aβ-. CN older adults from the AIBL study (n=585) were followed for up to 8 years. Aβ+ was defined as PET SUVR ≥ 1.4. Participants whose clinical classification or Aβ status fluctuated between study visits were excluded. Cause-specific Cox proportional hazards modelling was run within the Aβ- and Aβ+ groups to examine risk factors for progression by Aβ status. Progression to MCI/dementia was coded as events, and death or study withdrawal was right-censored. Time to event or censoring was entered in months from the baseline visit. Predictor variables were PET SUVR and factors that differed between Aβ groups to isolate the contribution of Aβ to progression risk (age, BMI, hypertension, APOE-ε4). Medical history of diabetes and stroke/TIA were also included. All statistical assumptions were met. Models were compared by assessment of confidence intervals. Seventy participants progressed over 8 years (26 Aβ-, 44 Aβ+). Significant risk factors of progression in Aβ+ were age, PET SUVR and APOE-ε4 (see Figure). Confidence interval overlaps were observed between the Aβ groups for all predictor variables except PET SUVR. Aβ- progressors were not near the threshold for Aβ+ (median PET SUVR = 1.16).
On the use of the Bayesian information criterion in multiple speaker detection (2001)

An efficient scheme, based on the Bayesian information criterion (BIC), for the detection of speaker changes in an audio stream is introduced and investigated. BIC has been the subject of considerable attention in recent years due to its effectiveness for speaker change detection (SCD) as well as the detection of other forms of acoustic changes. A main difficulty in BIC-based SCD has been reported to be that of the computational complexity. The scheme proposed here tackles this problem by reducing the computational load in the previously proposed algorithms significantly, without compromising their effectiveness. The paper describes the new scheme thoroughly and analyses its performance. Experiments are based on 3 hours of broadcast news with 416 speaker changes. With this data, the proposed scheme has been found to be capable of running in about 0.06 times real-time whilst keeping the rate of each of misdetection and false alarm close to 9%.
Clinical Use of Biologics and Biosimilars in Oncology Settings (2022)

The use of biologics has revolutionized cancer therapy with highly promising results and better patient compliance. However, these are some of the most expensive prescription drugs on the market which limits the accessibility for necessary treatment in the case of many patients. With the advent of biosimilars, tough market competition has begun which helped in decreasing the cost burden to cancer patients. Regulatory guidelines for biosimilars have now been established and are constantly being revised to address any issues, facilitating their robust development. Moreover, many scientific societies offer guidance to help stake holders better understand current regulations and biosimilar's safety. In this chapter, we briefly discussed the difference between biologics and biosimilars, the current biosimilar market, approved oncology biosimilars in the United States and Europe along the country-specific regulatory guidelines.
Solutions of fully exfoliated individual graphene flakes in low boiling point solvents (2012)

Graphenide solutions (solutions of negatively charged graphene flakes) have been prepared in low boiling point solvents such as tetrahydrofuran (THF) by dissolution of the graphite intercalation compound (GIC) KC8. The presence of two-dimensional objects in solution, with an average lateral size of over one micron, is evidenced by light scattering analysis. High resolution transmission electron microscopy analysis shows that the solubilized graphene flakes are exclusively single and double layers with no evidence for thicker species. Molecular dynamics simulations support the graphene folding, observed in TEM, and suggest it is triggered by solvent nanodrops.
The Black Box of Technological Outcome Measures: An Example in Duchenne Muscular Dystrophy (2022)

Only ACTIVE qualified as potential outcome measure in non-ambulant DMD patients, although the SRM was below the commonly used threshold of 0.8. Lack of insight in technological constraints due to intellectual property and software updates made the technology behind these outcome measures a kind of black box that could jeopardize long-term use in clinical development.
Robotic assisted placement of hepatic artery infusion pump is a safe and feasible approach (2016)

Robotic assisted placement of HAI pump placement is safe, feasible, and obviates the need for major laparotomy. J. Surg. Oncol. 2016;114:342-347. © 2016 Wiley Periodicals, Inc.
Non-M3, MHC Ib-restricted CD8<sup>+</sup> T cells exhibit polyfunctional characteristics. (2016)

&lt;p&gt;CD8&lt;sup&gt;+&lt;/sup&gt; T cells from the lung or spleen of C57BL/6 and K&lt;sup&gt;b-/-&lt;/sup&gt;D&lt;sup&gt;b-/-&lt;/sup&gt;M&lt;sup&gt;3-/-&lt;/sup&gt; mice were stimulated &lt;i&gt;ex vivo&lt;/i&gt; for 18h with Mtb antigen-pulsed C57BL/6 and K&lt;sup&gt;b-/-&lt;/sup&gt;D&lt;sup&gt;b-/-&lt;/sup&gt;M3&lt;sup&gt;-/-&lt;/sup&gt; BMDCs, respectively, then harvested for intracellular staining of IFN-γ, TNF-α and IL-2. (A) Representative dot-plots of multiple cytokine-producing CD8&lt;sup&gt;+&lt;/sup&gt; T cells in the lung of C57BL/6 and K&lt;sup&gt;b-/-&lt;/sup&gt;D&lt;sup&gt;b-/-&lt;/sup&gt;M3&lt;sup&gt;-/-&lt;/sup&gt; mice at day 30 after infection upon stimulation with Mtb culture filtrate proteins (CFP). (B) Pie graphs show relative proportion of TNF-α&lt;sup&gt;+&lt;/sup&gt;, IL-2&lt;sup&gt;+&lt;/sup&gt; and TNF-α&lt;sup&gt;+&lt;/sup&gt;IL-2&lt;sup&gt;+&lt;/sup&gt; CD8&lt;sup&gt;+&lt;/sup&gt; T cells among IFN-γ&lt;sup&gt;+&lt;/sup&gt;CD8&lt;sup&gt;+&lt;/sup&gt; T cells from the lung of Mtb-infected K&lt;sup&gt;b-/-&lt;/sup&gt;D&lt;sup&gt;b-/-&lt;/sup&gt;M3&lt;sup&gt;-/-&lt;/sup&gt; and C57BL/6 mice. (C) IL-17A production from enriched CD8&lt;sup&gt;+&lt;/sup&gt; T cells in Mtb-infected K&lt;sup&gt;b-/-&lt;/sup&gt;D&lt;sup&gt;b-/-&lt;/sup&gt;M3&lt;sup&gt;-/-&lt;/sup&gt; mice detected by ELISA after stimulation with CFP. ***&lt;i&gt;P&lt;/i&gt; &lt;0.001.&lt;/p&gt;
Investigating the use of nonattenuation corrected PET images for the attenuation correction of PET data (2013)

Preliminary results suggest that PET-NAC for the AC of PET images is feasible. Such an approach can potentially be used for dedicated PET or PET∕MR hybrid systems while minimizing scan time or potential image artifacts, respectively.
Spoken Content Retrieval Using Distance Combination and Spoken Term Detection Using Hash Function for NTCIR10 SpokenDoc2 Task (2013)

In this paper we describe a spoken content retrieval (SCR) and a spoken term detection (STD) which were used in the 2nd round of the IR (Information Retrieval) for Spoken Documents (SpokenDoc2) task. Our SCR method maps the target documents into multiple vector spaces, which include a word-based vector space for word-based speech recognition results and a syllable-based vector space for syllablebased speech recognition results. The syllable-based space is spanned by axes extracted using latent semantic indexing (LSI). We also apply query expansion and morpheme weighting to the word-based space. Finally, the distance between the query and the documents in each vector space are combined and ranked for retrieving the documents. On the other hand, our STD method extracts sub-sequences from the target documents and converts them into bit sequences using the hash function. The query is also converted into a bit sequence in the same way. Candidates are detected by calculating the hamming distance between the bit sequence of the query and that of the target documents. Then, our method calculates the distances between the query and the candidates using DP (Dynamic Programming) matching. To evaluate the proposed methods, we conducted spoken document retrieval experiments using the SpokenDoc task from the NTCIR-9 meeting. Using these experimental results to set our parameters, we submitted the results for the SpokenDoc2 task at NTCIR-10.
Controllable hydrothermal synthesis of Ni/H-BEA with a hierarchical core–shell structure and highly enhanced biomass hydrodeoxygenation performance (2017)

Ni based catalysts are wildly used in catalytic industrial processes due to their low costs and high activities. The design of highly hierarchical core-shell structured Ni/HBEA is achieved using a sustainable, simple, and easy-tunable hydrothermal synthesis approach using combined NH<sub>4</sub>Cl and NH<sub>3</sub>·H<sub>2</sub>O as a co-precipitation agent at 120 °C. Starting from a single-crystalline hierarchical H<sup>+</sup>-exchanged beta polymorph zeolite (HBEA), the adjustment of the precipitate conditions shows that mixed NH<sub>4</sub>Cl and NH<sub>3</sub>·H<sub>2</sub>O precipitates with proper concentrations are vital in the hydrothermal synthesis for preserving a good crystalline morphology of HBEA and generating abundant highly-dispersed Ni nanoparticles (loading: 41 wt%, 5.9 ± 0.7 nm) encapsulated onto/into the support. NH<sub>4</sub>Cl solution without an alkali is unable to generate abundant Ni nanoparticles from Ni salts under the hydrothermal conditions, whereas NH<sub>3</sub>·H<sub>2</sub>O seriously damages the pore structure. After studying the in situ changes in infrared, X-ray diffractometry, temperature-programmed reduction, and scanning electron microscopy measurements, as well as variations in the filtrate pH, Si/Al ratios, and solid sample Ni loading, a two-step dissolution-recrystallization process is proposed. The process consists of Si dissolution and no change in elemental Al, and after the dissolved Si(iv) concentrations have promoted Ni phyllosilicate nanosheet solubility, further growth of multilayered Ni phyllosilicate nanosheets commences. The precursor Ni phyllosilicate is changeable between Ni<sub>3</sub>Si<sub>2</sub>O<sub>5</sub>(OH)<sub>4</sub> and Ni<sub>3</sub>Si<sub>4</sub>O<sub>10</sub>(OH)<sub>2</sub>, because of competition in kinetically-favored and thermodynamically-controlled species caused by different basic agents. The superior catalytic performance is demonstrated in the metal/acid catalyzed biomass derived bulky stearic acid hydrodeoxygenation with 90% octadecane selectivity and a promising rate of 54 g g<sup>-1</sup> h<sup>-1</sup>, which highly excels the reported rates catalyzed by Ni catalysts. Significant improvements in activity and selectivity are related to the highly dispersive Ni nanoparticles onto/into intra-mesopores of hierarchical HBEA, hence enhance the accessibility of bulky substrates to metal sites and mass transfer capacity.
Platelet and BM-1. The inhibition mechanism of BM-1 on aggregation of platelet. (1989)

In vitro, the effects of BM-1 (extracts from the mackerel) on platelet aggregation induced in platelet rich plasma (PRP) by ADP, collagen, epinephrine and A. A. (arachidonic acid) was inhibited by BM-1. But platelet aggregation by PMA (phorbol 12, 13-myristate acetate) was not inhibited by BM-1.In the platelet suspension, when BM-1 was removed from the medium, inhibition of platelet aggregation by BM-1 was not observed.Cytoplasmic free Ca2+ was measured in human platelets using the intracellularlytrapped fluorescent indicator Fura-2.Thrombin-induced increase in cytoplasmic free Ca2+ was inhibited by BM-1. When BM-1 was removed from the medium, inhibition of the rise in cytoplasmic free Ca2+ was not found.The present findings would suggest that there were unknown factors in BM-1 which inhibited the aggregation of platelet and the rise in cytoplasmic free Ca2+ of platelets.
Serotonin receptors and systems: endless diversity? (2002)

Serotonin is probably unique among the monoamines in that its effects are subserved by as many as 13 distinct heptahelical, G protein-coupled receptors (GPCRs) and a ligand-gated ion channel family (5-HT3). These receptors are divided into seven distinct classes (5-HT1 to 5-HT7) largely on the basis of their structural, transductional and operational char- acteristics. While this degree of physical diversity clearly underscores the physiological importance of serotonin, evidence for an even greater degree of operational diversity continues to emerge. Here, we will review this diversity and its physiological and possibly pathophysiological consequences. Indeed, 5-HT research which is about 50 years old, has resulted in numerous therapeutic agents, some of which have a major impact on disease man- agement. Thus, selective 5-HT reuptake inhibitors (SSRIs) are among the most widely used drugs in depression and other disorders such as anxiety, social phobia, panic disorders, or obsessive compulsive disorders (OCDs) to name a few. The discovery of 5-HT1B/1D receptor agonists (the triptans) for treating migraine, 5-HT3 receptor antagonists for chemotherapy and radiation-induced emesis, and finally the emergence of 5-HT3 / 5-HT4 ligands to treat irritable bowel syndrome (IBS), all represent major advances in the field. Finally, the role of 5-HT in the mechanism of action of antipsychotic agents still is a topic of intense research, which promises better treatments for schizophrenia.
Reverse Polarity Reductive Functionalization of Tertiary Amides via a Dual Iridium Catalyzed Hydrosilylation & SET Strategy (2020)

A new strategy for the mild generation of synthetically valuable α-amino radicals from robust tertiary amide building blocks has been developed. By combining Vaska’s complex-catalyzed tertiary amide reductive activation and photochemical single electron reduction into a streamlined tandem process, metastable hemiaminal intermediates were successfully transformed into nucleophilic α-amino free radical species. This umpolung approach to such reactive intermediates was exemplified through coupling with an electrophilic dehydroalanine acceptor, resulting in the synthesis of an array of α-functionalized tertiary amine derivatives, previously inaccessible from the amide starting materials. The utility of the strategy was expanded to include secondary amide substrates, intramolecular variants and late stage functionalization of an active pharmaceutical ingredient. DFT analyses were used to establish the reaction mechanism and elements of the chemical system that were responsible for the reaction’s efficiency.
2′,5′-Dideoxyadenosine 3′-Polyphosphates Are Potent Inhibitors of Adenylyl Cyclases (1996)

2',5'-Dideoxyadenosine 3'-di- and triphosphates were tested as inhibitors of brain adenylyl cyclases. With an IC50 approximately 40 nM, 2',5'-dideoxy-3'-ATP is the most potent nonprotein synthetic regulator of adenylyl cyclases thus far described. Neither 2',5'-dideoxy-3'-ADP nor 2',5'-dideoxy-3'-ATP inhibited activity by competition with substrate, and the linear noncompetitive inhibition observed was consistent with interaction via a distinct domain. The availability of this ligand will permit the development of a variety of probes that will be extremely useful in investigating adenylyl cyclase structure and the role(s) that this class of compound may play in physiologically regulating cell function.
ChemInform Abstract: Solvatochromic Study of the Effect of Chain Length, Chain Branching, and Polymethylation of Alkylbenzenes on Solvent Polarizability (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Fluorination and Fluoroalkylation of Organolithium, Magnesium, and Zinc Reagents (2016)

Abstract Review: 124 refs.